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
10155,ERR5236196,ERX5039563,ERS5672247,ERP126773,PRJEB42852,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E-MTAB-10068,Transcriptome Analysis,Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore  we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected  with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,,Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Zebrafish WT 3,SAMEA7984965,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA",ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984965|INSDC center alias:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC center name:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E MTAB 10068:Zebrafish WT 3 p,Zebrafish WT 3 p,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were  lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA.  RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP126773,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,Zebrafish_WT_3_1.fastq.gz Zebrafish_WT_3_2.fastq.gz,fastq fastq,7150981594.0,23678747.0,E MTAB 10068:Zebrafish WT 3 ,0:151 1:151,A:1885053833;C:1690814929;G:1772259046;T:1802798453;N:55333,151,151,,,1885053833,1690814929,1772259046,1802798453,55333,ERX5039563,ERS5672247,ERA3400155,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive","Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive",2,0.95124,0.95221,0.08338,0.08285,0.69181,0.69256,0.46157,0.46139,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2022-01-26,Larval,Larval,Eye,Sensory System
10156,ERR5236195,ERX5039562,ERS5672246,ERP126773,PRJEB42852,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E-MTAB-10068,Transcriptome Analysis,Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore  we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected  with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,,Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Zebrafish WT 2,SAMEA7984964,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA",ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984964|INSDC center alias:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC center name:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E MTAB 10068:Zebrafish WT 2 p,Zebrafish WT 2 p,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were  lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA.  RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP126773,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,Zebrafish_WT_2_1.fastq.gz Zebrafish_WT_2_2.fastq.gz,fastq fastq,7214044026.0,23887563.0,E MTAB 10068:Zebrafish WT 2 ,0:151 1:151,A:1902219751;C:1705162605;G:1795933407;T:1810669383;N:58880,151,151,,,1902219751,1705162605,1795933407,1810669383,58880,ERX5039562,ERS5672246,ERA3400155,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive","Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive",2,0.95311,0.95386,0.07898,0.07845,0.69045,0.69061,0.46066,0.4628,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2022-01-26,Larval,Larval,Eye,Sensory System
10157,ERR5236194,ERX5039561,ERS5672245,ERP126773,PRJEB42852,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E-MTAB-10068,Transcriptome Analysis,Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore  we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected  with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,,Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Zebrafish WT 1,SAMEA7984963,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA",ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984963|INSDC center alias:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC center name:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E MTAB 10068:Zebrafish WT 1 p,Zebrafish WT 1 p,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were  lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA.  RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP126773,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,Zebrafish_WT_1_1.fastq.gz Zebrafish_WT_1_2.fastq.gz,fastq fastq,6632043216.0,21960408.0,E MTAB 10068:Zebrafish WT 1 ,0:151 1:151,A:1763732625;C:1547925091;G:1636588945;T:1683739270;N:57285,151,151,,,1763732625,1547925091,1636588945,1683739270,57285,ERX5039561,ERS5672245,ERA3400155,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive","Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive",2,0.9495,0.95025,0.08958,0.08856,0.68661,0.68598,0.46029,0.46171,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2022-01-26,Larval,Larval,Eye,Sensory System
10158,ERR5236193,ERX5039560,ERS5672244,ERP126773,PRJEB42852,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E-MTAB-10068,Transcriptome Analysis,Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore  we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected  with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,,Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Zebrafish mab21l1 3,SAMEA7984962,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA",ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984962|INSDC center alias:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC center name:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish mab21l1 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:homozygous mab21l1 c.107delA|organism part:eye|sample name:E MTAB 10068:Zebrafish mab21l1 3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E MTAB 10068:Zebrafish mab21l1 3 p,Zebrafish mab21l1 3 p,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were  lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA.  RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Experimental Factor: genotype:homozygous mab21l1 c.107delA,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP126773,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,Zebrafish_mab21l1_3_1.fastq.gz Zebrafish_mab21l1_3_2.fastq.gz,fastq fastq,6182833618.0,20472959.0,E MTAB 10068:Zebrafish mab21l1 3 ,0:151 1:151,A:1613191835;C:1471874932;G:1547131522;T:1550575662;N:59667,151,151,,,1613191835,1471874932,1547131522,1550575662,59667,ERX5039560,ERS5672244,ERA3400155,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive","Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive",2,0.95645,0.95788,0.0697,0.06969,0.70096,0.70033,0.43342,0.43242,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2022-01-26,Larval,Larval,Eye,Sensory System
10159,ERR5236192,ERX5039559,ERS5672243,ERP126773,PRJEB42852,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E-MTAB-10068,Transcriptome Analysis,Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore  we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected  with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,,Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Zebrafish mab21l1 2,SAMEA7984961,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA",ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984961|INSDC center alias:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC center name:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish mab21l1 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:homozygous mab21l1 c.107delA|organism part:eye|sample name:E MTAB 10068:Zebrafish mab21l1 2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E MTAB 10068:Zebrafish mab21l1 2 p,Zebrafish mab21l1 2 p,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were  lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA.  RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Experimental Factor: genotype:homozygous mab21l1 c.107delA,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP126773,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,Zebrafish_mab21l1_2_1.fastq.gz Zebrafish_mab21l1_2_2.fastq.gz,fastq fastq,6989382602.0,23143651.0,E MTAB 10068:Zebrafish mab21l1 2 ,0:151 1:151,A:1841093814;C:1660652130;G:1754262273;T:1733319973;N:54412,151,151,,,1841093814,1660652130,1754262273,1733319973,54412,ERX5039559,ERS5672243,ERA3400155,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive","Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive",2,0.95595,0.95712,0.07199,0.07107,0.70485,0.70431,0.42033,0.42681,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2022-01-26,Larval,Larval,Eye,Sensory System
10160,ERR5236191,ERX5039558,ERS5672242,ERP126773,PRJEB42852,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E-MTAB-10068,Transcriptome Analysis,Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore  we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected  with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure.,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,,Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Zebrafish mab21l1 1,SAMEA7984960,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA",ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984960|INSDC center alias:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC center name:Department of Pediatrics and Cell Biology  Neurobiology and Anatomy  The Medical College of Wisconsin  Milwaukee  WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish mab21l1 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:homozygous mab21l1 c.107delA|organism part:eye|sample name:E MTAB 10068:Zebrafish mab21l1 1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,E MTAB 10068:Zebrafish mab21l1 1 p,Zebrafish mab21l1 1 p,RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype  and each sample contained 50 eyes. To isolate RNA  whole eye samples were  lysed and homogenized in TRI Reagent. Then  the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA.  RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide  Part # 15031047 Rev. E.,Experimental Factor: genotype:homozygous mab21l1 c.107delA,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP126773,Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf,ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26,Zebrafish_mab21l1_1_1.fastq.gz Zebrafish_mab21l1_1_2.fastq.gz,fastq fastq,6882371922.0,22789311.0,E MTAB 10068:Zebrafish mab21l1 1 ,0:151 1:151,A:1803380739;C:1630414039;G:1732263332;T:1716255495;N:58317,151,151,,,1803380739,1630414039,1732263332,1716255495,58317,ERX5039558,ERS5672242,ERA3400155,"Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive","Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive",2,0.95518,0.95612,0.07088,0.07032,0.70526,0.70457,0.42942,0.4302,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2022-01-26,Larval,Larval,Eye,Sensory System
19087,ERR13834862,ERX13237628,ERS21098715,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48HC1 S20 R1 001.fastq.gz,SAMEA116100635,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC1|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 48 HC1,webin reads 48 HC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 HC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48HC1_S20_R1_001.fastq.gz,fastq,3768442091.0,38065677.0,webin reads 48 HC1,0:99.00,A:1055463738;C:792073627;G:817607736;T:1103223790;N:73200,99,,,,1055463738,792073627,817607736,1103223790,73200,ERX13237628,ERS21098715,ERA30883416,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Hatching,Embryo,Eye,Sensory System
19088,ERR13834951,ERX13237717,ERS21098721,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58PR3 S26 R1 001.fastq.gz,58 PR3,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 PR3,webin reads 58 PR3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 PR3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58PR3_S26_R1_001.fastq.gz,fastq,3869469736.0,38850717.0,webin reads 58 PR3,0:99.60,A:1103909449;C:804146524;G:827344036;T:1134036010;N:33717,99,,,,1103909449,804146524,827344036,1134036010,33717,ERX13237717,ERS21098721,ERA30883529,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19089,ERR13835010,ERX13237776,ERS21098726,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58AC4 S31 R1 001.fastq.gz,SAMEA116100646,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 AC4|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 AC4|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 58 AC4,webin reads 58 AC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 AC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58AC4_S31_R1_001.fastq.gz,fastq,3607648651.0,36331933.0,webin reads 58 AC4,0:99.30,A:1038047870;C:736262498;G:759315202;T:1073962987;N:60094,99,,,,1038047870,736262498,759315202,1073962987,60094,ERX13237776,ERS21098726,ERA30883721,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Hatching,Embryo,Eye,Sensory System
19090,ERR13822794,ERX13225546,ERS21098708,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48PR2 S13 R1 001.fastq.gz,48 PR2,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 PR2,webin reads 48 PR2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 PR2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48PR2_S13_R1_001.fastq.gz,fastq,3809299607.0,38404185.0,webin reads 48 PR2,0:99.19,A:1067728192;C:802585802;G:828435932;T:1110435904;N:113777,99,,,,1067728192,802585802,828435932,1110435904,113777,ERX13225546,ERS21098708,ERA30879682,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19091,ERR13834854,ERX13237620,ERS21098714,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48AC4 S19 R1 001.fastq.gz,48 AC4,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 AC4,webin reads 48 AC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 AC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48AC4_S19_R1_001.fastq.gz,fastq,3410801894.0,34443068.0,webin reads 48 AC4,0:99.03,A:966160063;C:707754156;G:733039262;T:1003772756;N:75657,99,,,,966160063,707754156,733039262,1003772756,75657,ERX13237620,ERS21098714,ERA30883390,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19092,ERR13828824,ERX13231590,ERS21098710,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48PR4 S15 R1 001.fastq.gz,48 PR4,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 PR4,webin reads 48 PR4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 PR4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48PR4_S15_R1_001.fastq.gz,fastq,4365943927.0,44278278.0,webin reads 48 PR4,0:98.60,A:1214448497;C:927512154;G:957491418;T:1266385355;N:106503,98,,,,1214448497,927512154,957491418,1266385355,106503,ERX13231590,ERS21098710,ERA30883309,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19093,ERR13834993,ERX13237759,ERS21098723,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58AC1 S28 R1 001.fastq.gz,58 AC1,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 AC1,webin reads 58 AC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 AC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58AC1_S28_R1_001.fastq.gz,fastq,3710768269.0,37364763.0,webin reads 58 AC1,0:99.31,A:1060419097;C:761984557;G:786533722;T:1101603428;N:227465,99,,,,1060419097,761984557,786533722,1101603428,227465,ERX13237759,ERS21098723,ERA30883659,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19094,ERR13834875,ERX13237641,ERS21098717,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48HC3 S22 R1 001.fastq.gz,48 HC3,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 HC3,webin reads 48 HC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 HC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48HC3_S22_R1_001.fastq.gz,fastq,3083078586.0,31073491.0,webin reads 48 HC3,0:99.22,A:856250957;C:655140994;G:677078911;T:894558582;N:49142,99,,,,856250957,655140994,677078911,894558582,49142,ERX13237641,ERS21098717,ERA30883447,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19095,ERR13834899,ERX13237665,ERS21098720,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58PR2 S25 R1 001.fastq.gz,58 PR2,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 PR2,webin reads 58 PR2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 PR2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58PR2_S25_R1_001.fastq.gz,fastq,3849571818.0,38706841.0,webin reads 58 PR2,0:99.45,A:1089593011;C:803322469;G:827777017;T:1128836774;N:42547,99,,,,1089593011,803322469,827777017,1128836774,42547,ERX13237665,ERS21098720,ERA30883518,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19096,ERR13834889,ERX13237655,ERS21098719,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58PR1 S24 R1 001.fastq.gz,58 PR1,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 PR1,webin reads 58 PR1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 PR1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58PR1_S24_R1_001.fastq.gz,fastq,3945671240.0,39514922.0,webin reads 58 PR1,0:99.85,A:1135075173;C:807489123;G:827964380;T:1175109762;N:32802,99,,,,1135075173,807489123,827964380,1175109762,32802,ERX13237655,ERS21098719,ERA30883497,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19097,ERR13835019,ERX13237785,ERS21098728,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58HC2 S33 R1 001.fastq.gz,SAMEA116100648,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 HC2|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 HC2|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 58 HC2,webin reads 58 HC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 HC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58HC2_S33_R1_001.fastq.gz,fastq,3711237069.0,37217240.0,webin reads 58 HC2,0:99.72,A:1070592288;C:757099665;G:780689044;T:1102575310;N:280762,99,,,,1070592288,757099665,780689044,1102575310,280762,ERX13237785,ERS21098728,ERA30883748,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Hatching,Embryo,Eye,Sensory System
19098,ERR13822110,ERX13224862,ERS21098697,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR2 S2 R1 001.fastq.gz,38 PR2,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 PR2,webin reads 38 PR2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR2_S2_R1_001.fastq.gz,fastq,3463281109.0,34821985.0,webin reads 38 PR2,0:99.46,A:969862466;C:733798241;G:755135957;T:1004440555;N:43890,99,,,,969862466,733798241,755135957,1004440555,43890,ERX13224862,ERS21098697,ERA30879238,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19099,ERR13822784,ERX13225536,ERS21098706,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC3 S11 R1 001.fastq.gz,38 HC3,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 HC3,webin reads 38 HC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC3_S11_R1_001.fastq.gz,fastq,4360921873.0,44107486.0,webin reads 38 HC3,0:98.87,A:1222778761;C:918257887;G:948838973;T:1270939370;N:106882,98,,,,1222778761,918257887,948838973,1270939370,106882,ERX13225536,ERS21098706,ERA30879613,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19100,ERR13828836,ERX13231602,ERS21098712,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48AC2 S17 R1 001.fastq.gz,48 AC2,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 AC2,webin reads 48 AC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 AC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48AC2_S17_R1_001.fastq.gz,fastq,3205206588.0,32424632.0,webin reads 48 AC2,0:98.85,A:902438127;C:672433401;G:694813369;T:935445436;N:76255,98,,,,902438127,672433401,694813369,935445436,76255,ERX13231602,ERS21098712,ERA30883343,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19101,ERR13835004,ERX13237770,ERS21098725,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58AC3 S30 R1 001.fastq.gz,58 AC3,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 AC3,webin reads 58 AC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 AC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58AC3_S30_R1_001.fastq.gz,fastq,3782993133.0,38295959.0,webin reads 58 AC3,0:98.78,A:1080745150;C:779903026;G:803258485;T:1118994941;N:91531,98,,,,1080745150,779903026,803258485,1118994941,91531,ERX13237770,ERS21098725,ERA30883697,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19102,ERR13834868,ERX13237634,ERS21098716,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48HC2 S21 R1 001.fastq.gz,SAMEA116100636,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC2|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC2|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 48 HC2,webin reads 48 HC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 HC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48HC2_S21_R1_001.fastq.gz,fastq,3424347865.0,34510204.0,webin reads 48 HC2,0:99.23,A:959488173;C:721171249;G:745705870;T:997922014;N:60559,99,,,,959488173,721171249,745705870,997922014,60559,ERX13237634,ERS21098716,ERA30883434,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Hatching,Embryo,Eye,Sensory System
19103,ERR13822197,ERX13224949,ERS21098704,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC1 S9 R1 001.fastq.gz,SAMEA116100624,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 HC1|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 38 HC1,webin reads 38 HC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC1_S9_R1_001.fastq.gz,fastq,3784641498.0,38331162.0,webin reads 38 HC1,0:98.74,A:1064199311;C:791310791;G:818910597;T:1110118632;N:102167,98,,,,1064199311,791310791,818910597,1110118632,102167,ERX13224949,ERS21098704,ERA30879548,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Pharyngula,Embryo,Eye,Sensory System
19104,ERR13834880,ERX13237646,ERS21098718,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48HC4 S23 R1 001.fastq.gz,48 HC4,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 HC4,webin reads 48 HC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 HC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48HC4_S23_R1_001.fastq.gz,fastq,3660674315.0,36821474.0,webin reads 48 HC4,0:99.42,A:1035049987;C:763030378;G:788062167;T:1074303516;N:228267,99,,,,1035049987,763030378,788062167,1074303516,228267,ERX13237646,ERS21098718,ERA30883470,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19105,ERR13822867,ERX13225633,ERS21098709,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48PR3 S14 R1 001.fastq.gz,48 PR3,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 PR3,webin reads 48 PR3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 PR3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48PR3_S14_R1_001.fastq.gz,fastq,4232170464.0,42534853.0,webin reads 48 PR3,0:99.50,A:1195251409;C:889346003;G:917240118;T:1230272855;N:60079,99,,,,1195251409,889346003,917240118,1230272855,60079,ERX13225633,ERS21098709,ERA30879704,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19106,ERR13822131,ERX13224883,ERS21098700,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC1 S5 R1 001.fastq.gz,SAMEA116100620,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 AC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 AC1|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 38 AC1,webin reads 38 AC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC1_S5_R1_001.fastq.gz,fastq,3836921113.0,38702139.0,webin reads 38 AC1,0:99.14,A:1066720805;C:818958589;G:843762182;T:1107403844;N:75693,99,,,,1066720805,818958589,843762182,1107403844,75693,ERX13224883,ERS21098700,ERA30879356,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Pharyngula,Embryo,Eye,Sensory System
19107,ERR13822143,ERX13224895,ERS21098702,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC3 S7 R1 001.fastq.gz,38 AC3,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 AC3,webin reads 38 AC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC3_S7_R1_001.fastq.gz,fastq,3452707377.0,34902410.0,webin reads 38 AC3,0:98.92,A:970868997;C:726795179;G:750560378;T:1004408693;N:74130,98,,,,970868997,726795179,750560378,1004408693,74130,ERX13224895,ERS21098702,ERA30879451,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19108,ERR13828843,ERX13234350,ERS21098713,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48AC3 S18 R1 001.fastq.gz,48 AC3,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 AC3,webin reads 48 AC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 AC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48AC3_S18_R1_001.fastq.gz,fastq,3733628911.0,37779462.0,webin reads 48 AC3,0:98.83,A:1047204450;C:786943605;G:812327274;T:1086893109;N:260473,98,,,,1047204450,786943605,812327274,1086893109,260473,ERX13234350,ERS21098713,ERA30883366,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19109,ERR13822153,ERX13224905,ERS21098703,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC4 S8 R1 001.fastq.gz,38 AC4,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 AC4,webin reads 38 AC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC4_S8_R1_001.fastq.gz,fastq,4130629624.0,41794865.0,webin reads 38 AC4,0:98.83,A:1156746387;C:877063962;G:905379690;T:1191264308;N:175277,98,,,,1156746387,877063962,905379690,1191264308,175277,ERX13224905,ERS21098703,ERA30879532,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19110,ERR13822201,ERX13224953,ERS21098705,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC2 S10 R1 001.fastq.gz,38 HC2,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 HC2,webin reads 38 HC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC2_S10_R1_001.fastq.gz,fastq,4221340137.0,42584743.0,webin reads 38 HC2,0:99.13,A:1195817135;C:879958039;G:908085464;T:1237394738;N:84761,99,,,,1195817135,879958039,908085464,1237394738,84761,ERX13224953,ERS21098705,ERA30879582,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19111,ERR13822114,ERX13224866,ERS21098698,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR3 S3 R1 001.fastq.gz,SAMEA116100618,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 PR3|collected by:Jaakko Lehtimaki|collection date:2021 12 07|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 PR3|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 38 PR3,webin reads 38 PR3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR3_S3_R1_001.fastq.gz,fastq,3894010106.0,39196855.0,webin reads 38 PR3,0:99.34,A:1093221995;C:818047738;G:843661747;T:1138957138;N:121488,99,,,,1093221995,818047738,843661747,1138957138,121488,ERX13224866,ERS21098698,ERA30879273,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Pharyngula,Embryo,Eye,Sensory System
19112,ERR13822135,ERX13224887,ERS21098701,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC2 S6 R1 001.fastq.gz,38 AC2,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 AC2,webin reads 38 AC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC2_S6_R1_001.fastq.gz,fastq,3913343007.0,39682834.0,webin reads 38 AC2,0:98.62,A:1089960083;C:827936673;G:855955684;T:1139372607;N:117960,98,,,,1089960083,827936673,855955684,1139372607,117960,ERX13224887,ERS21098701,ERA30879382,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19113,ERR13835032,ERX13237798,ERS21098730,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58HC4 S35 R1 001.fastq.gz,58 HC4,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 HC4,webin reads 58 HC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 HC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58HC4_S35_R1_001.fastq.gz,fastq,4418556015.0,44331835.0,webin reads 58 HC4,0:99.67,A:1255080581;C:916490847;G:946212615;T:1300735054;N:36918,99,,,,1255080581,916490847,946212615,1300735054,36918,ERX13237798,ERS21098730,ERA30883773,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19114,ERR13828829,ERX13231595,ERS21098711,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48AC1 S16 R1 001.fastq.gz,48 AC1,,organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 48 AC1,webin reads 48 AC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 AC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48AC1_S16_R1_001.fastq.gz,fastq,3933669121.0,39695406.0,webin reads 48 AC1,0:99.10,A:1105258159;C:824538054;G:854253688;T:1149538152;N:81068,99,,,,1105258159,824538054,854253688,1149538152,81068,ERX13231595,ERS21098711,ERA30883326,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19115,ERR13822099,ERX13224851,ERS21098696,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR1 S1 R1 001.fastq.gz,38 PR1,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 PR1,webin reads 38 PR1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR1_S1_R1_001.fastq.gz,fastq,4256158288.0,42658127.0,webin reads 38 PR1,0:99.77,A:1193880575;C:899261652;G:926114030;T:1236860186;N:41845,99,,,,1193880575,899261652,926114030,1236860186,41845,ERX13224851,ERS21098696,ERA30879152,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19116,ERR13822119,ERX13224871,ERS21098699,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR4 S4 R1 001.fastq.gz,38 PR4,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 PR4,webin reads 38 PR4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR4_S4_R1_001.fastq.gz,fastq,3726308046.0,37591038.0,webin reads 38 PR4,0:99.13,A:1043231302;C:789255840;G:812957881;T:1080801843;N:61180,99,,,,1043231302,789255840,812957881,1080801843,61180,ERX13224871,ERS21098699,ERA30879302,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19117,ERR13835025,ERX13237791,ERS21098729,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58HC3 S34 R1 001.fastq.gz,58 HC3,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 HC3,webin reads 58 HC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 HC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58HC3_S34_R1_001.fastq.gz,fastq,3523899212.0,35292613.0,webin reads 58 HC3,0:99.85,A:1012516999;C:723225071;G:745152410;T:1042976092;N:28640,99,,,,1012516999,723225071,745152410,1042976092,28640,ERX13237791,ERS21098729,ERA30883757,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19118,ERR13835014,ERX13237780,ERS21098727,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58HC1 S32 R1 001.fastq.gz,58 HC1,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 HC1,webin reads 58 HC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 HC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58HC1_S32_R1_001.fastq.gz,fastq,3436493821.0,34597887.0,webin reads 58 HC1,0:99.33,A:980894291;C:707196785;G:729948858;T:1018400124;N:53763,99,,,,980894291,707196785,729948858,1018400124,53763,ERX13237780,ERS21098727,ERA30883731,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19119,ERR13834987,ERX13237753,ERS21098722,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58PR4 S27 R1 001.fastq.gz,58 PR4,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 PR4,webin reads 58 PR4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 PR4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58PR4_S27_R1_001.fastq.gz,fastq,3069040814.0,30923422.0,webin reads 58 PR4,0:99.25,A:875776938;C:633951750;G:653308475;T:905949639;N:54012,99,,,,875776938,633951750,653308475,905949639,54012,ERX13237753,ERS21098722,ERA30883641,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System
19120,ERR13822788,ERX13225540,ERS21098707,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC4 S12 R1 001.fastq.gz,38 HC4,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 HC4,webin reads 38 HC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC4_S12_R1_001.fastq.gz,fastq,3353994440.0,33744828.0,webin reads 38 HC4,0:99.39,A:939537209;C:709367668;G:731849729;T:973193819;N:46015,99,,,,939537209,709367668,731849729,973193819,46015,ERX13225540,ERS21098707,ERA30879650,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19121,ERR13834997,ERX13237763,ERS21098724,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,58AC2 S29 R1 001.fastq.gz,58 AC2,,organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 58 AC2,webin reads 58 AC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 AC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58AC2_S29_R1_001.fastq.gz,fastq,3872162091.0,38898173.0,webin reads 58 AC2,0:99.55,A:1111663794;C:793747086;G:817730996;T:1148980297;N:39918,99,,,,1111663794,793747086,817730996,1148980297,39918,ERX13237763,ERS21098724,ERA30883678,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,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
30230,SRR27730907,SRX23396554,SRS20257429,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,4dpi40Hz+biological replicate 2,,4dpi40Hz 2,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:10|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165700aR1AL1A,M23165700aR1AL1A,4 xxx post injury+40Hz,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,4dpi40Hz_2_1.fq.gz 4dpi40Hz_2_2.fq.gz,fastq fastq,7794055500.0,25980185.0,4dpi40Hz 2 1.fq.gz,0:150 1:150,A:2129184357;C:1759642251;G:1791618685;T:2113568820;N:41387,150,150,,,2129184357,1759642251,1791618685,2113568820,41387,SRX23396554,SRS20257429,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System
30231,SRR27730908,SRX23396553,SRS20257428,SRP486007,PRJNA1069290,Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish,PRJNA1069290,Other,In the present study  we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC  promoted dendritic remodeling and axonal regeneration of RGCs  and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general  our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs  as well as the recovery of visual function  which is related to the activation of microglia and enhancement of neural plasticity.,,,4dpi40Hz+biological replicate 1,,4dpi40Hz 1,,strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:9|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: retina,M23165699aR1AL1A,M23165699aR1AL1A,4 xxx post injury+40Hz,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP486007,,,4dpi40Hz_1_1.fq.gz 4dpi40Hz_1_2.fq.gz,fastq fastq,7508652600.0,25028842.0,4dpi40Hz 1 1.fq.gz,0:150 1:150,A:2057198043;C:1689714910;G:1722042670;T:2039656491;N:40486,150,150,,,2057198043,1689714910,1722042670,2039656491,40486,SRX23396553,SRS20257428,SRA1791874,Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology,Affiliated Eye Hospital of Nanchang University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-01-25,Adult,Adult,Eye,Sensory System