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
29107,SRR27151543,SRX22833143,SRS19813583,SRP476691,PRJNA1050282,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye],GSE249751,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,5 dpf larval eyes  samd7 /   rep3,GSM7963641,,source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing,5 dpf larval eyes  samd7 /   rep3,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf larval eyes. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / ,GSM7963641,GSM7963641: 5 dpf larval eyes  samd7 /   rep3; Danio rerio; RNA Seq,GSM7963641 r1,GSM7963641,1,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476691,,loader:fastq load.py,k7.AGGTATTCGG-GAGTCGCTTC.H37F5DSX2_AGGTATTCGG-GAGTCGCTTC_L003_R1.fastq.gz k7.AGGTATTCGG-GAGTCGCTTC.H37F5DSX2_AGGTATTCGG-GAGTCGCTTC_L003_R2.fastq.gz,fastq fastq,10747100652.0,35586426.0,GSM7963641 r1,0:151 1:151,A:2879574125;C:2414500329;G:2693618198;T:2759237631;N:170369,151,151,,,2879574125,2414500329,2693618198,2759237631,170369,SRX22833143,SRS19813583,SRA1765718,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.95486,0.95989,0.05038,0.05167,0.73018,0.73438,0.41476,0.42743,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
29108,SRR27151544,SRX22833142,SRS19813582,SRP476691,PRJNA1050282,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye],GSE249751,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,5 dpf larval eyes  samd7 /   rep2,GSM7963640,,source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing,5 dpf larval eyes  samd7 /   rep2,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf larval eyes. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / ,GSM7963640,GSM7963640: 5 dpf larval eyes  samd7 /   rep2; Danio rerio; RNA Seq,GSM7963640 r1,GSM7963640,1,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476691,,loader:fastq load.py,k10.AATCGAACTC-TTAGACCTTC.H37F5DSX2_AATCGAACTC-TTAGACCTTC_L003_R1.fastq.gz k10.AATCGAACTC-TTAGACCTTC.H37F5DSX2_AATCGAACTC-TTAGACCTTC_L003_R2.fastq.gz,fastq fastq,10739126946.0,35560023.0,GSM7963640 r1,0:151 1:151,A:2888527520;C:2418475992;G:2670968816;T:2760983764;N:170854,151,151,,,2888527520,2418475992,2670968816,2760983764,170854,SRX22833142,SRS19813582,SRA1765718,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.95306,0.95846,0.05658,0.05746,0.73269,0.73714,0.42191,0.43088,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
29109,SRR27151545,SRX22833141,SRS19813581,SRP476691,PRJNA1050282,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye],GSE249751,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,5 dpf larval eyes  samd7 /   rep1,GSM7963639,,source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing,5 dpf larval eyes  samd7 /   rep1,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf larval eyes. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / ,GSM7963639,GSM7963639: 5 dpf larval eyes  samd7 /   rep1; Danio rerio; RNA Seq,GSM7963639 r1,GSM7963639,1,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476691,,loader:fastq load.py,k11.CCGAAGATAA-TGGATTAACG.H37F5DSX2_CCGAAGATAA-TGGATTAACG_L003_R1.fastq.gz k11.CCGAAGATAA-TGGATTAACG.H37F5DSX2_CCGAAGATAA-TGGATTAACG_L003_R2.fastq.gz,fastq fastq,10514289154.0,34815527.0,GSM7963639 r1,0:151 1:151,A:2862247233;C:2377266250;G:2528917605;T:2745692826;N:165240,151,151,,,2862247233,2377266250,2528917605,2745692826,165240,SRX22833141,SRS19813581,SRA1765718,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.95376,0.95966,0.05526,0.05681,0.72965,0.73273,0.42276,0.43148,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
29110,SRR27151546,SRX22833140,SRS19813578,SRP476691,PRJNA1050282,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye],GSE249751,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,5 dpf larval eyes  WT  rep3,GSM7963638,,source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing,5 dpf larval eyes  WT  rep3,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf larval eyes. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:eye|developmental stage:5 dpf larvae|genotype:WT,GSM7963638,GSM7963638: 5 dpf larval eyes  WT  rep3; Danio rerio; RNA Seq,GSM7963638 r1,GSM7963638,1,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476691,,loader:fastq load.py,w6.CCTTGCCGTA-TAGTACACAG.H37F5DSX2_CCTTGCCGTA-TAGTACACAG_L003_R1.fastq.gz w6.CCTTGCCGTA-TAGTACACAG.H37F5DSX2_CCTTGCCGTA-TAGTACACAG_L003_R2.fastq.gz,fastq fastq,11943994904.0,39549652.0,GSM7963638 r1,0:151 1:151,A:3182349655;C:2708994785;G:2976982793;T:3075478468;N:189203,151,151,,,3182349655,2708994785,2976982793,3075478468,189203,SRX22833140,SRS19813578,SRA1765718,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.95522,0.96109,0.04859,0.04955,0.74247,0.74799,0.42424,0.43226,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
29111,SRR27151547,SRX22833139,SRS19813579,SRP476691,PRJNA1050282,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye],GSE249751,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,5 dpf larval eyes  WT  rep2,GSM7963637,,source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing,5 dpf larval eyes  WT  rep2,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf larval eyes. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:eye|developmental stage:5 dpf larvae|genotype:WT,GSM7963637,GSM7963637: 5 dpf larval eyes  WT  rep2; Danio rerio; RNA Seq,GSM7963637 r1,GSM7963637,1,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476691,,loader:fastq load.py,w8.AATCTCAGGC-TCACCAGGAC.H37F5DSX2_AATCTCAGGC-TCACCAGGAC_L003_R1.fastq.gz w8.AATCTCAGGC-TCACCAGGAC.H37F5DSX2_AATCTCAGGC-TCACCAGGAC_L003_R2.fastq.gz,fastq fastq,10471048190.0,34672345.0,GSM7963637 r1,0:151 1:151,A:2767212261;C:2402799397;G:2644524852;T:2656347723;N:163957,151,151,,,2767212261,2402799397,2644524852,2656347723,163957,SRX22833139,SRS19813579,SRA1765718,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.95909,0.96443,0.04132,0.04289,0.74217,0.74631,0.40379,0.41076,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
29112,SRR27151548,SRX22833138,SRS19813580,SRP476691,PRJNA1050282,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye],GSE249751,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,5 dpf larval eyes  WT  rep1,GSM7963636,,source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing,5 dpf larval eyes  WT  rep1,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf larval eyes. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:eye|developmental stage:5 dpf larvae|genotype:WT,GSM7963636,GSM7963636: 5 dpf larval eyes  WT  rep1; Danio rerio; RNA Seq,GSM7963636 r1,GSM7963636,1,To perform RNA seq on 5 dpf larvae  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine  anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C  and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed  eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen  then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total  with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476691,,loader:fastq load.py,w15.AACAGGCAAG-TTCATGGAAG.H37F5DSX2_AACAGGCAAG-TTCATGGAAG_L003_R1.fastq.gz w15.AACAGGCAAG-TTCATGGAAG.H37F5DSX2_AACAGGCAAG-TTCATGGAAG_L003_R2.fastq.gz,fastq fastq,11852131940.0,39245470.0,GSM7963636 r1,0:151 1:151,A:3157263060;C:2691924686;G:2998627934;T:3004129760;N:186500,151,151,,,3157263060,2691924686,2998627934,3004129760,186500,SRX22833138,SRS19813580,SRA1765718,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.95652,0.96043,0.05012,0.05113,0.73198,0.73637,0.42361,0.41636,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,random_priming,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
29113,SRR27151348,SRX22832950,SRS19813390,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  samd7 /   rep3,GSM7963654,,source name:retina|tissue:retina|developmental stage:adult|genotype:samd7 / |geo loc name:missing|collection date:missing,Adult retina  samd7 /   rep3,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:samd7 / ,GSM7963654,GSM7963654: Adult retina  samd7 /   rep3; Danio rerio; RNA Seq,GSM7963654 r1,GSM7963654,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,samd7 3.GTCGACTCCT-ACCTTAGCCG.HJNJTDSX3_GTCGACTCCT-ACCTTAGCCG_L003_R2.fastq.gz samd7 3.GTCGACTCCT-ACCTTAGCCG.HJNJTDSX3_GTCGACTCCT-ACCTTAGCCG_L003_R1.fastq.gz,fastq fastq,12350621596.0,40896098.0,GSM7963654 r1,0:151 1:151,A:3311452403;C:2805529783;G:3049468848;T:3184114382;N:56180,151,151,,,3311452403,2805529783,3049468848,3184114382,56180,SRX22832950,SRS19813390,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.9517,0.9527,0.08772,0.08879,0.73342,0.73574,0.50684,0.51229,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
29114,SRR27151349,SRX22832949,SRS19813389,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  samd7 /   rep2,GSM7963653,,source name:retina|tissue:retina|developmental stage:adult|genotype:samd7 / |geo loc name:missing|collection date:missing,Adult retina  samd7 /   rep2,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:samd7 / ,GSM7963653,GSM7963653: Adult retina  samd7 /   rep2; Danio rerio; RNA Seq,GSM7963653 r1,GSM7963653,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,samd7 2.AACACCAATG-GCACTTACAA.HJNJTDSX3_AACACCAATG-GCACTTACAA_L003_R2.fastq.gz samd7 2.AACACCAATG-GCACTTACAA.HJNJTDSX3_AACACCAATG-GCACTTACAA_L003_R1.fastq.gz,fastq fastq,10779711820.0,35694410.0,GSM7963653 r1,0:151 1:151,A:2944031330;C:2416631581;G:2607925305;T:2811076060;N:47544,151,151,,,2944031330,2416631581,2607925305,2811076060,47544,SRX22832949,SRS19813389,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.94587,0.94807,0.0994,0.10023,0.73837,0.74052,0.50262,0.50849,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
29115,SRR27151350,SRX22832948,SRS19813387,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  samd7 /   rep1,GSM7963652,,source name:retina|tissue:retina|developmental stage:adult|genotype:samd7 / |geo loc name:missing|collection date:missing,Adult retina  samd7 /   rep1,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:samd7 / ,GSM7963652,GSM7963652: Adult retina  samd7 /   rep1; Danio rerio; RNA Seq,GSM7963652 r1,GSM7963652,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,samd7 1.AGAACTGGTG-TGGATTGTAG.HJNJTDSX3_AGAACTGGTG-TGGATTGTAG_L003_R1.fastq.gz samd7 1.AGAACTGGTG-TGGATTGTAG.HJNJTDSX3_AGAACTGGTG-TGGATTGTAG_L003_R2.fastq.gz,fastq fastq,10592879520.0,35075760.0,GSM7963652 r1,0:151 1:151,A:2902239961;C:2373635807;G:2559549595;T:2757407466;N:46691,151,151,,,2902239961,2373635807,2559549595,2757407466,46691,SRX22832948,SRS19813387,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.94718,0.94948,0.09134,0.09292,0.7291,0.73117,0.51985,0.52005,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
29116,SRR27151351,SRX22832947,SRS19813388,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  WT  rep3,GSM7963651,,source name:retina|tissue:retina|developmental stage:adult|genotype:WT|geo loc name:missing|collection date:missing,Adult retina  WT  rep3,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:WT,GSM7963651,GSM7963651: Adult retina  WT  rep3; Danio rerio; RNA Seq,GSM7963651 r1,GSM7963651,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,wt 3.TCCGAAGTGG-ACACAATGGT.HJNJTDSX3_TCCGAAGTGG-ACACAATGGT_L003_R1.fastq.gz wt 3.TCCGAAGTGG-ACACAATGGT.HJNJTDSX3_TCCGAAGTGG-ACACAATGGT_L003_R2.fastq.gz,fastq fastq,11864600916.0,39286758.0,GSM7963651 r1,0:151 1:151,A:3134961848;C:2656797227;G:3067645293;T:3005143714;N:52834,151,151,,,3134961848,2656797227,3067645293,3005143714,52834,SRX22832947,SRS19813388,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.94961,0.95129,0.08731,0.08788,0.75465,0.75739,0.52752,0.51933,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
29117,SRR27151352,SRX22832946,SRS19813385,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  WT  rep2,GSM7963650,,source name:retina|tissue:retina|developmental stage:adult|genotype:WT|geo loc name:missing|collection date:missing,Adult retina  WT  rep2,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:WT,GSM7963650,GSM7963650: Adult retina  WT  rep2; Danio rerio; RNA Seq,GSM7963650 r1,GSM7963650,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,wt 2.CGATAGCAGG-TAAGTGTCGA.HJNJTDSX3_CGATAGCAGG-TAAGTGTCGA_L003_R1.fastq.gz wt 2.CGATAGCAGG-TAAGTGTCGA.HJNJTDSX3_CGATAGCAGG-TAAGTGTCGA_L003_R2.fastq.gz,fastq fastq,11537286672.0,38202936.0,GSM7963650 r1,0:151 1:151,A:3128579183;C:2619829672;G:2797531802;T:2991294275;N:51740,151,151,,,3128579183,2619829672,2797531802,2991294275,51740,SRX22832946,SRS19813385,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.95108,0.9523,0.08612,0.08648,0.754,0.75643,0.5265,0.51457,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
29118,SRR27151353,SRX22832945,SRS19813386,SRP476686,PRJNA1050286,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [adult],GSE249754,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces.,parent bioproject:PRJNA1050288,pubmed:39531499,,Adult retina  WT  rep1,GSM7963649,,source name:retina|tissue:retina|developmental stage:adult|genotype:WT|geo loc name:missing|collection date:missing,Adult retina  WT  rep1,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from adult retina. Genes are ranked by p adj.,retina,,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,tissue:retina|developmental stage:adult|genotype:WT,GSM7963649,GSM7963649: Adult retina  WT  rep1; Danio rerio; RNA Seq,GSM7963649 r1,GSM7963649,1,To perform RNA seq on 3 mpf adult retinas  samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring and grown to maturity. post adults were genotyped  pairs of retinas from three male WT and samd7stl888/stl888 zebrafish were dissected. The pair of retinas from an individual zebrafish were then combined to make one replicate  and RNA was extracted using the RNEasy Mini Kit Qiagen with on column DNAse treatment using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 20 37 ng/µl 600 1100 ng total  with RIN scores ranging from 9 9.5; there was minimal RNA degradation as shown by Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476686,,loader:fastq load.py,wt 1.AACACCGGTT-ACGAGACGTC.HJNJTDSX3_AACACCGGTT-ACGAGACGTC_L003_R2.fastq.gz wt 1.AACACCGGTT-ACGAGACGTC.HJNJTDSX3_AACACCGGTT-ACGAGACGTC_L003_R1.fastq.gz,fastq fastq,15142192118.0,50139709.0,GSM7963649 r1,0:151 1:151,A:4123269688;C:3413024919;G:3665579705;T:3940250217;N:67589,151,151,,,4123269688,3413024919,3665579705,3940250217,67589,SRX22832945,SRS19813386,SRA1765771,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.94752,0.94913,0.08393,0.08515,0.75446,0.75672,0.46043,0.506,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Adult,Adult,Eye,Sensory System
29119,SRR27151354,SRX22832956,SRS19813396,SRP476687,PRJNA1050291,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td],GSE249755,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4.,parent bioproject:PRJNA1050288,pubmed:39531499,,thrb:tdTomato+ cells from 5 dpf larval eyes  samd7 /   rep3,GSM7963660,,source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing,thrb:tdTomato+ cells from 5 dpf larval eyes  samd7 /   rep3,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / ,GSM7963660,GSM7963660: thrb:tdTomato+ cells from 5 dpf larval eyes  samd7 /   rep3; Danio rerio; RNA Seq,GSM7963660 r1,GSM7963660,1,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476687,,loader:fastq load.py,samd7_1_rna_6_2_22.AGAAGGAACA-TGGTAGATGC.HNGJJDSX3_AGAAGGAACA-TGGTAGATGC_L003_R1.fastq.gz samd7_1_rna_6_2_22.AGAAGGAACA-TGGTAGATGC.HNGJJDSX3_AGAAGGAACA-TGGTAGATGC_L003_R2.fastq.gz,fastq fastq,10483631624.0,34714012.0,GSM7963660 r1,0:151 1:151,A:2778161057;C:2394557806;G:2692864342;T:2618022344;N:26075,151,151,,,2778161057,2394557806,2692864342,2618022344,26075,SRX22832956,SRS19813396,SRA1765707,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.91943,0.91641,0.08589,0.08581,0.78748,0.79774,0.5086,0.50263,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
29120,SRR27151355,SRX22832955,SRS19813395,SRP476687,PRJNA1050291,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td],GSE249755,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4.,parent bioproject:PRJNA1050288,pubmed:39531499,,thrb:tdTomato+ cells from 5 dpf larval eyes  samd7 /   rep2,GSM7963659,,source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing,thrb:tdTomato+ cells from 5 dpf larval eyes  samd7 /   rep2,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / ,GSM7963659,GSM7963659: thrb:tdTomato+ cells from 5 dpf larval eyes  samd7 /   rep2; Danio rerio; RNA Seq,GSM7963659 r1,GSM7963659,1,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476687,,loader:fastq load.py,samd7_1_rna_6_1_22.AGACAGACGT-TATCAGTGCA.HNGJJDSX3_AGACAGACGT-TATCAGTGCA_L003_R1.fastq.gz samd7_1_rna_6_1_22.AGACAGACGT-TATCAGTGCA.HNGJJDSX3_AGACAGACGT-TATCAGTGCA_L003_R2.fastq.gz,fastq fastq,12234446424.0,40511412.0,GSM7963659 r1,0:151 1:151,A:3397427491;C:2650252489;G:2963872812;T:3222862933;N:30699,151,151,,,3397427491,2650252489,2963872812,3222862933,30699,SRX22832955,SRS19813395,SRA1765707,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.89702,0.8967,0.14358,0.14658,0.77309,0.77962,0.5468,0.44645,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
29121,SRR27151356,SRX22832954,SRS19813394,SRP476687,PRJNA1050291,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td],GSE249755,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4.,parent bioproject:PRJNA1050288,pubmed:39531499,,thrb:tdTomato+ cells from 5 dpf larval eyes  samd7 /   rep1,GSM7963658,,source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing,thrb:tdTomato+ cells from 5 dpf larval eyes  samd7 /   rep1,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / ,GSM7963658,GSM7963658: thrb:tdTomato+ cells from 5 dpf larval eyes  samd7 /   rep1; Danio rerio; RNA Seq,GSM7963658 r1,GSM7963658,1,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476687,,loader:fastq load.py,samd7_rna_5_10_22.CAATTCACGC-ACATCCTGCG.HNGJJDSX3_CAATTCACGC-ACATCCTGCG_L003_R1.fastq.gz samd7_rna_5_10_22.CAATTCACGC-ACATCCTGCG.HNGJJDSX3_CAATTCACGC-ACATCCTGCG_L003_R2.fastq.gz,fastq fastq,11352128660.0,37589830.0,GSM7963658 r1,0:151 1:151,A:3035915425;C:2447970512;G:2970538003;T:2897676299;N:28421,151,151,,,3035915425,2447970512,2970538003,2897676299,28421,SRX22832954,SRS19813394,SRA1765707,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.90706,0.91061,0.09833,0.102,0.78186,0.78948,0.54785,0.47215,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
29122,SRR27151357,SRX22832953,SRS19813393,SRP476687,PRJNA1050291,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td],GSE249755,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4.,parent bioproject:PRJNA1050288,pubmed:39531499,,thrb:tdTomato+ cells from 5 dpf larval eyes  WT  rep3,GSM7963657,,source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing,thrb:tdTomato+ cells from 5 dpf larval eyes  WT  rep3,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT,GSM7963657,GSM7963657: thrb:tdTomato+ cells from 5 dpf larval eyes  WT  rep3; Danio rerio; RNA Seq,GSM7963657 r1,GSM7963657,1,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476687,,loader:fastq load.py,wt_3_a_rna_5_12_22.CACCATTGTA-TACCAATTGC.HNGJJDSX3_CACCATTGTA-TACCAATTGC_L003_R1.fastq.gz wt_3_a_rna_5_12_22.CACCATTGTA-TACCAATTGC.HNGJJDSX3_CACCATTGTA-TACCAATTGC_L003_R2.fastq.gz,fastq fastq,9723911364.0,32198382.0,GSM7963657 r1,0:151 1:151,A:2610813507;C:2104688166;G:2520224929;T:2488160661;N:24101,151,151,,,2610813507,2104688166,2520224929,2488160661,24101,SRX22832953,SRS19813393,SRA1765707,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.62594,0.60745,0.07012,0.07039,0.81728,0.82578,0.50983,0.57347,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
29123,SRR27151358,SRX22832952,SRS19813392,SRP476687,PRJNA1050291,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td],GSE249755,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4.,parent bioproject:PRJNA1050288,pubmed:39531499,,thrb:tdTomato+ cells from 5 dpf larval eyes  WT  rep2,GSM7963656,,source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing,thrb:tdTomato+ cells from 5 dpf larval eyes  WT  rep2,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT,GSM7963656,GSM7963656: thrb:tdTomato+ cells from 5 dpf larval eyes  WT  rep2; Danio rerio; RNA Seq,GSM7963656 r1,GSM7963656,1,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476687,,loader:fastq load.py,wt_2_b_rna_5_12_22.AAGACTCTCG-TAAGTCTGGC.HNGJJDSX3_AAGACTCTCG-TAAGTCTGGC_L003_R1.fastq.gz wt_2_b_rna_5_12_22.AAGACTCTCG-TAAGTCTGGC.HNGJJDSX3_AAGACTCTCG-TAAGTCTGGC_L003_R2.fastq.gz,fastq fastq,10722667946.0,35505523.0,GSM7963656 r1,0:151 1:151,A:2872256957;C:2358147851;G:2771142656;T:2721093653;N:26829,151,151,,,2872256957,2358147851,2771142656,2721093653,26829,SRX22832952,SRS19813392,SRA1765707,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.90028,0.8986,0.10012,0.10225,0.7973,0.80389,0.56209,0.56007,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
29124,SRR27151359,SRX22832951,SRS19813391,SRP476687,PRJNA1050291,Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td],GSE249755,Transcriptome Analysis,The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here  we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 /  retina  red cones are transformed to hybrid red/UV sensitive cones  green cones are transfated to blue cones  and the number of rods is greatly reduced. In the mouse Samd7 /  retina  dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether  Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones  thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4.,parent bioproject:PRJNA1050288,pubmed:39531499,,thrb:tdTomato+ cells from 5 dpf larval eyes  WT  rep1,GSM7963655,,source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing,thrb:tdTomato+ cells from 5 dpf larval eyes  WT  rep1,Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next  Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression  DESeq2 1.34.0 was used in R 4.1.3  using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific  manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 /  adult retina Table S3  we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 /  and WT replicates  derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj.,eye,,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT,GSM7963655,GSM7963655: thrb:tdTomato+ cells from 5 dpf larval eyes  WT  rep1; Danio rerio; RNA Seq,GSM7963655 r1,GSM7963655,1,To perform RNA seq on 5 dpf thrb:tdTomato+ cells  the following crosses were performed: WT × WT;thrb:tdTomato+/  or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen  and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total  with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples  and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18  duty factor 20%  cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase  Klenow Fragment DNA Polymerase  and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo   and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples  and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags  using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP476687,,loader:fastq load.py,wt_rna_5_10_22.CCACCTTCAA-ACCATCGAGG.HNGJJDSX3_CCACCTTCAA-ACCATCGAGG_L003_R1.fastq.gz wt_rna_5_10_22.CCACCTTCAA-ACCATCGAGG.HNGJJDSX3_CCACCTTCAA-ACCATCGAGG_L003_R2.fastq.gz,fastq fastq,9875387618.0,32699959.0,GSM7963655 r1,0:151 1:151,A:2640364023;C:2083842037;G:2621465276;T:2529691405;N:24877,151,151,,,2640364023,2083842037,2621465276,2529691405,24877,SRX22832951,SRS19813391,SRA1765707,"Pathology and Immunology, Washington University School of Medicine","Pathology and Immunology, Washington University School of Medicine",2,0.90131,0.90429,0.10837,0.1106,0.79523,0.80182,0.50934,0.58039,151,151,B,B,biological fallback assumption,illumina,novaseq_era,3prime,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2023-12-08,Larval,Larval,Eye,Sensory System
33202,SRR29848463,SRX25346228,SRS22013442,SRP520276,PRJNA1136505,Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish,GSE272355,Transcriptome Analysis,Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.,,pubmed:39742644,,IPP 120hpf eye replicate4,GSM8399280,,source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing,IPP 120hpf eye replicate4,Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample,Dissected eye,Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,Embryos were spawned and maintained in system water,tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf,GSM8399280,GSM8399280: IPP 120hpf eye replicate4; Danio rerio; RNA Seq,GSM8399280 r1,GSM8399280,1,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP520276,,,IPP_eye_4_1.fq.gz IPP_eye_4_2.fq.gz,fastq fastq,7072359000.0,23574530.0,GSM8399280 r1,0:150 1:150,A:1896065137;C:1651795911;G:1640296836;T:1877949054;N:6252062,150,150,,,1896065137,1651795911,1640296836,1877949054,6252062,SRX25346228,SRS22013442,SRA1925887,"Dasgupta lab, Biological Sciences, Clemson University","Dasgupta lab, Biological Sciences, Clemson University",2,0.90538,0.89728,0.10331,0.10225,0.70593,0.70688,0.44853,0.44733,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2024-07-16,Multi-stage,Multi-stage,Eye,Sensory System
33203,SRR29848464,SRX25346227,SRS22013441,SRP520276,PRJNA1136505,Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish,GSE272355,Transcriptome Analysis,Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.,,pubmed:39742644,,IPP 120hpf eye replicate3,GSM8399279,,source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing,IPP 120hpf eye replicate3,Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample,Dissected eye,Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,Embryos were spawned and maintained in system water,tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf,GSM8399279,GSM8399279: IPP 120hpf eye replicate3; Danio rerio; RNA Seq,GSM8399279 r1,GSM8399279,1,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP520276,,,IPP_eye_3_1.fq.gz IPP_eye_3_2.fq.gz,fastq fastq,6537519300.0,21791731.0,GSM8399279 r1,0:150 1:150,A:1760227857;C:1520738786;G:1507946481;T:1742862368;N:5743808,150,150,,,1760227857,1520738786,1507946481,1742862368,5743808,SRX25346227,SRS22013441,SRA1925887,"Dasgupta lab, Biological Sciences, Clemson University","Dasgupta lab, Biological Sciences, Clemson University",2,0.90945,0.90902,0.10894,0.10846,0.70431,0.7055,0.44535,0.43463,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2024-07-16,Multi-stage,Multi-stage,Eye,Sensory System
33204,SRR29848465,SRX25346226,SRS22013440,SRP520276,PRJNA1136505,Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish,GSE272355,Transcriptome Analysis,Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.,,pubmed:39742644,,IPP 120hpf eye replicate2,GSM8399278,,source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing,IPP 120hpf eye replicate2,Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample,Dissected eye,Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,Embryos were spawned and maintained in system water,tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf,GSM8399278,GSM8399278: IPP 120hpf eye replicate2; Danio rerio; RNA Seq,GSM8399278 r1,GSM8399278,1,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP520276,,,IPP_eye_2_1.fq.gz IPP_eye_2_2.fq.gz,fastq fastq,7374435900.0,24581453.0,GSM8399278 r1,0:150 1:150,A:1986621253;C:1713862328;G:1699590477;T:1967874898;N:6486944,150,150,,,1986621253,1713862328,1699590477,1967874898,6486944,SRX25346226,SRS22013440,SRA1925887,"Dasgupta lab, Biological Sciences, Clemson University","Dasgupta lab, Biological Sciences, Clemson University",2,0.9091,0.90128,0.11122,0.1097,0.70201,0.70266,0.44395,0.4416,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2024-07-16,Multi-stage,Multi-stage,Eye,Sensory System
33205,SRR29848466,SRX25346225,SRS22013439,SRP520276,PRJNA1136505,Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish,GSE272355,Transcriptome Analysis,Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.,,pubmed:39742644,,IPP 120hpf eye replicate1,GSM8399277,,source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing,IPP 120hpf eye replicate1,Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample,Dissected eye,Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,Embryos were spawned and maintained in system water,tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf,GSM8399277,GSM8399277: IPP 120hpf eye replicate1; Danio rerio; RNA Seq,GSM8399277 r1,GSM8399277,1,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP520276,,,IPP_eye_1_1.fq.gz IPP_eye_1_2.fq.gz,fastq fastq,6538011600.0,21793372.0,GSM8399277 r1,0:150 1:150,A:1758764189;C:1520242338;G:1510361700;T:1742917780;N:5725593,150,150,,,1758764189,1520242338,1510361700,1742917780,5725593,SRX25346225,SRS22013439,SRA1925887,"Dasgupta lab, Biological Sciences, Clemson University","Dasgupta lab, Biological Sciences, Clemson University",2,0.91402,0.90585,0.11702,0.11558,0.70029,0.70094,0.45385,0.45435,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2024-07-16,Multi-stage,Multi-stage,Eye,Sensory System
33206,SRR29848467,SRX25346224,SRS22013438,SRP520276,PRJNA1136505,Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish,GSE272355,Transcriptome Analysis,Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.,,pubmed:39742644,,DMSO 120hpf eye replicate4,GSM8399276,,source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing,DMSO 120hpf eye replicate4,Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample,Dissected eye,Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,Embryos were spawned and maintained in system water,tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf,GSM8399276,GSM8399276: DMSO 120hpf eye replicate4; Danio rerio; RNA Seq,GSM8399276 r1,GSM8399276,1,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP520276,,,Ctrl_eye_4_1.fq.gz Ctrl_eye_4_2.fq.gz,fastq fastq,7198057200.0,23993524.0,GSM8399276 r1,0:150 1:150,A:1929066670;C:1680279530;G:1672121671;T:1910263876;N:6325453,150,150,,,1929066670,1680279530,1672121671,1910263876,6325453,SRX25346224,SRS22013438,SRA1925887,"Dasgupta lab, Biological Sciences, Clemson University","Dasgupta lab, Biological Sciences, Clemson University",2,0.91947,0.90384,0.11309,0.11094,0.69576,0.69779,0.45803,0.45394,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2024-07-16,Multi-stage,Multi-stage,Eye,Sensory System
33207,SRR29848468,SRX25346223,SRS22013437,SRP520276,PRJNA1136505,Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish,GSE272355,Transcriptome Analysis,Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.,,pubmed:39742644,,DMSO 120hpf eye replicate3,GSM8399275,,source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing,DMSO 120hpf eye replicate3,Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample,Dissected eye,Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,Embryos were spawned and maintained in system water,tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf,GSM8399275,GSM8399275: DMSO 120hpf eye replicate3; Danio rerio; RNA Seq,GSM8399275 r1,GSM8399275,1,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP520276,,,Ctrl_eye_3_1.fq.gz Ctrl_eye_3_2.fq.gz,fastq fastq,6349681200.0,21165604.0,GSM8399275 r1,0:150 1:150,A:1713020668;C:1474226584;G:1462505802;T:1694350186;N:5577960,150,150,,,1713020668,1474226584,1462505802,1694350186,5577960,SRX25346223,SRS22013437,SRA1925887,"Dasgupta lab, Biological Sciences, Clemson University","Dasgupta lab, Biological Sciences, Clemson University",2,0.89548,0.89606,0.09628,0.09664,0.71102,0.71161,0.44199,0.4354,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2024-07-16,Multi-stage,Multi-stage,Eye,Sensory System
33208,SRR29848469,SRX25346222,SRS22013436,SRP520276,PRJNA1136505,Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish,GSE272355,Transcriptome Analysis,Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.,,pubmed:39742644,,DMSO 120hpf eye replicate2,GSM8399274,,source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing,DMSO 120hpf eye replicate2,Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample,Dissected eye,Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,Embryos were spawned and maintained in system water,tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf,GSM8399274,GSM8399274: DMSO 120hpf eye replicate2; Danio rerio; RNA Seq,GSM8399274 r1,GSM8399274,1,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP520276,,,Ctrl_eye_2_1.fq.gz Ctrl_eye_2_2.fq.gz,fastq fastq,6861299400.0,22870998.0,GSM8399274 r1,0:150 1:150,A:1839006136;C:1604484415;G:1591747628;T:1820307442;N:5753779,150,150,,,1839006136,1604484415,1591747628,1820307442,5753779,SRX25346222,SRS22013436,SRA1925887,"Dasgupta lab, Biological Sciences, Clemson University","Dasgupta lab, Biological Sciences, Clemson University",2,0.84164,0.83344,0.09914,0.09758,0.72034,0.72088,0.44273,0.4389,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2024-07-16,Multi-stage,Multi-stage,Eye,Sensory System
33209,SRR29848470,SRX25346221,SRS22013435,SRP520276,PRJNA1136505,Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish,GSE272355,Transcriptome Analysis,Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.,,pubmed:39742644,,DMSO 120hpf eye replicate1,GSM8399273,,source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing,DMSO 120hpf eye replicate1,Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample,Dissected eye,Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,Embryos were spawned and maintained in system water,tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf,GSM8399273,GSM8399273: DMSO 120hpf eye replicate1; Danio rerio; RNA Seq,GSM8399273 r1,GSM8399273,1,Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP520276,,,Ctrl_eye_1_1.fq.gz Ctrl_eye_1_2.fq.gz,fastq fastq,6544491000.0,21814970.0,GSM8399273 r1,0:150 1:150,A:1774622867;C:1510819173;G:1498655117;T:1754689449;N:5704394,150,150,,,1774622867,1510819173,1498655117,1754689449,5704394,SRX25346221,SRS22013435,SRA1925887,"Dasgupta lab, Biological Sciences, Clemson University","Dasgupta lab, Biological Sciences, Clemson University",2,0.86147,0.86095,0.11217,0.11159,0.71319,0.71352,0.44434,0.43886,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2024-07-16,Multi-stage,Multi-stage,Eye,Sensory System
33274,SRR29884407,SRX25380711,SRS22046064,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  wh5  Male 5,GSM8406321,,source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing,Brain  wh5  Male 5,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:wh5,GSM8406321,GSM8406321: Brain  wh5  Male 5; Danio rerio; RNA Seq,GSM8406321 r1,GSM8406321,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample20KOMaleBrain_R1.fastq Sample20KOMaleBrain_R2.fastq,fastq fastq,5509276088.0,27917150.0,GSM8406321 r1,0:98.67 1:98.67,A:1498190193;C:1242495192;G:1267229536;T:1499431726;N:1929441,98,98,,,1498190193,1242495192,1267229536,1499431726,1929441,SRX25380711,SRS22046064,SRA1927371,Oregon State University,Oregon State University,2,0.94576,0.94515,0.14102,0.13871,0.69187,0.69077,0.52554,0.53007,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33275,SRR29884408,SRX25380710,SRS22046063,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  wh5  Male 4,GSM8406320,,source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing,Brain  wh5  Male 4,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:wh5,GSM8406320,GSM8406320: Brain  wh5  Male 4; Danio rerio; RNA Seq,GSM8406320 r1,GSM8406320,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample19KOMaleBrain_R1.fastq Sample19KOMaleBrain_R2.fastq,fastq fastq,6985356408.0,35379007.0,GSM8406320 r1,0:98.72 1:98.72,A:1889039547;C:1582622229;G:1620512342;T:1890746302;N:2435988,98,98,,,1889039547,1582622229,1620512342,1890746302,2435988,SRX25380710,SRS22046063,SRA1927371,Oregon State University,Oregon State University,2,0.94197,0.94411,0.14763,0.14597,0.69852,0.69826,0.54705,0.54822,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33276,SRR29884409,SRX25380709,SRS22046062,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  wh5  Male 3,GSM8406319,,source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing,Brain  wh5  Male 3,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:wh5,GSM8406319,GSM8406319: Brain  wh5  Male 3; Danio rerio; RNA Seq,GSM8406319 r1,GSM8406319,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample18KOMaleBrain_R1.fastq Sample18KOMaleBrain_R2.fastq,fastq fastq,5864072768.0,29837549.0,GSM8406319 r1,0:98.27 1:98.27,A:1609423180;C:1310248473;G:1328624911;T:1613750029;N:2026175,98,98,,,1609423180,1310248473,1328624911,1613750029,2026175,SRX25380709,SRS22046062,SRA1927371,Oregon State University,Oregon State University,2,0.94007,0.94233,0.14021,0.1386,0.69376,0.69317,0.51507,0.52214,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33277,SRR29884410,SRX25380708,SRS22046061,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  wh5  Male 2,GSM8406318,,source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing,Brain  wh5  Male 2,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:wh5,GSM8406318,GSM8406318: Brain  wh5  Male 2; Danio rerio; RNA Seq,GSM8406318 r1,GSM8406318,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample17KOMaleBrain_R1.fastq Sample17KOMaleBrain_R2.fastq,fastq fastq,5841328432.0,29860768.0,GSM8406318 r1,0:97.81 1:97.81,A:1606036785;C:1302920703;G:1321021765;T:1609306125;N:2043054,97,97,,,1606036785,1302920703,1321021765,1609306125,2043054,SRX25380708,SRS22046061,SRA1927371,Oregon State University,Oregon State University,2,0.9429,0.94295,0.14247,0.14023,0.69808,0.69739,0.51804,0.51798,69,69,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33278,SRR29884411,SRX25380707,SRS22046060,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  wh5  Male 1,GSM8406317,,source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing,Brain  wh5  Male 1,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:wh5,GSM8406317,GSM8406317: Brain  wh5  Male 1; Danio rerio; RNA Seq,GSM8406317 r1,GSM8406317,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample16KOMaleBrain_R1.fastq Sample16KOMaleBrain_R2.fastq,fastq fastq,6061816166.0,30929476.0,GSM8406317 r1,0:97.99 1:97.99,A:1666435568;C:1352308656;G:1373281492;T:1667671946;N:2118504,97,97,,,1666435568,1352308656,1373281492,1667671946,2118504,SRX25380707,SRS22046060,SRA1927371,Oregon State University,Oregon State University,2,0.94198,0.9434,0.14745,0.14621,0.69201,0.69138,0.52388,0.52247,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33279,SRR29884412,SRX25380706,SRS22046059,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  wh5  Female 5,GSM8406316,,source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing,Brain  wh5  Female 5,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:wh5,GSM8406316,GSM8406316: Brain  wh5  Female 5; Danio rerio; RNA Seq,GSM8406316 r1,GSM8406316,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample15KOFemaleBrain_R1.fastq Sample15KOFemaleBrain_R2.fastq,fastq fastq,5830172008.0,29715950.0,GSM8406316 r1,0:98.10 1:98.10,A:1585225847;C:1316585087;G:1339955604;T:1586384657;N:2020813,98,98,,,1585225847,1316585087,1339955604,1586384657,2020813,SRX25380706,SRS22046059,SRA1927371,Oregon State University,Oregon State University,2,0.94307,0.94571,0.13598,0.13423,0.69341,0.69309,0.52103,0.50706,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33280,SRR29884413,SRX25380705,SRS22046058,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  wh5  Female 4,GSM8406315,,source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing,Brain  wh5  Female 4,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:wh5,GSM8406315,GSM8406315: Brain  wh5  Female 4; Danio rerio; RNA Seq,GSM8406315 r1,GSM8406315,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample14KOFemaleBrain_R1.fastq Sample14KOFemaleBrain_R2.fastq,fastq fastq,6700791892.0,34096304.0,GSM8406315 r1,0:98.26 1:98.26,A:1817874372;C:1516000049;G:1546573687;T:1818017657;N:2326127,98,98,,,1817874372,1516000049,1546573687,1818017657,2326127,SRX25380705,SRS22046058,SRA1927371,Oregon State University,Oregon State University,2,0.94342,0.94623,0.13719,0.13523,0.69313,0.69254,0.53293,0.53816,84,84,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33281,SRR29884414,SRX25380704,SRS22046057,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  wh5  Female 3,GSM8406314,,source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing,Brain  wh5  Female 3,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:wh5,GSM8406314,GSM8406314: Brain  wh5  Female 3; Danio rerio; RNA Seq,GSM8406314 r1,GSM8406314,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample13KOFemaleBrain_R2.fastq Sample13KOFemaleBrain_R1.fastq,fastq fastq,6308152444.0,32040291.0,GSM8406314 r1,0:98.44 1:98.44,A:1698706705;C:1436132175;G:1472501608;T:1698611730;N:2200226,98,98,,,1698706705,1436132175,1472501608,1698611730,2200226,SRX25380704,SRS22046057,SRA1927371,Oregon State University,Oregon State University,2,0.94654,0.94476,0.1362,0.13304,0.694,0.69321,0.54515,0.53479,91,91,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33282,SRR29884415,SRX25380703,SRS22046056,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  wh5  Female 2,GSM8406313,,source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing,Brain  wh5  Female 2,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:wh5,GSM8406313,GSM8406313: Brain  wh5  Female 2; Danio rerio; RNA Seq,GSM8406313 r1,GSM8406313,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample12KOFemaleBrain_R1.fastq Sample12KOFemaleBrain_R2.fastq,fastq fastq,6503673262.0,33197897.0,GSM8406313 r1,0:97.95 1:97.95,A:1781196226;C:1457467194;G:1479672271;T:1783090598;N:2246973,97,97,,,1781196226,1457467194,1479672271,1783090598,2246973,SRX25380703,SRS22046056,SRA1927371,Oregon State University,Oregon State University,2,0.94227,0.94462,0.13793,0.13614,0.69359,0.69355,0.52971,0.52982,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33283,SRR29884416,SRX25380702,SRS22046055,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  wh5  Female 1,GSM8406312,,source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing,Brain  wh5  Female 1,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:wh5,GSM8406312,GSM8406312: Brain  wh5  Female 1; Danio rerio; RNA Seq,GSM8406312 r1,GSM8406312,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample11KOFemaleBrain_R1.fastq Sample11KOFemaleBrain_R2.fastq,fastq fastq,5803578222.0,29408217.0,GSM8406312 r1,0:98.67 1:98.67,A:1586553028;C:1303184285;G:1323602566;T:1588219875;N:2018468,98,98,,,1586553028,1303184285,1323602566,1588219875,2018468,SRX25380702,SRS22046055,SRA1927371,Oregon State University,Oregon State University,2,0.94183,0.94513,0.1442,0.14286,0.6942,0.6942,0.51627,0.51673,93,93,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33284,SRR29884417,SRX25380701,SRS22046053,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  WT  Male 5,GSM8406311,,source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing,Brain  WT  Male 5,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:WT,GSM8406311,GSM8406311: Brain  WT  Male 5; Danio rerio; RNA Seq,GSM8406311 r1,GSM8406311,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample10WTMaleBrain_R1.fastq Sample10WTMaleBrain_R2.fastq,fastq fastq,4558024898.0,24051338.0,GSM8406311 r1,0:94.76 1:94.76,A:1220269093;C:1048518583;G:1068311203;T:1219299559;N:1626460,94,94,,,1220269093,1048518583,1068311203,1219299559,1626460,SRX25380701,SRS22046053,SRA1927371,Oregon State University,Oregon State University,2,0.93188,0.93167,0.1413,0.13958,0.70814,0.70875,0.52962,0.53051,80,80,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33285,SRR29884418,SRX25380700,SRS22046052,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  WT  Male 4,GSM8406310,,source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing,Brain  WT  Male 4,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:WT,GSM8406310,GSM8406310: Brain  WT  Male 4; Danio rerio; RNA Seq,GSM8406310 r1,GSM8406310,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample9WTMaleBrain_R1.fastq Sample9WTMaleBrain_R2.fastq,fastq fastq,5130577372.0,26157026.0,GSM8406310 r1,0:98.07 1:98.07,A:1409899035;C:1143333235;G:1163465644;T:1412102322;N:1777136,98,98,,,1409899035,1143333235,1163465644,1412102322,1777136,SRX25380700,SRS22046052,SRA1927371,Oregon State University,Oregon State University,2,0.94388,0.94533,0.13794,0.13603,0.69907,0.69867,0.52585,0.51928,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33286,SRR29884419,SRX25380699,SRS22046054,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  WT  Male 3,GSM8406309,,source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing,Brain  WT  Male 3,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:WT,GSM8406309,GSM8406309: Brain  WT  Male 3; Danio rerio; RNA Seq,GSM8406309 r1,GSM8406309,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample8WTMaleBrain_R1.fastq Sample8WTMaleBrain_R2.fastq,fastq fastq,7972815402.0,40447690.0,GSM8406309 r1,0:98.56 1:98.56,A:2168632819;C:1797135023;G:1834247957;T:2170022014;N:2777589,98,98,,,2168632819,1797135023,1834247957,2170022014,2777589,SRX25380699,SRS22046054,SRA1927371,Oregon State University,Oregon State University,2,0.94357,0.94705,0.13542,0.13436,0.69915,0.69863,0.52491,0.53063,81,81,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33287,SRR29884420,SRX25380698,SRS22046051,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  WT  Male 2,GSM8406308,,source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing,Brain  WT  Male 2,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:WT,GSM8406308,GSM8406308: Brain  WT  Male 2; Danio rerio; RNA Seq,GSM8406308 r1,GSM8406308,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample7WTMaleBrain_R1.fastq Sample7WTMaleBrain_R2.fastq,fastq fastq,7049713238.0,35734267.0,GSM8406308 r1,0:98.64 1:98.64,A:1906626428;C:1601451933;G:1627879106;T:1911302856;N:2452915,98,98,,,1906626428,1601451933,1627879106,1911302856,2452915,SRX25380698,SRS22046051,SRA1927371,Oregon State University,Oregon State University,2,0.9436,0.94611,0.15189,0.14982,0.70272,0.70293,0.54976,0.55028,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33288,SRR29884421,SRX25380697,SRS22046050,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  WT  Male 1,GSM8406307,,source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing,Brain  WT  Male 1,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:WT,GSM8406307,GSM8406307: Brain  WT  Male 1; Danio rerio; RNA Seq,GSM8406307 r1,GSM8406307,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample6WTMaleBrain_R1.fastq Sample6WTMaleBrain_R2.fastq,fastq fastq,5957369076.0,30406342.0,GSM8406307 r1,0:97.96 1:97.96,A:1609314070;C:1357455510;G:1376051649;T:1612447643;N:2100204,97,97,,,1609314070,1357455510,1376051649,1612447643,2100204,SRX25380697,SRS22046050,SRA1927371,Oregon State University,Oregon State University,2,0.94515,0.94596,0.13859,0.13741,0.69459,0.69386,0.5113,0.50829,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33289,SRR29884422,SRX25380696,SRS22046048,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  WT  Female 5,GSM8406306,,source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing,Brain  WT  Female 5,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:WT,GSM8406306,GSM8406306: Brain  WT  Female 5; Danio rerio; RNA Seq,GSM8406306 r1,GSM8406306,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample5WTFemaleBrain_R1.fastq Sample5WTFemaleBrain_R2.fastq,fastq fastq,6253800764.0,31754862.0,GSM8406306 r1,0:98.47 1:98.47,A:1706349321;C:1408396210;G:1425535859;T:1711348232;N:2171142,98,98,,,1706349321,1408396210,1425535859,1711348232,2171142,SRX25380696,SRS22046048,SRA1927371,Oregon State University,Oregon State University,2,0.94054,0.9433,0.13645,0.13468,0.69351,0.69268,0.50849,0.50886,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33290,SRR29884423,SRX25380695,SRS22046047,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  WT  Female 4,GSM8406305,,source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing,Brain  WT  Female 4,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:WT,GSM8406305,GSM8406305: Brain  WT  Female 4; Danio rerio; RNA Seq,GSM8406305 r1,GSM8406305,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample4WTFemaleBrain_R1.fastq Sample4WTFemaleBrain_R2.fastq,fastq fastq,6326747176.0,32181924.0,GSM8406305 r1,0:98.30 1:98.30,A:1726705163;C:1423533467;G:1441282364;T:1733022638;N:2203544,98,98,,,1726705163,1423533467,1441282364,1733022638,2203544,SRX25380695,SRS22046047,SRA1927371,Oregon State University,Oregon State University,2,0.94564,0.9463,0.13279,0.13015,0.69329,0.69264,0.52131,0.52995,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33291,SRR29884424,SRX25380694,SRS22046049,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  WT  Female 3,GSM8406304,,source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing,Brain  WT  Female 3,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:WT,GSM8406304,GSM8406304: Brain  WT  Female 3; Danio rerio; RNA Seq,GSM8406304 r1,GSM8406304,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample3WTFemaleBrain_R1.fastq Sample3WTFemaleBrain_R2.fastq,fastq fastq,6158432042.0,31268580.0,GSM8406304 r1,0:98.48 1:98.48,A:1663143400;C:1401049481;G:1427904493;T:1664192587;N:2142081,98,98,,,1663143400,1401049481,1427904493,1664192587,2142081,SRX25380694,SRS22046049,SRA1927371,Oregon State University,Oregon State University,2,0.94243,0.94497,0.13191,0.13006,0.68454,0.68335,0.53268,0.53362,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33292,SRR29884425,SRX25380693,SRS22046046,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  WT  Female 2,GSM8406303,,source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing,Brain  WT  Female 2,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:WT,GSM8406303,GSM8406303: Brain  WT  Female 2; Danio rerio; RNA Seq,GSM8406303 r1,GSM8406303,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample2WTFemaleBrain_R1.fastq Sample2WTFemaleBrain_R2.fastq,fastq fastq,5029227086.0,25468404.0,GSM8406303 r1,0:98.73 1:98.73,A:1373457097;C:1129749557;G:1148614258;T:1375648797;N:1757377,98,98,,,1373457097,1129749557,1148614258,1375648797,1757377,SRX25380693,SRS22046046,SRA1927371,Oregon State University,Oregon State University,2,0.94244,0.94484,0.14143,0.13943,0.69414,0.69292,0.52985,0.53107,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33293,SRR29884426,SRX25380692,SRS22046045,SRP520852,PRJNA1137393,Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles  affecting ocular and neurobehavioral function,GSE272589,Transcriptome Analysis,Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG  however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays  untargeted metabolomics  and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid  steroid  amino acid  and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays  however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex  genotype WT or KO wh5  and organ for a total of 40 samples.,,pubmed:39890032,,Brain  WT  Female 1,GSM8406302,,source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing,Brain  WT  Female 1,quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al.  2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included   alignIntronMin 15    alignIntronMax 250000 and   quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design =  Sex + Group  where the groups included brain KO wh5  brain WT  eye KO wh5  and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes  MDS and heatmap plots. Sample10 brain  WT  male was an outlier in all three plots. In addition  Sample3 brain  WT  female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples  it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx  raw counts of all samples and types Supplementary files format and content: .csv  separate DEG analysis results table for eye and brain with sample 3 and 10 removed,eye,,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,tissue:eye|genotype:WT,GSM8406302,GSM8406302: Brain  WT  Female 1; Danio rerio; RNA Seq,GSM8406302 r1,GSM8406302,1,RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP520852,,,Sample1WTFemaleBrain_R1.fastq Sample1WTFemaleBrain_R2.fastq,fastq fastq,6137098342.0,31214791.0,GSM8406302 r1,0:98.30 1:98.30,A:1678153918;C:1372921889;G:1402049594;T:1681827427;N:2145514,98,98,,,1678153918,1372921889,1402049594,1681827427,2145514,SRX25380692,SRS22046045,SRA1927371,Oregon State University,Oregon State University,2,0.93905,0.94293,0.14999,0.14877,0.69376,0.69292,0.52265,0.5227,101,101,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-07-18,Undetermined,Multi-stage,Eye,Sensory System
33846,SRR30769771,SRX26172026,SRS22716039,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 20dpi Rep 3,GSM8530629,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 20dpi Rep 3,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530629,GSM8530629: NMDA+Senolytic 20dpi Rep 3; Danio rerio; RNA Seq,GSM8530629 r1,GSM8530629,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0018_S1_L005_R1_001.fastq.gz 11384-GK-0018_S1_L005_R2_001.fastq.gz,fastq fastq,22610089492.0,74867846.0,GSM8530629 r1,0:151 1:151,A:6096322158;C:5038348469;G:5495879212;T:5975532315;N:4007338,151,151,,,6096322158,5038348469,5495879212,5975532315,4007338,SRX26172026,SRS22716039,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33847,SRR30769772,SRX26172025,SRS22716040,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 20dpi Rep 2,GSM8530628,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 20dpi Rep 2,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530628,GSM8530628: NMDA+Senolytic 20dpi Rep 2; Danio rerio; RNA Seq,GSM8530628 r1,GSM8530628,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0017_S1_L005_R1_001.fastq.gz 11384-GK-0017_S1_L005_R2_001.fastq.gz,fastq fastq,15883255120.0,52593560.0,GSM8530628 r1,0:151 1:151,A:4234691081;C:3596643174;G:3921904429;T:4127066479;N:2949957,151,151,,,4234691081,3596643174,3921904429,4127066479,2949957,SRX26172025,SRS22716040,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33848,SRR30769773,SRX26172024,SRS22716038,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 20dpi Rep 1,GSM8530627,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 20dpi Rep 1,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530627,GSM8530627: NMDA+Senolytic 20dpi Rep 1; Danio rerio; RNA Seq,GSM8530627 r1,GSM8530627,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0016_S1_L005_R1_001.fastq.gz 11384-GK-0016_S1_L005_R2_001.fastq.gz,fastq fastq,20074224484.0,66470942.0,GSM8530627 r1,0:151 1:151,A:5366083942;C:4521905793;G:4941071454;T:5241584345;N:3578950,151,151,,,5366083942,4521905793,4941071454,5241584345,3578950,SRX26172024,SRS22716038,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33849,SRR30769774,SRX26172023,SRS22716037,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 20dpi Rep 3,GSM8530626,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 20dpi Rep 3,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530626,GSM8530626: NMDA Only 20dpi Rep 3; Danio rerio; RNA Seq,GSM8530626 r1,GSM8530626,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0015_S1_L005_R1_001.fastq.gz 11384-GK-0015_S1_L005_R2_001.fastq.gz,fastq fastq,16764864392.0,55512796.0,GSM8530626 r1,0:151 1:151,A:4465019974;C:3832519977;G:4089874744;T:4374403116;N:3046581,151,151,,,4465019974,3832519977,4089874744,4374403116,3046581,SRX26172023,SRS22716037,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33850,SRR30769775,SRX26172022,SRS22716036,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 20dpi Rep 2,GSM8530625,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 20dpi Rep 2,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530625,GSM8530625: NMDA Only 20dpi Rep 2; Danio rerio; RNA Seq,GSM8530625 r1,GSM8530625,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0014_S1_L005_R1_001.fastq.gz 11384-GK-0014_S1_L005_R2_001.fastq.gz,fastq fastq,17587013488.0,58235144.0,GSM8530625 r1,0:151 1:151,A:4702159471;C:3973231615;G:4291531323;T:4616815802;N:3275277,151,151,,,4702159471,3973231615,4291531323,4616815802,3275277,SRX26172022,SRS22716036,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33851,SRR30769776,SRX26172021,SRS22716035,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 20dpi Rep 1,GSM8530624,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 20dpi Rep 1,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530624,GSM8530624: NMDA Only 20dpi Rep 1; Danio rerio; RNA Seq,GSM8530624 r1,GSM8530624,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0013_S1_L005_R1_001.fastq.gz 11384-GK-0013_S1_L005_R2_001.fastq.gz,fastq fastq,17211645306.0,56992203.0,GSM8530624 r1,0:151 1:151,A:4570848139;C:3941519932;G:4229510898;T:4466558031;N:3208306,151,151,,,4570848139,3941519932,4229510898,4466558031,3208306,SRX26172021,SRS22716035,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33852,SRR30769777,SRX26172020,SRS22716034,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 12dpi Rep 3,GSM8530623,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 12dpi Rep 3,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530623,GSM8530623: NMDA+Senolytic 12dpi Rep 3; Danio rerio; RNA Seq,GSM8530623 r1,GSM8530623,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0012_S1_L005_R1_001.fastq.gz 11384-GK-0012_S1_L005_R2_001.fastq.gz,fastq fastq,19519830400.0,64635200.0,GSM8530623 r1,0:151 1:151,A:5213575107;C:4426193150;G:4758365858;T:5118199883;N:3496402,151,151,,,5213575107,4426193150,4758365858,5118199883,3496402,SRX26172020,SRS22716034,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33853,SRR30769778,SRX26172019,SRS22716032,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 12dpi Rep 2,GSM8530622,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 12dpi Rep 2,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530622,GSM8530622: NMDA+Senolytic 12dpi Rep 2; Danio rerio; RNA Seq,GSM8530622 r1,GSM8530622,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0011_S1_L005_R1_001.fastq.gz 11384-GK-0011_S1_L005_R2_001.fastq.gz,fastq fastq,15020818318.0,49737809.0,GSM8530622 r1,0:151 1:151,A:4035098361;C:3327301881;G:3685533773;T:3970171718;N:2712585,151,151,,,4035098361,3327301881,3685533773,3970171718,2712585,SRX26172019,SRS22716032,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33854,SRR30769779,SRX26172018,SRS22716033,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 12dpi Rep 1,GSM8530621,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 12dpi Rep 1,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530621,GSM8530621: NMDA+Senolytic 12dpi Rep 1; Danio rerio; RNA Seq,GSM8530621 r1,GSM8530621,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0010_S1_L005_R1_001.fastq.gz 11384-GK-0010_S1_L005_R2_001.fastq.gz,fastq fastq,21313476652.0,70574426.0,GSM8530621 r1,0:151 1:151,A:5681259287;C:4844892428;G:5203514513;T:5579854696;N:3955728,151,151,,,5681259287,4844892428,5203514513,5579854696,3955728,SRX26172018,SRS22716033,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33855,SRR30769780,SRX26172017,SRS22716030,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 12dpi Rep 3,GSM8530620,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 12dpi Rep 3,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530620,GSM8530620: NMDA Only 12dpi Rep 3; Danio rerio; RNA Seq,GSM8530620 r1,GSM8530620,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0009_S1_L005_R1_001.fastq.gz 11384-GK-0009_S1_L005_R2_001.fastq.gz,fastq fastq,15559919726.0,51522913.0,GSM8530620 r1,0:151 1:151,A:4218748488;C:3440121432;G:3770196530;T:4128045704;N:2807572,151,151,,,4218748488,3440121432,3770196530,4128045704,2807572,SRX26172017,SRS22716030,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33856,SRR30769781,SRX26172016,SRS22716028,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 12dpi Rep 2,GSM8530619,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 12dpi Rep 2,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530619,GSM8530619: NMDA Only 12dpi Rep 2; Danio rerio; RNA Seq,GSM8530619 r1,GSM8530619,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0008_S1_L005_R1_001.fastq.gz 11384-GK-0008_S1_L005_R2_001.fastq.gz,fastq fastq,16929495162.0,56057931.0,GSM8530619 r1,0:151 1:151,A:4580671833;C:3751371251;G:4108279016;T:4486053060;N:3120002,151,151,,,4580671833,3751371251,4108279016,4486053060,3120002,SRX26172016,SRS22716028,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33857,SRR30769782,SRX26172015,SRS22716029,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 12dpi Rep 1,GSM8530618,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 12dpi Rep 1,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530618,GSM8530618: NMDA Only 12dpi Rep 1; Danio rerio; RNA Seq,GSM8530618 r1,GSM8530618,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0007_S1_L005_R1_001.fastq.gz 11384-GK-0007_S1_L005_R2_001.fastq.gz,fastq fastq,14797480862.0,48998281.0,GSM8530618 r1,0:151 1:151,A:3900528784;C:3418459440;G:3652120707;T:3823647040;N:2724891,151,151,,,3900528784,3418459440,3652120707,3823647040,2724891,SRX26172015,SRS22716029,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33858,SRR30769783,SRX26172014,SRS22716031,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 3dpi Rep 3,GSM8530617,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 3dpi Rep 3,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530617,GSM8530617: NMDA+Senolytic 3dpi Rep 3; Danio rerio; RNA Seq,GSM8530617 r1,GSM8530617,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0006_S1_L005_R1_001.fastq.gz 11384-GK-0006_S1_L005_R2_001.fastq.gz,fastq fastq,21007284892.0,69560546.0,GSM8530617 r1,0:151 1:151,A:5599691886;C:4713794227;G:5216907301;T:5473147077;N:3744401,151,151,,,5599691886,4713794227,5216907301,5473147077,3744401,SRX26172014,SRS22716031,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33859,SRR30769784,SRX26172013,SRS22716027,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 3dpi Rep 2,GSM8530616,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 3dpi Rep 2,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530616,GSM8530616: NMDA+Senolytic 3dpi Rep 2; Danio rerio; RNA Seq,GSM8530616 r1,GSM8530616,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0005_S1_L005_R1_001.fastq.gz 11384-GK-0005_S1_L005_R2_001.fastq.gz,fastq fastq,21284313418.0,70477859.0,GSM8530616 r1,0:151 1:151,A:5662907550;C:4819337573;G:5250600393;T:5547505694;N:3962208,151,151,,,5662907550,4819337573,5250600393,5547505694,3962208,SRX26172013,SRS22716027,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33860,SRR30769785,SRX26172012,SRS22716026,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 3dpi Rep 1,GSM8530615,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 3dpi Rep 1,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530615,GSM8530615: NMDA+Senolytic 3dpi Rep 1; Danio rerio; RNA Seq,GSM8530615 r1,GSM8530615,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0004_S1_L005_R1_001.fastq.gz 11384-GK-0004_S1_L005_R2_001.fastq.gz,fastq fastq,21278249862.0,70457781.0,GSM8530615 r1,0:151 1:151,A:5702525360;C:4765542588;G:5213022165;T:5593300201;N:3859548,151,151,,,5702525360,4765542588,5213022165,5593300201,3859548,SRX26172012,SRS22716026,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System