RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

786 rows where technology = "unknown" and tissue_curation_coarse = "Sensory System"

✎ View and edit SQL

This data as json, CSV (advanced)

devstage_curation 8

experiment.library_selection 7

devstage_curation_coarse 6

experiment.platform 3

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Sensory System · 786 ✖

tissue_curation 1

technology 1

  • unknown · 786 ✖

experiment.library_source 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 10155 ERR5236196 ERX5039563 ERS5672247 ERP126773 PRJEB42852 RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E-MTAB-10068 Transcriptome Analysis Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26   Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Zebrafish WT 3 SAMEA7984965 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984965|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 3                 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E MTAB 10068:Zebrafish WT 3 p Zebrafish WT 3 p RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP126773 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 Zebrafish_WT_3_1.fastq.gz Zebrafish_WT_3_2.fastq.gz fastq fastq 7150981594.0 23678747.0 E MTAB 10068:Zebrafish WT 3 0:151 1:151 A:1885053833;C:1690814929;G:1772259046;T:1802798453;N:55333 151 151     1885053833 1690814929 1772259046 1802798453 55333 ERX5039563 ERS5672247 ERA3400155 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive 2 0.95124 0.95221 0.08338 0.08285 0.69181 0.69256 0.46157 0.46139 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2022-01-26 Larval Larval Eye Sensory System
10156 10156 ERR5236195 ERX5039562 ERS5672246 ERP126773 PRJEB42852 RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E-MTAB-10068 Transcriptome Analysis Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26   Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Zebrafish WT 2 SAMEA7984964 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984964|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 2                 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E MTAB 10068:Zebrafish WT 2 p Zebrafish WT 2 p RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP126773 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 Zebrafish_WT_2_1.fastq.gz Zebrafish_WT_2_2.fastq.gz fastq fastq 7214044026.0 23887563.0 E MTAB 10068:Zebrafish WT 2 0:151 1:151 A:1902219751;C:1705162605;G:1795933407;T:1810669383;N:58880 151 151     1902219751 1705162605 1795933407 1810669383 58880 ERX5039562 ERS5672246 ERA3400155 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive 2 0.95311 0.95386 0.07898 0.07845 0.69045 0.69061 0.46066 0.4628 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2022-01-26 Larval Larval Eye Sensory System
10157 10157 ERR5236194 ERX5039561 ERS5672245 ERP126773 PRJEB42852 RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E-MTAB-10068 Transcriptome Analysis Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26   Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Zebrafish WT 1 SAMEA7984963 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984963|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish WT 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:wild type genotype|organism part:eye|sample name:E MTAB 10068:Zebrafish WT 1                 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E MTAB 10068:Zebrafish WT 1 p Zebrafish WT 1 p RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP126773 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 Zebrafish_WT_1_1.fastq.gz Zebrafish_WT_1_2.fastq.gz fastq fastq 6632043216.0 21960408.0 E MTAB 10068:Zebrafish WT 1 0:151 1:151 A:1763732625;C:1547925091;G:1636588945;T:1683739270;N:57285 151 151     1763732625 1547925091 1636588945 1683739270 57285 ERX5039561 ERS5672245 ERA3400155 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive 2 0.9495 0.95025 0.08958 0.08856 0.68661 0.68598 0.46029 0.46171 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2022-01-26 Larval Larval Eye Sensory System
10158 10158 ERR5236193 ERX5039560 ERS5672244 ERP126773 PRJEB42852 RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E-MTAB-10068 Transcriptome Analysis Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26   Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Zebrafish mab21l1 3 SAMEA7984962 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984962|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish mab21l1 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:homozygous mab21l1 c.107delA|organism part:eye|sample name:E MTAB 10068:Zebrafish mab21l1 3                 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E MTAB 10068:Zebrafish mab21l1 3 p Zebrafish mab21l1 3 p RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Experimental Factor: genotype:homozygous mab21l1 c.107delA RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP126773 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 Zebrafish_mab21l1_3_1.fastq.gz Zebrafish_mab21l1_3_2.fastq.gz fastq fastq 6182833618.0 20472959.0 E MTAB 10068:Zebrafish mab21l1 3 0:151 1:151 A:1613191835;C:1471874932;G:1547131522;T:1550575662;N:59667 151 151     1613191835 1471874932 1547131522 1550575662 59667 ERX5039560 ERS5672244 ERA3400155 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive 2 0.95645 0.95788 0.0697 0.06969 0.70096 0.70033 0.43342 0.43242 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2022-01-26 Larval Larval Eye Sensory System
10159 10159 ERR5236192 ERX5039559 ERS5672243 ERP126773 PRJEB42852 RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E-MTAB-10068 Transcriptome Analysis Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26   Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Zebrafish mab21l1 2 SAMEA7984961 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984961|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish mab21l1 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:homozygous mab21l1 c.107delA|organism part:eye|sample name:E MTAB 10068:Zebrafish mab21l1 2                 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E MTAB 10068:Zebrafish mab21l1 2 p Zebrafish mab21l1 2 p RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Experimental Factor: genotype:homozygous mab21l1 c.107delA RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP126773 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 Zebrafish_mab21l1_2_1.fastq.gz Zebrafish_mab21l1_2_2.fastq.gz fastq fastq 6989382602.0 23143651.0 E MTAB 10068:Zebrafish mab21l1 2 0:151 1:151 A:1841093814;C:1660652130;G:1754262273;T:1733319973;N:54412 151 151     1841093814 1660652130 1754262273 1733319973 54412 ERX5039559 ERS5672243 ERA3400155 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive 2 0.95595 0.95712 0.07199 0.07107 0.70485 0.70431 0.42033 0.42681 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2022-01-26 Larval Larval Eye Sensory System
10160 10160 ERR5236191 ERX5039558 ERS5672242 ERP126773 PRJEB42852 RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E-MTAB-10068 Transcriptome Analysis Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26   Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Zebrafish mab21l1 1 SAMEA7984960 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984960|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish mab21l1 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:homozygous mab21l1 c.107delA|organism part:eye|sample name:E MTAB 10068:Zebrafish mab21l1 1                 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E MTAB 10068:Zebrafish mab21l1 1 p Zebrafish mab21l1 1 p RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Experimental Factor: genotype:homozygous mab21l1 c.107delA RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP126773 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 Zebrafish_mab21l1_1_1.fastq.gz Zebrafish_mab21l1_1_2.fastq.gz fastq fastq 6882371922.0 22789311.0 E MTAB 10068:Zebrafish mab21l1 1 0:151 1:151 A:1803380739;C:1630414039;G:1732263332;T:1716255495;N:58317 151 151     1803380739 1630414039 1732263332 1716255495 58317 ERX5039558 ERS5672242 ERA3400155 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive 2 0.95518 0.95612 0.07088 0.07032 0.70526 0.70457 0.42942 0.4302 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2022-01-26 Larval Larval Eye Sensory System
29092 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 29107 SRR27151543 SRX22833143 SRS19813583 SRP476691 PRJNA1050282 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye] GSE249751 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. parent bioproject:PRJNA1050288 pubmed:39531499   5 dpf larval eyes samd7 / rep3 GSM7963641   source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing 5 dpf larval eyes samd7 / rep3 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / GSM7963641 GSM7963641: 5 dpf larval eyes samd7 / rep3; Danio rerio; RNA Seq GSM7963641 r1 GSM7963641 1 To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476691   loader:fastq load.py k7.AGGTATTCGG-GAGTCGCTTC.H37F5DSX2_AGGTATTCGG-GAGTCGCTTC_L003_R1.fastq.gz k7.AGGTATTCGG-GAGTCGCTTC.H37F5DSX2_AGGTATTCGG-GAGTCGCTTC_L003_R2.fastq.gz fastq fastq 10747100652.0 35586426.0 GSM7963641 r1 0:151 1:151 A:2879574125;C:2414500329;G:2693618198;T:2759237631;N:170369 151 151     2879574125 2414500329 2693618198 2759237631 170369 SRX22833143 SRS19813583 SRA1765718 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.95486 0.95989 0.05038 0.05167 0.73018 0.73438 0.41476 0.42743 151 151 B B biological fallback assumption illumina novaseq_era 3prime random_priming smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
29108 29108 SRR27151544 SRX22833142 SRS19813582 SRP476691 PRJNA1050282 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye] GSE249751 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. parent bioproject:PRJNA1050288 pubmed:39531499   5 dpf larval eyes samd7 / rep2 GSM7963640   source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing 5 dpf larval eyes samd7 / rep2 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / GSM7963640 GSM7963640: 5 dpf larval eyes samd7 / rep2; Danio rerio; RNA Seq GSM7963640 r1 GSM7963640 1 To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476691   loader:fastq load.py k10.AATCGAACTC-TTAGACCTTC.H37F5DSX2_AATCGAACTC-TTAGACCTTC_L003_R1.fastq.gz k10.AATCGAACTC-TTAGACCTTC.H37F5DSX2_AATCGAACTC-TTAGACCTTC_L003_R2.fastq.gz fastq fastq 10739126946.0 35560023.0 GSM7963640 r1 0:151 1:151 A:2888527520;C:2418475992;G:2670968816;T:2760983764;N:170854 151 151     2888527520 2418475992 2670968816 2760983764 170854 SRX22833142 SRS19813582 SRA1765718 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.95306 0.95846 0.05658 0.05746 0.73269 0.73714 0.42191 0.43088 151 151 B B biological fallback assumption illumina novaseq_era 3prime random_priming smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
29109 29109 SRR27151545 SRX22833141 SRS19813581 SRP476691 PRJNA1050282 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye] GSE249751 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. parent bioproject:PRJNA1050288 pubmed:39531499   5 dpf larval eyes samd7 / rep1 GSM7963639   source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing 5 dpf larval eyes samd7 / rep1 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / GSM7963639 GSM7963639: 5 dpf larval eyes samd7 / rep1; Danio rerio; RNA Seq GSM7963639 r1 GSM7963639 1 To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476691   loader:fastq load.py k11.CCGAAGATAA-TGGATTAACG.H37F5DSX2_CCGAAGATAA-TGGATTAACG_L003_R1.fastq.gz k11.CCGAAGATAA-TGGATTAACG.H37F5DSX2_CCGAAGATAA-TGGATTAACG_L003_R2.fastq.gz fastq fastq 10514289154.0 34815527.0 GSM7963639 r1 0:151 1:151 A:2862247233;C:2377266250;G:2528917605;T:2745692826;N:165240 151 151     2862247233 2377266250 2528917605 2745692826 165240 SRX22833141 SRS19813581 SRA1765718 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.95376 0.95966 0.05526 0.05681 0.72965 0.73273 0.42276 0.43148 151 151 B B biological fallback assumption illumina novaseq_era 3prime random_priming smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
29110 29110 SRR27151546 SRX22833140 SRS19813578 SRP476691 PRJNA1050282 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye] GSE249751 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. parent bioproject:PRJNA1050288 pubmed:39531499   5 dpf larval eyes WT rep3 GSM7963638   source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing 5 dpf larval eyes WT rep3 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   tissue:eye|developmental stage:5 dpf larvae|genotype:WT GSM7963638 GSM7963638: 5 dpf larval eyes WT rep3; Danio rerio; RNA Seq GSM7963638 r1 GSM7963638 1 To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476691   loader:fastq load.py w6.CCTTGCCGTA-TAGTACACAG.H37F5DSX2_CCTTGCCGTA-TAGTACACAG_L003_R1.fastq.gz w6.CCTTGCCGTA-TAGTACACAG.H37F5DSX2_CCTTGCCGTA-TAGTACACAG_L003_R2.fastq.gz fastq fastq 11943994904.0 39549652.0 GSM7963638 r1 0:151 1:151 A:3182349655;C:2708994785;G:2976982793;T:3075478468;N:189203 151 151     3182349655 2708994785 2976982793 3075478468 189203 SRX22833140 SRS19813578 SRA1765718 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.95522 0.96109 0.04859 0.04955 0.74247 0.74799 0.42424 0.43226 151 151 B B biological fallback assumption illumina novaseq_era 3prime random_priming smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
29111 29111 SRR27151547 SRX22833139 SRS19813579 SRP476691 PRJNA1050282 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye] GSE249751 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. parent bioproject:PRJNA1050288 pubmed:39531499   5 dpf larval eyes WT rep2 GSM7963637   source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing 5 dpf larval eyes WT rep2 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   tissue:eye|developmental stage:5 dpf larvae|genotype:WT GSM7963637 GSM7963637: 5 dpf larval eyes WT rep2; Danio rerio; RNA Seq GSM7963637 r1 GSM7963637 1 To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476691   loader:fastq load.py w8.AATCTCAGGC-TCACCAGGAC.H37F5DSX2_AATCTCAGGC-TCACCAGGAC_L003_R1.fastq.gz w8.AATCTCAGGC-TCACCAGGAC.H37F5DSX2_AATCTCAGGC-TCACCAGGAC_L003_R2.fastq.gz fastq fastq 10471048190.0 34672345.0 GSM7963637 r1 0:151 1:151 A:2767212261;C:2402799397;G:2644524852;T:2656347723;N:163957 151 151     2767212261 2402799397 2644524852 2656347723 163957 SRX22833139 SRS19813579 SRA1765718 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.95909 0.96443 0.04132 0.04289 0.74217 0.74631 0.40379 0.41076 151 151 B B biological fallback assumption illumina novaseq_era 3prime random_priming smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
29112 29112 SRR27151548 SRX22833138 SRS19813580 SRP476691 PRJNA1050282 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf whole eye] GSE249751 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. parent bioproject:PRJNA1050288 pubmed:39531499   5 dpf larval eyes WT rep1 GSM7963636   source name:eye|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing 5 dpf larval eyes WT rep1 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf larval eyes. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   tissue:eye|developmental stage:5 dpf larvae|genotype:WT GSM7963636 GSM7963636: 5 dpf larval eyes WT rep1; Danio rerio; RNA Seq GSM7963636 r1 GSM7963636 1 To perform RNA seq on 5 dpf larvae samd7stl888/+ heterozygous were intercrossed to produce mixed genotype offspring. Larvae were euthanized by exposure to tricaine anterior halves of the body were collected in RNAlater Invitrogen and stored at 4°C and corresponding posterior halves were collected in 50 mM NaOH for genotyping. Once genotypes were confirmed eyes were dissected from the anterior body halves. The eyes from an individual larva constituted one replicate. Three WT and samd7stl888/stl888 replicates were collected and RNA extracted using the RNeasy Micro Kit Qiagen then DNAse treated and repurified using the Rneasy MinElute Cleanup Kit Qiagen. RNA concentrations ranged from 1.5 2.2 ng/µl 20 ng RNA total with prominent 18/28S peaks and minimal RNA degradation in Bioanalyzer traces. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476691   loader:fastq load.py w15.AACAGGCAAG-TTCATGGAAG.H37F5DSX2_AACAGGCAAG-TTCATGGAAG_L003_R1.fastq.gz w15.AACAGGCAAG-TTCATGGAAG.H37F5DSX2_AACAGGCAAG-TTCATGGAAG_L003_R2.fastq.gz fastq fastq 11852131940.0 39245470.0 GSM7963636 r1 0:151 1:151 A:3157263060;C:2691924686;G:2998627934;T:3004129760;N:186500 151 151     3157263060 2691924686 2998627934 3004129760 186500 SRX22833138 SRS19813580 SRA1765718 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.95652 0.96043 0.05012 0.05113 0.73198 0.73637 0.42361 0.41636 151 151 B B biological fallback assumption illumina novaseq_era 3prime random_priming smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
29113 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 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 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 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 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 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 29119 SRR27151354 SRX22832956 SRS19813396 SRP476687 PRJNA1050291 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td] GSE249755 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. parent bioproject:PRJNA1050288 pubmed:39531499   thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep3 GSM7963660   source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep3 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / GSM7963660 GSM7963660: thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep3; Danio rerio; RNA Seq GSM7963660 r1 GSM7963660 1 To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476687   loader:fastq load.py samd7_1_rna_6_2_22.AGAAGGAACA-TGGTAGATGC.HNGJJDSX3_AGAAGGAACA-TGGTAGATGC_L003_R1.fastq.gz samd7_1_rna_6_2_22.AGAAGGAACA-TGGTAGATGC.HNGJJDSX3_AGAAGGAACA-TGGTAGATGC_L003_R2.fastq.gz fastq fastq 10483631624.0 34714012.0 GSM7963660 r1 0:151 1:151 A:2778161057;C:2394557806;G:2692864342;T:2618022344;N:26075 151 151     2778161057 2394557806 2692864342 2618022344 26075 SRX22832956 SRS19813396 SRA1765707 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.91943 0.91641 0.08589 0.08581 0.78748 0.79774 0.5086 0.50263 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
29120 29120 SRR27151355 SRX22832955 SRS19813395 SRP476687 PRJNA1050291 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td] GSE249755 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. parent bioproject:PRJNA1050288 pubmed:39531499   thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep2 GSM7963659   source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep2 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / GSM7963659 GSM7963659: thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep2; Danio rerio; RNA Seq GSM7963659 r1 GSM7963659 1 To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476687   loader:fastq load.py samd7_1_rna_6_1_22.AGACAGACGT-TATCAGTGCA.HNGJJDSX3_AGACAGACGT-TATCAGTGCA_L003_R1.fastq.gz samd7_1_rna_6_1_22.AGACAGACGT-TATCAGTGCA.HNGJJDSX3_AGACAGACGT-TATCAGTGCA_L003_R2.fastq.gz fastq fastq 12234446424.0 40511412.0 GSM7963659 r1 0:151 1:151 A:3397427491;C:2650252489;G:2963872812;T:3222862933;N:30699 151 151     3397427491 2650252489 2963872812 3222862933 30699 SRX22832955 SRS19813395 SRA1765707 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.89702 0.8967 0.14358 0.14658 0.77309 0.77962 0.5468 0.44645 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
29121 29121 SRR27151356 SRX22832954 SRS19813394 SRP476687 PRJNA1050291 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td] GSE249755 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. parent bioproject:PRJNA1050288 pubmed:39531499   thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep1 GSM7963658   source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / |geo loc name:missing|collection date:missing thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep1 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:samd7 / GSM7963658 GSM7963658: thrb:tdTomato+ cells from 5 dpf larval eyes samd7 / rep1; Danio rerio; RNA Seq GSM7963658 r1 GSM7963658 1 To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476687   loader:fastq load.py samd7_rna_5_10_22.CAATTCACGC-ACATCCTGCG.HNGJJDSX3_CAATTCACGC-ACATCCTGCG_L003_R1.fastq.gz samd7_rna_5_10_22.CAATTCACGC-ACATCCTGCG.HNGJJDSX3_CAATTCACGC-ACATCCTGCG_L003_R2.fastq.gz fastq fastq 11352128660.0 37589830.0 GSM7963658 r1 0:151 1:151 A:3035915425;C:2447970512;G:2970538003;T:2897676299;N:28421 151 151     3035915425 2447970512 2970538003 2897676299 28421 SRX22832954 SRS19813394 SRA1765707 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.90706 0.91061 0.09833 0.102 0.78186 0.78948 0.54785 0.47215 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
29122 29122 SRR27151357 SRX22832953 SRS19813393 SRP476687 PRJNA1050291 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td] GSE249755 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. parent bioproject:PRJNA1050288 pubmed:39531499   thrb:tdTomato+ cells from 5 dpf larval eyes WT rep3 GSM7963657   source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing thrb:tdTomato+ cells from 5 dpf larval eyes WT rep3 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT GSM7963657 GSM7963657: thrb:tdTomato+ cells from 5 dpf larval eyes WT rep3; Danio rerio; RNA Seq GSM7963657 r1 GSM7963657 1 To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476687   loader:fastq load.py wt_3_a_rna_5_12_22.CACCATTGTA-TACCAATTGC.HNGJJDSX3_CACCATTGTA-TACCAATTGC_L003_R1.fastq.gz wt_3_a_rna_5_12_22.CACCATTGTA-TACCAATTGC.HNGJJDSX3_CACCATTGTA-TACCAATTGC_L003_R2.fastq.gz fastq fastq 9723911364.0 32198382.0 GSM7963657 r1 0:151 1:151 A:2610813507;C:2104688166;G:2520224929;T:2488160661;N:24101 151 151     2610813507 2104688166 2520224929 2488160661 24101 SRX22832953 SRS19813393 SRA1765707 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.62594 0.60745 0.07012 0.07039 0.81728 0.82578 0.50983 0.57347 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
29123 29123 SRR27151358 SRX22832952 SRS19813392 SRP476687 PRJNA1050291 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td] GSE249755 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. parent bioproject:PRJNA1050288 pubmed:39531499   thrb:tdTomato+ cells from 5 dpf larval eyes WT rep2 GSM7963656   source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing thrb:tdTomato+ cells from 5 dpf larval eyes WT rep2 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT GSM7963656 GSM7963656: thrb:tdTomato+ cells from 5 dpf larval eyes WT rep2; Danio rerio; RNA Seq GSM7963656 r1 GSM7963656 1 To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476687   loader:fastq load.py wt_2_b_rna_5_12_22.AAGACTCTCG-TAAGTCTGGC.HNGJJDSX3_AAGACTCTCG-TAAGTCTGGC_L003_R1.fastq.gz wt_2_b_rna_5_12_22.AAGACTCTCG-TAAGTCTGGC.HNGJJDSX3_AAGACTCTCG-TAAGTCTGGC_L003_R2.fastq.gz fastq fastq 10722667946.0 35505523.0 GSM7963656 r1 0:151 1:151 A:2872256957;C:2358147851;G:2771142656;T:2721093653;N:26829 151 151     2872256957 2358147851 2771142656 2721093653 26829 SRX22832952 SRS19813392 SRA1765707 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.90028 0.8986 0.10012 0.10225 0.7973 0.80389 0.56209 0.56007 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
29124 29124 SRR27151359 SRX22832951 SRS19813391 SRP476687 PRJNA1050291 Samd7 preserves cell identity and enforces the 'one neuron one receptor' rule in vertebrate photoreceptors [5dpf td] GSE249755 Transcriptome Analysis The exclusive expression of single sensory receptors in individual neurons the 'one neuron one receptor' rule is essential for vision and other sensory systems. Here we show that the transcriptional corepressor Samd7 enforces this rule in vertebrate red cones and acts in other photoreceptor types to maintain cell identity. In the zebrafish samd7 / retina red cones are transformed to hybrid red/UV sensitive cones green cones are transfated to blue cones and the number of rods is greatly reduced. In the mouse Samd7 / retina dorsal M cones are transformed to hybrid M/S cones—analogous to the transformation of red to red/UV cones that occurs in zebrafish—and rods aberrantly express cone genes including S opsin. Altogether Samd7 acts to repress short wavelength cone gene expression in long wavelength sensitive cones thereby sustaining the mutually exclusive patterns of opsin expression and cone identity required for color vision. Overall design: To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS as described in another section. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. parent bioproject:PRJNA1050288 pubmed:39531499   thrb:tdTomato+ cells from 5 dpf larval eyes WT rep1 GSM7963655   source name:eye|cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT|geo loc name:missing|collection date:missing thrb:tdTomato+ cells from 5 dpf larval eyes WT rep1 Sequencing adapters were trimmed using trimgalore 0.6.1 https://github.com/FelixKrueger/TrimGalore61. RNA seq reads were then aligned to danRer10 using STAR 2.7.2b with an index prepared for 150 bp reads62. Next Htseq 0.9.1 was used to generate normalized read counts63. To calculate differential gene expression DESeq2 1.34.0 was used in R 4.1.3 using a log2 fold change threshold of 0 and an FDR p adj of 0.164. Volcano plots were then labeled to identify genes with p adj < 0.05. To identify genes as photoreceptor subtype specific manual curation was performed using publicly available RNA seq data from adult zebrafish photoreceptor subtypes4 5. To identify rod specific gene dysregulated in the samd7 / adult retina Table S3 we manually cross referenced the top 40 most enriched rod specific genes and mafba from Ogawa et al5. Assembly: danRer10 Supplementary files format and content: csv file of DESeq2 normalized counts and averages from three samd7 / and WT replicates derived from 5dpf thrb:tdTomato+ cells. Genes are ranked by p adj. eye   To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer’s protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the 3’ ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   cell type:thrb:tdTomato+ cells|tissue:eye|developmental stage:5 dpf larvae|genotype:WT GSM7963655 GSM7963655: thrb:tdTomato+ cells from 5 dpf larval eyes WT rep1; Danio rerio; RNA Seq GSM7963655 r1 GSM7963655 1 To perform RNA seq on 5 dpf thrb:tdTomato+ cells the following crosses were performed: WT × WT;thrb:tdTomato+/ or samd7stl888/stl888 × samd7stl888/stl888;thrb:tdTomato+/ . A subset of larvae were genotyped from each resultant clutch. TdTomato+ larvae were then separated for subsequent dissociation. 40 50 eyes from 20 25 larvae were dissected from each clutch as an individual replicate. The eyes were then dissociated into single cells and subjected to FACS. 10 000 25 000 cells were collected and sorted directly to buffer RLT from the Rneasy minElute Cleanup Kit Qiagen; RNA was then extracted using the Rneasy Micro Kit Qiagen and on column DNAse treatment performed using the Rnase Free Dnase Set Qiagen. RNA concentrations ranged from 40 190 pg/µl 0.3 1.8 ng total with RNA integrity RIN scores ranging from 7.4 8.4. Library preparation was performed with 10 ng of total RNA for 5 dpf whole eye and adult retina samples and with 300 pg of total RNA for 5 dpf thrb:tdTomato+ cells. Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing Takara Clontech per manufacturer's protocol using 12 amplification cycles for 5 dpf whole eye and adult retina samples and 14 amplification cycles for 5 dpf thrb:tdTomato+ cell samples. cDNA was fragmented using a Covaris E220 sonicator with peak incident power 18 duty factor 20% cycles per burst 50 for 120 seconds. cDNA was blunt ended using a combination of T4 DNA Polymerase Klenow Fragment DNA Polymerase and T4 PolyNucleotide Kinase; an A base was added to the three prime ends using Klenow three prime five prime exo and Illumina sequencing adapters were ligated to the ends using T4 DNA ligase Qiagen Enzymatics. Ligated fragments were then amplified for 12 cycles for 5 dpf whole eye samples and 15 cycles for adult retina and 5 dpf thrb:tdTomato+ cell samples using primers incorporating unique dual index tags using 2X VeraSeq PCR mix. DNA was sequenced on an Illumina NovaSeq 6000 using 150 bp paired end reads.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP476687   loader:fastq load.py wt_rna_5_10_22.CCACCTTCAA-ACCATCGAGG.HNGJJDSX3_CCACCTTCAA-ACCATCGAGG_L003_R1.fastq.gz wt_rna_5_10_22.CCACCTTCAA-ACCATCGAGG.HNGJJDSX3_CCACCTTCAA-ACCATCGAGG_L003_R2.fastq.gz fastq fastq 9875387618.0 32699959.0 GSM7963655 r1 0:151 1:151 A:2640364023;C:2083842037;G:2621465276;T:2529691405;N:24877 151 151     2640364023 2083842037 2621465276 2529691405 24877 SRX22832951 SRS19813391 SRA1765707 Pathology and Immunology, Washington University School of Medicine Pathology and Immunology, Washington University School of Medicine 2 0.90131 0.90429 0.10837 0.1106 0.79523 0.80182 0.50934 0.58039 151 151 B B biological fallback assumption illumina novaseq_era 3prime cdna_unspecified smarter bulk unknown unknown   United States 2023-12-08 Larval Larval Eye Sensory System
30230 30230 SRR27730907 SRX23396554 SRS20257429 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     4dpi40Hz+biological replicate 2   4dpi40Hz 2   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:10|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165700aR1AL1A M23165700aR1AL1A 4 xxx post injury+40Hz     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     4dpi40Hz_2_1.fq.gz 4dpi40Hz_2_2.fq.gz fastq fastq 7794055500.0 25980185.0 4dpi40Hz 2 1.fq.gz 0:150 1:150 A:2129184357;C:1759642251;G:1791618685;T:2113568820;N:41387 150 150     2129184357 1759642251 1791618685 2113568820 41387 SRX23396554 SRS20257429 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30231 30231 SRR27730908 SRX23396553 SRS20257428 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     4dpi40Hz+biological replicate 1   4dpi40Hz 1   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:9|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165699aR1AL1A M23165699aR1AL1A 4 xxx post injury+40Hz     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     4dpi40Hz_1_1.fq.gz 4dpi40Hz_1_2.fq.gz fastq fastq 7508652600.0 25028842.0 4dpi40Hz 1 1.fq.gz 0:150 1:150 A:2057198043;C:1689714910;G:1722042670;T:2039656491;N:40486 150 150     2057198043 1689714910 1722042670 2039656491 40486 SRX23396553 SRS20257428 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30232 30232 SRR27730909 SRX23396552 SRS20257427 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     4dpi+biological replicate 4   4dpi 4   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:8|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165697aR1AL1A M23165697aR1AL1A 4 xxx post injury     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     4dpi_4_1.fq.gz 4dpi_4_2.fq.gz fastq fastq 7094977200.0 23649924.0 4dpi 4 1.fq.gz 0:150 1:150 A:1943019606;C:1597025881;G:1626301543;T:1928592039;N:38131 150 150     1943019606 1597025881 1626301543 1928592039 38131 SRX23396552 SRS20257427 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30233 30233 SRR27730910 SRX23396551 SRS20257426 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     4dpi+biological replicate 3   4dpi 3   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:7|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165696aR1AL1A M23165696aR1AL1A 4 xxx post injury     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     4dpi_3_1.fq.gz 4dpi_3_2.fq.gz fastq fastq 7386629700.0 24622099.0 4dpi 3 1.fq.gz 0:150 1:150 A:2031801635;C:1655982922;G:1683647412;T:2015157737;N:39994 150 150     2031801635 1655982922 1683647412 2015157737 39994 SRX23396551 SRS20257426 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30234 30234 SRR27730911 SRX23396550 SRS20257425 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     4dpi+biological replicate 2   4dpi 2   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:6|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165695aR1AL1A M23165695aR1AL1A 4 xxx post injury     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     4dpi_2_1.fq.gz 4dpi_2_2.fq.gz fastq fastq 6654237600.0 22180792.0 4dpi 2 1.fq.gz 0:150 1:150 A:1825547718;C:1496727215;G:1522459901;T:1809467151;N:35615 150 150     1825547718 1496727215 1522459901 1809467151 35615 SRX23396550 SRS20257425 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30235 30235 SRR27730912 SRX23396549 SRS20257424 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     4dpi+biological replicate 1   4dpi 1   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:5|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165694aR1AL1A M23165694aR1AL1A 4 xxx post injury     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     4dpi_1_1.fq.gz 4dpi_1_2.fq.gz fastq fastq 7023034200.0 23410114.0 4dpi 1 1.fq.gz 0:150 1:150 A:1928523555;C:1581982138;G:1606070304;T:1906420119;N:38084 150 150     1928523555 1581982138 1606070304 1906420119 38084 SRX23396549 SRS20257424 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30236 30236 SRR27730913 SRX23396548 SRS20257423 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     Con+biological replicate 4   Con 4   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:4|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165693aR1AL1A M23165693aR1AL1A Control     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     Con_4_1.fq.gz Con_4_2.fq.gz fastq fastq 6857548800.0 22858496.0 Con 4 1.fq.gz 0:150 1:150 A:1882601360;C:1546021101;G:1569334195;T:1859555495;N:36649 150 150     1882601360 1546021101 1569334195 1859555495 36649 SRX23396548 SRS20257423 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30237 30237 SRR27730914 SRX23396547 SRS20257422 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     Con+biological replicate 3   Con 3   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165692aR1AL1A M23165692aR1AL1A Control     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     Con_3_1.fq.gz Con_3_2.fq.gz fastq fastq 7458957900.0 24863193.0 Con 3 1.fq.gz 0:150 1:150 A:2038911157;C:1679971639;G:1712675120;T:2027359083;N:40901 150 150     2038911157 1679971639 1712675120 2027359083 40901 SRX23396547 SRS20257422 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30238 30238 SRR27730915 SRX23396546 SRS20257421 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     7dpi40Hz+biological replicate 4   7dpi40Hz 4   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:20|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165713aR1AL1A M23165713aR1AL1A 7 xxx post injury+40Hz     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     7dpi40Hz_4_1.fq.gz 7dpi40Hz_4_2.fq.gz fastq fastq 6691700400.0 22305668.0 7dpi40Hz 4 1.fq.gz 0:150 1:150 A:1868931421;C:1476540468;G:1501092489;T:1845097964;N:38058 150 150     1868931421 1476540468 1501092489 1845097964 38058 SRX23396546 SRS20257421 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30239 30239 SRR27730916 SRX23396545 SRS20257420 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     7dpi40Hz+biological replicate 3   7dpi40Hz 3   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:19|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165712aR1AL1A M23165712aR1AL1A 7 xxx post injury+40Hz     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     7dpi40Hz_3_1.fq.gz 7dpi40Hz_3_2.fq.gz fastq fastq 7212117000.0 24040390.0 7dpi40Hz 3 1.fq.gz 0:150 1:150 A:1992256057;C:1607062903;G:1637554739;T:1975202488;N:40813 150 150     1992256057 1607062903 1637554739 1975202488 40813 SRX23396545 SRS20257420 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30240 30240 SRR27730917 SRX23396544 SRS20257419 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     7dpi40Hz+biological replicate 2   7dpi40Hz 2   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:18|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165711aR1AL1A M23165711aR1AL1A 7 xxx post injury+40Hz     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     7dpi40Hz_2_1.fq.gz 7dpi40Hz_2_2.fq.gz fastq fastq 7457525100.0 24858417.0 7dpi40Hz 2 1.fq.gz 0:150 1:150 A:2040191437;C:1678135313;G:1713456206;T:2025700956;N:41188 150 150     2040191437 1678135313 1713456206 2025700956 41188 SRX23396544 SRS20257419 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30241 30241 SRR27730918 SRX23396543 SRS20257418 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     7dpi40Hz+biological replicate 1   7dpi40Hz 1   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:17|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165710aR1AL1A M23165710aR1AL1A 7 xxx post injury+40Hz     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     7dpi40Hz_1_1.fq.gz 7dpi40Hz_1_2.fq.gz fastq fastq 6855385800.0 22851286.0 7dpi40Hz 1 1.fq.gz 0:150 1:150 A:1880374717;C:1545013977;G:1569663640;T:1860295686;N:37780 150 150     1880374717 1545013977 1569663640 1860295686 37780 SRX23396543 SRS20257418 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30242 30242 SRR27730919 SRX23396542 SRS20257417 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     7dpi+biological replicate 4   7dpi 4   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:16|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165708aR1AL1A M23165708aR1AL1A 7 xxx post injury     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     7dpi_4_1.fq.gz 7dpi_4_2.fq.gz fastq fastq 6462470400.0 21541568.0 7dpi 4 1.fq.gz 0:150 1:150 A:1785795783;C:1441222995;G:1466593271;T:1768826748;N:31603 150 150     1785795783 1441222995 1466593271 1768826748 31603 SRX23396542 SRS20257417 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30243 30243 SRR27730920 SRX23396541 SRS20257416 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     7dpi+biological replicate 3   7dpi 3   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:15|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165706aR1AL1A M23165706aR1AL1A 7 xxx post injury     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     7dpi_3_1.fq.gz 7dpi_3_2.fq.gz fastq fastq 6710491200.0 22368304.0 7dpi 3 1.fq.gz 0:150 1:150 A:1831876501;C:1512529252;G:1544827061;T:1821200080;N:58306 150 150     1831876501 1512529252 1544827061 1821200080 58306 SRX23396541 SRS20257416 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30244 30244 SRR27730921 SRX23396540 SRS20257415 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     7dpi+biological replicate 2   7dpi 2   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:14|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165705aR1AL1A M23165705aR1AL1A 7 xxx post injury     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     7dpi_2_1.fq.gz 7dpi_2_2.fq.gz fastq fastq 6294917700.0 20983059.0 7dpi 2 1.fq.gz 0:150 1:150 A:1735431442;C:1394112982;G:1431966224;T:1733339379;N:67673 150 150     1735431442 1394112982 1431966224 1733339379 67673 SRX23396540 SRS20257415 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30245 30245 SRR27730922 SRX23396539 SRS20257414 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     7dpi+biological replicate 1   7dpi 1   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:13|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165704aR1AL1A M23165704aR1AL1A 7 xxx post injury     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     7dpi_1_1.fq.gz 7dpi_1_2.fq.gz fastq fastq 6694150800.0 22313836.0 7dpi 1 1.fq.gz 0:150 1:150 A:1824840998;C:1510909671;G:1543521247;T:1814842377;N:36507 150 150     1824840998 1510909671 1543521247 1814842377 36507 SRX23396539 SRS20257414 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30246 30246 SRR27730923 SRX23396538 SRS20257413 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     4dpi40Hz+biological replicate 4   4dpi40Hz 4   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:12|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165702aR1AL1A M23165702aR1AL1A 4 xxx post injury+40Hz     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     4dpi40Hz_4_1.fq.gz 4dpi40Hz_4_2.fq.gz fastq fastq 8672814300.0 28909381.0 4dpi40Hz 4 1.fq.gz 0:150 1:150 A:2372923011;C:1956760768;G:1989924842;T:2353159305;N:46374 150 150     2372923011 1956760768 1989924842 2353159305 46374 SRX23396538 SRS20257413 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30247 30247 SRR27730924 SRX23396537 SRS20257412 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     4dpi40Hz+biological replicate 3   4dpi40Hz 3   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:11|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165701aR1AL1A M23165701aR1AL1A 4 xxx post injury+40Hz     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     4dpi40Hz_3_1.fq.gz 4dpi40Hz_3_2.fq.gz fastq fastq 7566042300.0 25220141.0 4dpi40Hz 3 1.fq.gz 0:150 1:150 A:2073697374;C:1705150021;G:1733548148;T:2053605856;N:40901 150 150     2073697374 1705150021 1733548148 2053605856 40901 SRX23396537 SRS20257412 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30248 30248 SRR27730925 SRX23396536 SRS20257411 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     Con+biological replicate 2   Con 2   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165691aR1AL1A M23165691aR1AL1A Control     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     Con_2_1.fq.gz Con_2_2.fq.gz fastq fastq 7211639400.0 24038798.0 Con 2 1.fq.gz 0:150 1:150 A:1979869383;C:1617364490;G:1649637969;T:1964729059;N:38499 150 150     1979869383 1617364490 1649637969 1964729059 38499 SRX23396536 SRS20257411 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
30249 30249 SRR27730926 SRX23396535 SRS20257410 SRP486007 PRJNA1069290 Noninvasive light flicker stimulation promotes optic nerve regeneration by activating microglia and enhancing neural plasticity in zebrafish PRJNA1069290 Other In the present study we demonstrated that the optic nerve can spontaneously regenerate and that visual function can be restored post ONC in zebrafish. Forty Hertz light flicker stimulation modulated microglia in the zebrafish retina post ONC promoted dendritic remodeling and axonal regeneration of RGCs and restored visual function. Transcriptomic and qPCR results both indicated that 40 Hz light flicker stimulation increased the expression of genes related to neural plasticity. In general our study showed that 40 Hz light flicker stimulation promotes axonal and dendritic regeneration of RGCs as well as the recovery of visual function which is related to the activation of microglia and enhancement of neural plasticity.     Con+biological replicate 1   Con 1   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month 6 month|dev stage:3 month 6 month|collection date:2023 07|geo loc name:China:Nanchang|sex:pooled male and female|tissue:retina|ID:1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: retina M23165689aR1AL1A M23165689aR1AL1A Control     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP486007     Con_1_1.fq.gz Con_1_2.fq.gz fastq fastq 6217369800.0 20724566.0 Con 1 1.fq.gz 0:150 1:150 A:1714156006;C:1391042352;G:1415307378;T:1696831326;N:32738 150 150     1714156006 1391042352 1415307378 1696831326 32738 SRX23396535 SRS20257410 SRA1791874 Affiliated Eye Hospital of Nanchang University|Department of Ophthalmology Affiliated Eye Hospital of Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-01-25 Adult Adult Eye Sensory System
33202 33202 SRR29848463 SRX25346228 SRS22013442 SRP520276 PRJNA1136505 Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish GSE272355 Transcriptome Analysis Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…   pubmed:39742644   IPP 120hpf eye replicate4 GSM8399280   source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing IPP 120hpf eye replicate4 Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample Dissected eye Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification Embryos were spawned and maintained in system water tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf GSM8399280 GSM8399280: IPP 120hpf eye replicate4; Danio rerio; RNA Seq GSM8399280 r1 GSM8399280 1 Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     IPP_eye_4_1.fq.gz IPP_eye_4_2.fq.gz fastq fastq 7072359000.0 23574530.0 GSM8399280 r1 0:150 1:150 A:1896065137;C:1651795911;G:1640296836;T:1877949054;N:6252062 150 150     1896065137 1651795911 1640296836 1877949054 6252062 SRX25346228 SRS22013442 SRA1925887 Dasgupta lab, Biological Sciences, Clemson University Dasgupta lab, Biological Sciences, Clemson University 2 0.90538 0.89728 0.10331 0.10225 0.70593 0.70688 0.44853 0.44733 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   United States 2024-07-16 Multi-stage Multi-stage Eye Sensory System
33203 33203 SRR29848464 SRX25346227 SRS22013441 SRP520276 PRJNA1136505 Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish GSE272355 Transcriptome Analysis Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…   pubmed:39742644   IPP 120hpf eye replicate3 GSM8399279   source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing IPP 120hpf eye replicate3 Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample Dissected eye Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification Embryos were spawned and maintained in system water tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf GSM8399279 GSM8399279: IPP 120hpf eye replicate3; Danio rerio; RNA Seq GSM8399279 r1 GSM8399279 1 Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     IPP_eye_3_1.fq.gz IPP_eye_3_2.fq.gz fastq fastq 6537519300.0 21791731.0 GSM8399279 r1 0:150 1:150 A:1760227857;C:1520738786;G:1507946481;T:1742862368;N:5743808 150 150     1760227857 1520738786 1507946481 1742862368 5743808 SRX25346227 SRS22013441 SRA1925887 Dasgupta lab, Biological Sciences, Clemson University Dasgupta lab, Biological Sciences, Clemson University 2 0.90945 0.90902 0.10894 0.10846 0.70431 0.7055 0.44535 0.43463 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   United States 2024-07-16 Multi-stage Multi-stage Eye Sensory System
33204 33204 SRR29848465 SRX25346226 SRS22013440 SRP520276 PRJNA1136505 Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish GSE272355 Transcriptome Analysis Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…   pubmed:39742644   IPP 120hpf eye replicate2 GSM8399278   source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing IPP 120hpf eye replicate2 Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample Dissected eye Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification Embryos were spawned and maintained in system water tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf GSM8399278 GSM8399278: IPP 120hpf eye replicate2; Danio rerio; RNA Seq GSM8399278 r1 GSM8399278 1 Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     IPP_eye_2_1.fq.gz IPP_eye_2_2.fq.gz fastq fastq 7374435900.0 24581453.0 GSM8399278 r1 0:150 1:150 A:1986621253;C:1713862328;G:1699590477;T:1967874898;N:6486944 150 150     1986621253 1713862328 1699590477 1967874898 6486944 SRX25346226 SRS22013440 SRA1925887 Dasgupta lab, Biological Sciences, Clemson University Dasgupta lab, Biological Sciences, Clemson University 2 0.9091 0.90128 0.11122 0.1097 0.70201 0.70266 0.44395 0.4416 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   United States 2024-07-16 Multi-stage Multi-stage Eye Sensory System
33205 33205 SRR29848466 SRX25346225 SRS22013439 SRP520276 PRJNA1136505 Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish GSE272355 Transcriptome Analysis Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…   pubmed:39742644   IPP 120hpf eye replicate1 GSM8399277   source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing IPP 120hpf eye replicate1 Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample Dissected eye Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification Embryos were spawned and maintained in system water tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf GSM8399277 GSM8399277: IPP 120hpf eye replicate1; Danio rerio; RNA Seq GSM8399277 r1 GSM8399277 1 Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     IPP_eye_1_1.fq.gz IPP_eye_1_2.fq.gz fastq fastq 6538011600.0 21793372.0 GSM8399277 r1 0:150 1:150 A:1758764189;C:1520242338;G:1510361700;T:1742917780;N:5725593 150 150     1758764189 1520242338 1510361700 1742917780 5725593 SRX25346225 SRS22013439 SRA1925887 Dasgupta lab, Biological Sciences, Clemson University Dasgupta lab, Biological Sciences, Clemson University 2 0.91402 0.90585 0.11702 0.11558 0.70029 0.70094 0.45385 0.45435 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   United States 2024-07-16 Multi-stage Multi-stage Eye Sensory System
33206 33206 SRR29848467 SRX25346224 SRS22013438 SRP520276 PRJNA1136505 Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish GSE272355 Transcriptome Analysis Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…   pubmed:39742644   DMSO 120hpf eye replicate4 GSM8399276   source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing DMSO 120hpf eye replicate4 Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample Dissected eye Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification Embryos were spawned and maintained in system water tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf GSM8399276 GSM8399276: DMSO 120hpf eye replicate4; Danio rerio; RNA Seq GSM8399276 r1 GSM8399276 1 Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     Ctrl_eye_4_1.fq.gz Ctrl_eye_4_2.fq.gz fastq fastq 7198057200.0 23993524.0 GSM8399276 r1 0:150 1:150 A:1929066670;C:1680279530;G:1672121671;T:1910263876;N:6325453 150 150     1929066670 1680279530 1672121671 1910263876 6325453 SRX25346224 SRS22013438 SRA1925887 Dasgupta lab, Biological Sciences, Clemson University Dasgupta lab, Biological Sciences, Clemson University 2 0.91947 0.90384 0.11309 0.11094 0.69576 0.69779 0.45803 0.45394 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   United States 2024-07-16 Multi-stage Multi-stage Eye Sensory System
33207 33207 SRR29848468 SRX25346223 SRS22013437 SRP520276 PRJNA1136505 Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish GSE272355 Transcriptome Analysis Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…   pubmed:39742644   DMSO 120hpf eye replicate3 GSM8399275   source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing DMSO 120hpf eye replicate3 Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample Dissected eye Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification Embryos were spawned and maintained in system water tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf GSM8399275 GSM8399275: DMSO 120hpf eye replicate3; Danio rerio; RNA Seq GSM8399275 r1 GSM8399275 1 Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     Ctrl_eye_3_1.fq.gz Ctrl_eye_3_2.fq.gz fastq fastq 6349681200.0 21165604.0 GSM8399275 r1 0:150 1:150 A:1713020668;C:1474226584;G:1462505802;T:1694350186;N:5577960 150 150     1713020668 1474226584 1462505802 1694350186 5577960 SRX25346223 SRS22013437 SRA1925887 Dasgupta lab, Biological Sciences, Clemson University Dasgupta lab, Biological Sciences, Clemson University 2 0.89548 0.89606 0.09628 0.09664 0.71102 0.71161 0.44199 0.4354 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   United States 2024-07-16 Multi-stage Multi-stage Eye Sensory System
33208 33208 SRR29848469 SRX25346222 SRS22013436 SRP520276 PRJNA1136505 Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish GSE272355 Transcriptome Analysis Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…   pubmed:39742644   DMSO 120hpf eye replicate2 GSM8399274   source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing DMSO 120hpf eye replicate2 Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample Dissected eye Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification Embryos were spawned and maintained in system water tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf GSM8399274 GSM8399274: DMSO 120hpf eye replicate2; Danio rerio; RNA Seq GSM8399274 r1 GSM8399274 1 Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     Ctrl_eye_2_1.fq.gz Ctrl_eye_2_2.fq.gz fastq fastq 6861299400.0 22870998.0 GSM8399274 r1 0:150 1:150 A:1839006136;C:1604484415;G:1591747628;T:1820307442;N:5753779 150 150     1839006136 1604484415 1591747628 1820307442 5753779 SRX25346222 SRS22013436 SRA1925887 Dasgupta lab, Biological Sciences, Clemson University Dasgupta lab, Biological Sciences, Clemson University 2 0.84164 0.83344 0.09914 0.09758 0.72034 0.72088 0.44273 0.4389 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   United States 2024-07-16 Multi-stage Multi-stage Eye Sensory System
33209 33209 SRR29848470 SRX25346221 SRS22013435 SRP520276 PRJNA1136505 Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish GSE272355 Transcriptome Analysis Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture electronics automobiles plastics and children's products to slow down the spread of fire. The processing and distribution of IPP containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed range finding experiments with embryonic zebrafish exposed to 0 200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema yolk sac edema and spinal curvature at higher concentrations. Following this relying on secondary analyses of our whole embryo mRNA seq data we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite 3 methoxytyramine. We then conducted in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa but not RAR? and RAR?. For behavioral readouts we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally based on whole embryo RNA seq data we hypothesized that IPP affects the development of brain and eyes. Firstly we performed global DNA methylation in brain and eyes but did not find significant effects. Then we conducted mRNA sequencing on dissected brains and eyes and found 2 and 135 differentially expressed genes respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity synaptic transmission and neurotransmitter signaling. Collectively our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response potentially through RA inhibition and methylom…   pubmed:39742644   DMSO 120hpf eye replicate1 GSM8399273   source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf|geo loc name:missing|collection date:missing DMSO 120hpf eye replicate1 Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step clean data clean reads was obtainedbyremoving reads containing adapter reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample Dissected eye Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification Embryos were spawned and maintained in system water tissue:Dissected eye|genotype:wildtype|treatment:DMSO|time:120hpf GSM8399273 GSM8399273: DMSO 120hpf eye replicate1; Danio rerio; RNA Seq GSM8399273 r1 GSM8399273 1 Eyes and brains were dissected from whole embryos homogenized in RNA zol and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library it was ready post end repair A tailing adapter ligation size selection amplification and purification For the directional library it was ready post end repair A tailing adapter ligation size selection USER enzyme digestion amplification and purification   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP520276     Ctrl_eye_1_1.fq.gz Ctrl_eye_1_2.fq.gz fastq fastq 6544491000.0 21814970.0 GSM8399273 r1 0:150 1:150 A:1774622867;C:1510819173;G:1498655117;T:1754689449;N:5704394 150 150     1774622867 1510819173 1498655117 1754689449 5704394 SRX25346221 SRS22013435 SRA1925887 Dasgupta lab, Biological Sciences, Clemson University Dasgupta lab, Biological Sciences, Clemson University 2 0.86147 0.86095 0.11217 0.11159 0.71319 0.71352 0.44434 0.43886 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   United States 2024-07-16 Multi-stage Multi-stage Eye Sensory System
33274 33274 SRR29884407 SRX25380711 SRS22046064 SRP520852 PRJNA1137393 Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function GSE272589 Transcriptome Analysis Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.   pubmed:39890032   Brain wh5 Male 5 GSM8406321   source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing Brain wh5 Male 5 quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa… eye   RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   tissue:eye|genotype:wh5 GSM8406321 GSM8406321: Brain wh5 Male 5; Danio rerio; RNA Seq GSM8406321 r1 GSM8406321 1 RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP520852     Sample20KOMaleBrain_R1.fastq Sample20KOMaleBrain_R2.fastq fastq fastq 5509276088.0 27917150.0 GSM8406321 r1 0:98.67 1:98.67 A:1498190193;C:1242495192;G:1267229536;T:1499431726;N:1929441 98 98     1498190193 1242495192 1267229536 1499431726 1929441 SRX25380711 SRS22046064 SRA1927371 Oregon State University Oregon State University 2 0.94576 0.94515 0.14102 0.13871 0.69187 0.69077 0.52554 0.53007 101 101 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-07-18 Undetermined Multi-stage Eye Sensory System
33275 33275 SRR29884408 SRX25380710 SRS22046063 SRP520852 PRJNA1137393 Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function GSE272589 Transcriptome Analysis Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.   pubmed:39890032   Brain wh5 Male 4 GSM8406320   source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing Brain wh5 Male 4 quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa… eye   RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   tissue:eye|genotype:wh5 GSM8406320 GSM8406320: Brain wh5 Male 4; Danio rerio; RNA Seq GSM8406320 r1 GSM8406320 1 RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP520852     Sample19KOMaleBrain_R1.fastq Sample19KOMaleBrain_R2.fastq fastq fastq 6985356408.0 35379007.0 GSM8406320 r1 0:98.72 1:98.72 A:1889039547;C:1582622229;G:1620512342;T:1890746302;N:2435988 98 98     1889039547 1582622229 1620512342 1890746302 2435988 SRX25380710 SRS22046063 SRA1927371 Oregon State University Oregon State University 2 0.94197 0.94411 0.14763 0.14597 0.69852 0.69826 0.54705 0.54822 101 101 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-07-18 Undetermined Multi-stage Eye Sensory System
33276 33276 SRR29884409 SRX25380709 SRS22046062 SRP520852 PRJNA1137393 Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function GSE272589 Transcriptome Analysis Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.   pubmed:39890032   Brain wh5 Male 3 GSM8406319   source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing Brain wh5 Male 3 quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa… eye   RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   tissue:eye|genotype:wh5 GSM8406319 GSM8406319: Brain wh5 Male 3; Danio rerio; RNA Seq GSM8406319 r1 GSM8406319 1 RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP520852     Sample18KOMaleBrain_R1.fastq Sample18KOMaleBrain_R2.fastq fastq fastq 5864072768.0 29837549.0 GSM8406319 r1 0:98.27 1:98.27 A:1609423180;C:1310248473;G:1328624911;T:1613750029;N:2026175 98 98     1609423180 1310248473 1328624911 1613750029 2026175 SRX25380709 SRS22046062 SRA1927371 Oregon State University Oregon State University 2 0.94007 0.94233 0.14021 0.1386 0.69376 0.69317 0.51507 0.52214 101 101 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-07-18 Undetermined Multi-stage Eye Sensory System
33277 33277 SRR29884410 SRX25380708 SRS22046061 SRP520852 PRJNA1137393 Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function GSE272589 Transcriptome Analysis Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.   pubmed:39890032   Brain wh5 Male 2 GSM8406318   source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing Brain wh5 Male 2 quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa… eye   RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   tissue:eye|genotype:wh5 GSM8406318 GSM8406318: Brain wh5 Male 2; Danio rerio; RNA Seq GSM8406318 r1 GSM8406318 1 RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP520852     Sample17KOMaleBrain_R1.fastq Sample17KOMaleBrain_R2.fastq fastq fastq 5841328432.0 29860768.0 GSM8406318 r1 0:97.81 1:97.81 A:1606036785;C:1302920703;G:1321021765;T:1609306125;N:2043054 97 97     1606036785 1302920703 1321021765 1609306125 2043054 SRX25380708 SRS22046061 SRA1927371 Oregon State University Oregon State University 2 0.9429 0.94295 0.14247 0.14023 0.69808 0.69739 0.51804 0.51798 69 69 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-07-18 Undetermined Multi-stage Eye Sensory System
33278 33278 SRR29884411 SRX25380707 SRS22046060 SRP520852 PRJNA1137393 Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function GSE272589 Transcriptome Analysis Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.   pubmed:39890032   Brain wh5 Male 1 GSM8406317   source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing Brain wh5 Male 1 quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa… eye   RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   tissue:eye|genotype:wh5 GSM8406317 GSM8406317: Brain wh5 Male 1; Danio rerio; RNA Seq GSM8406317 r1 GSM8406317 1 RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP520852     Sample16KOMaleBrain_R1.fastq Sample16KOMaleBrain_R2.fastq fastq fastq 6061816166.0 30929476.0 GSM8406317 r1 0:97.99 1:97.99 A:1666435568;C:1352308656;G:1373281492;T:1667671946;N:2118504 97 97     1666435568 1352308656 1373281492 1667671946 2118504 SRX25380707 SRS22046060 SRA1927371 Oregon State University Oregon State University 2 0.94198 0.9434 0.14745 0.14621 0.69201 0.69138 0.52388 0.52247 101 101 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-07-18 Undetermined Multi-stage Eye Sensory System
33279 33279 SRR29884412 SRX25380706 SRS22046059 SRP520852 PRJNA1137393 Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function GSE272589 Transcriptome Analysis Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.   pubmed:39890032   Brain wh5 Female 5 GSM8406316   source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing Brain wh5 Female 5 quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa… eye   RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   tissue:eye|genotype:wh5 GSM8406316 GSM8406316: Brain wh5 Female 5; Danio rerio; RNA Seq GSM8406316 r1 GSM8406316 1 RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP520852     Sample15KOFemaleBrain_R1.fastq Sample15KOFemaleBrain_R2.fastq fastq fastq 5830172008.0 29715950.0 GSM8406316 r1 0:98.10 1:98.10 A:1585225847;C:1316585087;G:1339955604;T:1586384657;N:2020813 98 98     1585225847 1316585087 1339955604 1586384657 2020813 SRX25380706 SRS22046059 SRA1927371 Oregon State University Oregon State University 2 0.94307 0.94571 0.13598 0.13423 0.69341 0.69309 0.52103 0.50706 101 101 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-07-18 Undetermined Multi-stage Eye Sensory System
33280 33280 SRR29884413 SRX25380705 SRS22046058 SRP520852 PRJNA1137393 Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function GSE272589 Transcriptome Analysis Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.   pubmed:39890032   Brain wh5 Female 4 GSM8406315   source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing Brain wh5 Female 4 quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa… eye   RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   tissue:eye|genotype:wh5 GSM8406315 GSM8406315: Brain wh5 Female 4; Danio rerio; RNA Seq GSM8406315 r1 GSM8406315 1 RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP520852     Sample14KOFemaleBrain_R1.fastq Sample14KOFemaleBrain_R2.fastq fastq fastq 6700791892.0 34096304.0 GSM8406315 r1 0:98.26 1:98.26 A:1817874372;C:1516000049;G:1546573687;T:1818017657;N:2326127 98 98     1817874372 1516000049 1546573687 1818017657 2326127 SRX25380705 SRS22046058 SRA1927371 Oregon State University Oregon State University 2 0.94342 0.94623 0.13719 0.13523 0.69313 0.69254 0.53293 0.53816 84 84 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-07-18 Undetermined Multi-stage Eye Sensory System
33281 33281 SRR29884414 SRX25380704 SRS22046057 SRP520852 PRJNA1137393 Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function GSE272589 Transcriptome Analysis Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.   pubmed:39890032   Brain wh5 Female 3 GSM8406314   source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing Brain wh5 Female 3 quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa… eye   RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   tissue:eye|genotype:wh5 GSM8406314 GSM8406314: Brain wh5 Female 3; Danio rerio; RNA Seq GSM8406314 r1 GSM8406314 1 RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP520852     Sample13KOFemaleBrain_R2.fastq Sample13KOFemaleBrain_R1.fastq fastq fastq 6308152444.0 32040291.0 GSM8406314 r1 0:98.44 1:98.44 A:1698706705;C:1436132175;G:1472501608;T:1698611730;N:2200226 98 98     1698706705 1436132175 1472501608 1698611730 2200226 SRX25380704 SRS22046057 SRA1927371 Oregon State University Oregon State University 2 0.94654 0.94476 0.1362 0.13304 0.694 0.69321 0.54515 0.53479 91 91 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-07-18 Undetermined Multi-stage Eye Sensory System
33282 33282 SRR29884415 SRX25380703 SRS22046056 SRP520852 PRJNA1137393 Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function GSE272589 Transcriptome Analysis Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.   pubmed:39890032   Brain wh5 Female 2 GSM8406313   source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing Brain wh5 Female 2 quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value ≤ 0.05 and log2fold change ≥ |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sa… eye   RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   tissue:eye|genotype:wh5 GSM8406313 GSM8406313: Brain wh5 Female 2; Danio rerio; RNA Seq GSM8406313 r1 GSM8406313 1 RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP520852     Sample12KOFemaleBrain_R1.fastq Sample12KOFemaleBrain_R2.fastq fastq fastq 6503673262.0 33197897.0 GSM8406313 r1 0:97.95 1:97.95 A:1781196226;C:1457467194;G:1479672271;T:1783090598;N:2246973 97 97     1781196226 1457467194 1479672271 1783090598 2246973 SRX25380703 SRS22046056 SRA1927371 Oregon State University Oregon State University 2 0.94227 0.94462 0.13793 0.13614 0.69359 0.69355 0.52971 0.52982 101 101 B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-07-18 Undetermined Multi-stage Eye Sensory System

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;