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244 rows where devstage_curation_coarse = "Embryo" and tissue_curation_coarse = "Sensory System"

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technology 4

devstage_curation 4

experiment.library_selection 3

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Sensory System · 244 ✖

tissue_curation 1

experiment.platform 1

devstage_curation_coarse 1

  • Embryo · 244 ✖
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
19087 19087 ERR13834862 ERX13237628 ERS21098715 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC1 S20 R1 001.fastq.gz SAMEA116100635 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC1|scientific name:Danio rerio|tissue type:retina                 Raw reads: 48 HC1 webin reads 48 HC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC1_S20_R1_001.fastq.gz fastq 3768442091.0 38065677.0 webin reads 48 HC1 0:99.00 A:1055463738;C:792073627;G:817607736;T:1103223790;N:73200 99       1055463738 792073627 817607736 1103223790 73200 ERX13237628 ERS21098715 ERA30883416 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19088 19088 ERR13834951 ERX13237717 ERS21098721 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR3 S26 R1 001.fastq.gz 58 PR3   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR3 webin reads 58 PR3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR3_S26_R1_001.fastq.gz fastq 3869469736.0 38850717.0 webin reads 58 PR3 0:99.60 A:1103909449;C:804146524;G:827344036;T:1134036010;N:33717 99       1103909449 804146524 827344036 1134036010 33717 ERX13237717 ERS21098721 ERA30883529 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19089 19089 ERR13835010 ERX13237776 ERS21098726 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC4 S31 R1 001.fastq.gz SAMEA116100646 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 AC4|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 AC4|scientific name:Danio rerio|tissue type:retina                 Raw reads: 58 AC4 webin reads 58 AC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC4_S31_R1_001.fastq.gz fastq 3607648651.0 36331933.0 webin reads 58 AC4 0:99.30 A:1038047870;C:736262498;G:759315202;T:1073962987;N:60094 99       1038047870 736262498 759315202 1073962987 60094 ERX13237776 ERS21098726 ERA30883721 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19090 19090 ERR13822794 ERX13225546 ERS21098708 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48PR2 S13 R1 001.fastq.gz 48 PR2   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 PR2 webin reads 48 PR2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 PR2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48PR2_S13_R1_001.fastq.gz fastq 3809299607.0 38404185.0 webin reads 48 PR2 0:99.19 A:1067728192;C:802585802;G:828435932;T:1110435904;N:113777 99       1067728192 802585802 828435932 1110435904 113777 ERX13225546 ERS21098708 ERA30879682 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19091 19091 ERR13834854 ERX13237620 ERS21098714 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC4 S19 R1 001.fastq.gz 48 AC4   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC4 webin reads 48 AC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC4_S19_R1_001.fastq.gz fastq 3410801894.0 34443068.0 webin reads 48 AC4 0:99.03 A:966160063;C:707754156;G:733039262;T:1003772756;N:75657 99       966160063 707754156 733039262 1003772756 75657 ERX13237620 ERS21098714 ERA30883390 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19092 19092 ERR13828824 ERX13231590 ERS21098710 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48PR4 S15 R1 001.fastq.gz 48 PR4   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 PR4 webin reads 48 PR4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 PR4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48PR4_S15_R1_001.fastq.gz fastq 4365943927.0 44278278.0 webin reads 48 PR4 0:98.60 A:1214448497;C:927512154;G:957491418;T:1266385355;N:106503 98       1214448497 927512154 957491418 1266385355 106503 ERX13231590 ERS21098710 ERA30883309 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19093 19093 ERR13834993 ERX13237759 ERS21098723 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC1 S28 R1 001.fastq.gz 58 AC1   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 AC1 webin reads 58 AC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC1_S28_R1_001.fastq.gz fastq 3710768269.0 37364763.0 webin reads 58 AC1 0:99.31 A:1060419097;C:761984557;G:786533722;T:1101603428;N:227465 99       1060419097 761984557 786533722 1101603428 227465 ERX13237759 ERS21098723 ERA30883659 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19094 19094 ERR13834875 ERX13237641 ERS21098717 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC3 S22 R1 001.fastq.gz 48 HC3   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 HC3 webin reads 48 HC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC3_S22_R1_001.fastq.gz fastq 3083078586.0 31073491.0 webin reads 48 HC3 0:99.22 A:856250957;C:655140994;G:677078911;T:894558582;N:49142 99       856250957 655140994 677078911 894558582 49142 ERX13237641 ERS21098717 ERA30883447 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19095 19095 ERR13834899 ERX13237665 ERS21098720 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR2 S25 R1 001.fastq.gz 58 PR2   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR2 webin reads 58 PR2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR2_S25_R1_001.fastq.gz fastq 3849571818.0 38706841.0 webin reads 58 PR2 0:99.45 A:1089593011;C:803322469;G:827777017;T:1128836774;N:42547 99       1089593011 803322469 827777017 1128836774 42547 ERX13237665 ERS21098720 ERA30883518 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19096 19096 ERR13834889 ERX13237655 ERS21098719 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR1 S24 R1 001.fastq.gz 58 PR1   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR1 webin reads 58 PR1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR1_S24_R1_001.fastq.gz fastq 3945671240.0 39514922.0 webin reads 58 PR1 0:99.85 A:1135075173;C:807489123;G:827964380;T:1175109762;N:32802 99       1135075173 807489123 827964380 1175109762 32802 ERX13237655 ERS21098719 ERA30883497 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19097 19097 ERR13835019 ERX13237785 ERS21098728 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC2 S33 R1 001.fastq.gz SAMEA116100648 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 HC2|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 HC2|scientific name:Danio rerio|tissue type:retina                 Raw reads: 58 HC2 webin reads 58 HC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC2_S33_R1_001.fastq.gz fastq 3711237069.0 37217240.0 webin reads 58 HC2 0:99.72 A:1070592288;C:757099665;G:780689044;T:1102575310;N:280762 99       1070592288 757099665 780689044 1102575310 280762 ERX13237785 ERS21098728 ERA30883748 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19098 19098 ERR13822110 ERX13224862 ERS21098697 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR2 S2 R1 001.fastq.gz 38 PR2   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 PR2 webin reads 38 PR2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR2_S2_R1_001.fastq.gz fastq 3463281109.0 34821985.0 webin reads 38 PR2 0:99.46 A:969862466;C:733798241;G:755135957;T:1004440555;N:43890 99       969862466 733798241 755135957 1004440555 43890 ERX13224862 ERS21098697 ERA30879238 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19099 19099 ERR13822784 ERX13225536 ERS21098706 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC3 S11 R1 001.fastq.gz 38 HC3   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 HC3 webin reads 38 HC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC3_S11_R1_001.fastq.gz fastq 4360921873.0 44107486.0 webin reads 38 HC3 0:98.87 A:1222778761;C:918257887;G:948838973;T:1270939370;N:106882 98       1222778761 918257887 948838973 1270939370 106882 ERX13225536 ERS21098706 ERA30879613 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19100 19100 ERR13828836 ERX13231602 ERS21098712 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC2 S17 R1 001.fastq.gz 48 AC2   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC2 webin reads 48 AC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC2_S17_R1_001.fastq.gz fastq 3205206588.0 32424632.0 webin reads 48 AC2 0:98.85 A:902438127;C:672433401;G:694813369;T:935445436;N:76255 98       902438127 672433401 694813369 935445436 76255 ERX13231602 ERS21098712 ERA30883343 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19101 19101 ERR13835004 ERX13237770 ERS21098725 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC3 S30 R1 001.fastq.gz 58 AC3   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 AC3 webin reads 58 AC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC3_S30_R1_001.fastq.gz fastq 3782993133.0 38295959.0 webin reads 58 AC3 0:98.78 A:1080745150;C:779903026;G:803258485;T:1118994941;N:91531 98       1080745150 779903026 803258485 1118994941 91531 ERX13237770 ERS21098725 ERA30883697 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19102 19102 ERR13834868 ERX13237634 ERS21098716 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC2 S21 R1 001.fastq.gz SAMEA116100636 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC2|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC2|scientific name:Danio rerio|tissue type:retina                 Raw reads: 48 HC2 webin reads 48 HC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC2_S21_R1_001.fastq.gz fastq 3424347865.0 34510204.0 webin reads 48 HC2 0:99.23 A:959488173;C:721171249;G:745705870;T:997922014;N:60559 99       959488173 721171249 745705870 997922014 60559 ERX13237634 ERS21098716 ERA30883434 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19103 19103 ERR13822197 ERX13224949 ERS21098704 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC1 S9 R1 001.fastq.gz SAMEA116100624 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 HC1|scientific name:Danio rerio|tissue type:retina                 Raw reads: 38 HC1 webin reads 38 HC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC1_S9_R1_001.fastq.gz fastq 3784641498.0 38331162.0 webin reads 38 HC1 0:98.74 A:1064199311;C:791310791;G:818910597;T:1110118632;N:102167 98       1064199311 791310791 818910597 1110118632 102167 ERX13224949 ERS21098704 ERA30879548 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Pharyngula Embryo Eye Sensory System
19104 19104 ERR13834880 ERX13237646 ERS21098718 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC4 S23 R1 001.fastq.gz 48 HC4   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 HC4 webin reads 48 HC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC4_S23_R1_001.fastq.gz fastq 3660674315.0 36821474.0 webin reads 48 HC4 0:99.42 A:1035049987;C:763030378;G:788062167;T:1074303516;N:228267 99       1035049987 763030378 788062167 1074303516 228267 ERX13237646 ERS21098718 ERA30883470 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19105 19105 ERR13822867 ERX13225633 ERS21098709 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48PR3 S14 R1 001.fastq.gz 48 PR3   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 PR3 webin reads 48 PR3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 PR3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48PR3_S14_R1_001.fastq.gz fastq 4232170464.0 42534853.0 webin reads 48 PR3 0:99.50 A:1195251409;C:889346003;G:917240118;T:1230272855;N:60079 99       1195251409 889346003 917240118 1230272855 60079 ERX13225633 ERS21098709 ERA30879704 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19106 19106 ERR13822131 ERX13224883 ERS21098700 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC1 S5 R1 001.fastq.gz SAMEA116100620 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 AC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 AC1|scientific name:Danio rerio|tissue type:retina                 Raw reads: 38 AC1 webin reads 38 AC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC1_S5_R1_001.fastq.gz fastq 3836921113.0 38702139.0 webin reads 38 AC1 0:99.14 A:1066720805;C:818958589;G:843762182;T:1107403844;N:75693 99       1066720805 818958589 843762182 1107403844 75693 ERX13224883 ERS21098700 ERA30879356 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Pharyngula Embryo Eye Sensory System
19107 19107 ERR13822143 ERX13224895 ERS21098702 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC3 S7 R1 001.fastq.gz 38 AC3   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 AC3 webin reads 38 AC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC3_S7_R1_001.fastq.gz fastq 3452707377.0 34902410.0 webin reads 38 AC3 0:98.92 A:970868997;C:726795179;G:750560378;T:1004408693;N:74130 98       970868997 726795179 750560378 1004408693 74130 ERX13224895 ERS21098702 ERA30879451 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19108 19108 ERR13828843 ERX13234350 ERS21098713 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC3 S18 R1 001.fastq.gz 48 AC3   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC3 webin reads 48 AC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC3_S18_R1_001.fastq.gz fastq 3733628911.0 37779462.0 webin reads 48 AC3 0:98.83 A:1047204450;C:786943605;G:812327274;T:1086893109;N:260473 98       1047204450 786943605 812327274 1086893109 260473 ERX13234350 ERS21098713 ERA30883366 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19109 19109 ERR13822153 ERX13224905 ERS21098703 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC4 S8 R1 001.fastq.gz 38 AC4   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 AC4 webin reads 38 AC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC4_S8_R1_001.fastq.gz fastq 4130629624.0 41794865.0 webin reads 38 AC4 0:98.83 A:1156746387;C:877063962;G:905379690;T:1191264308;N:175277 98       1156746387 877063962 905379690 1191264308 175277 ERX13224905 ERS21098703 ERA30879532 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19110 19110 ERR13822201 ERX13224953 ERS21098705 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC2 S10 R1 001.fastq.gz 38 HC2   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 HC2 webin reads 38 HC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC2_S10_R1_001.fastq.gz fastq 4221340137.0 42584743.0 webin reads 38 HC2 0:99.13 A:1195817135;C:879958039;G:908085464;T:1237394738;N:84761 99       1195817135 879958039 908085464 1237394738 84761 ERX13224953 ERS21098705 ERA30879582 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19111 19111 ERR13822114 ERX13224866 ERS21098698 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR3 S3 R1 001.fastq.gz SAMEA116100618 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 PR3|collected by:Jaakko Lehtimaki|collection date:2021 12 07|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 PR3|scientific name:Danio rerio|tissue type:retina                 Raw reads: 38 PR3 webin reads 38 PR3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR3_S3_R1_001.fastq.gz fastq 3894010106.0 39196855.0 webin reads 38 PR3 0:99.34 A:1093221995;C:818047738;G:843661747;T:1138957138;N:121488 99       1093221995 818047738 843661747 1138957138 121488 ERX13224866 ERS21098698 ERA30879273 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Pharyngula Embryo Eye Sensory System
19112 19112 ERR13822135 ERX13224887 ERS21098701 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC2 S6 R1 001.fastq.gz 38 AC2   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 AC2 webin reads 38 AC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC2_S6_R1_001.fastq.gz fastq 3913343007.0 39682834.0 webin reads 38 AC2 0:98.62 A:1089960083;C:827936673;G:855955684;T:1139372607;N:117960 98       1089960083 827936673 855955684 1139372607 117960 ERX13224887 ERS21098701 ERA30879382 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19113 19113 ERR13835032 ERX13237798 ERS21098730 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC4 S35 R1 001.fastq.gz 58 HC4   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 HC4 webin reads 58 HC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC4_S35_R1_001.fastq.gz fastq 4418556015.0 44331835.0 webin reads 58 HC4 0:99.67 A:1255080581;C:916490847;G:946212615;T:1300735054;N:36918 99       1255080581 916490847 946212615 1300735054 36918 ERX13237798 ERS21098730 ERA30883773 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19114 19114 ERR13828829 ERX13231595 ERS21098711 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC1 S16 R1 001.fastq.gz 48 AC1   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC1 webin reads 48 AC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC1_S16_R1_001.fastq.gz fastq 3933669121.0 39695406.0 webin reads 48 AC1 0:99.10 A:1105258159;C:824538054;G:854253688;T:1149538152;N:81068 99       1105258159 824538054 854253688 1149538152 81068 ERX13231595 ERS21098711 ERA30883326 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19115 19115 ERR13822099 ERX13224851 ERS21098696 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR1 S1 R1 001.fastq.gz 38 PR1   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 PR1 webin reads 38 PR1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR1_S1_R1_001.fastq.gz fastq 4256158288.0 42658127.0 webin reads 38 PR1 0:99.77 A:1193880575;C:899261652;G:926114030;T:1236860186;N:41845 99       1193880575 899261652 926114030 1236860186 41845 ERX13224851 ERS21098696 ERA30879152 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19116 19116 ERR13822119 ERX13224871 ERS21098699 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR4 S4 R1 001.fastq.gz 38 PR4   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 PR4 webin reads 38 PR4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR4_S4_R1_001.fastq.gz fastq 3726308046.0 37591038.0 webin reads 38 PR4 0:99.13 A:1043231302;C:789255840;G:812957881;T:1080801843;N:61180 99       1043231302 789255840 812957881 1080801843 61180 ERX13224871 ERS21098699 ERA30879302 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19117 19117 ERR13835025 ERX13237791 ERS21098729 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC3 S34 R1 001.fastq.gz 58 HC3   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 HC3 webin reads 58 HC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC3_S34_R1_001.fastq.gz fastq 3523899212.0 35292613.0 webin reads 58 HC3 0:99.85 A:1012516999;C:723225071;G:745152410;T:1042976092;N:28640 99       1012516999 723225071 745152410 1042976092 28640 ERX13237791 ERS21098729 ERA30883757 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19118 19118 ERR13835014 ERX13237780 ERS21098727 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC1 S32 R1 001.fastq.gz 58 HC1   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 HC1 webin reads 58 HC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC1_S32_R1_001.fastq.gz fastq 3436493821.0 34597887.0 webin reads 58 HC1 0:99.33 A:980894291;C:707196785;G:729948858;T:1018400124;N:53763 99       980894291 707196785 729948858 1018400124 53763 ERX13237780 ERS21098727 ERA30883731 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19119 19119 ERR13834987 ERX13237753 ERS21098722 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR4 S27 R1 001.fastq.gz 58 PR4   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR4 webin reads 58 PR4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR4_S27_R1_001.fastq.gz fastq 3069040814.0 30923422.0 webin reads 58 PR4 0:99.25 A:875776938;C:633951750;G:653308475;T:905949639;N:54012 99       875776938 633951750 653308475 905949639 54012 ERX13237753 ERS21098722 ERA30883641 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19120 19120 ERR13822788 ERX13225540 ERS21098707 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC4 S12 R1 001.fastq.gz 38 HC4   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 HC4 webin reads 38 HC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC4_S12_R1_001.fastq.gz fastq 3353994440.0 33744828.0 webin reads 38 HC4 0:99.39 A:939537209;C:709367668;G:731849729;T:973193819;N:46015 99       939537209 709367668 731849729 973193819 46015 ERX13225540 ERS21098707 ERA30879650 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19121 19121 ERR13834997 ERX13237763 ERS21098724 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC2 S29 R1 001.fastq.gz 58 AC2   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 AC2 webin reads 58 AC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC2_S29_R1_001.fastq.gz fastq 3872162091.0 38898173.0 webin reads 58 AC2 0:99.55 A:1111663794;C:793747086;G:817730996;T:1148980297;N:39918 99       1111663794 793747086 817730996 1148980297 39918 ERX13237763 ERS21098724 ERA30883678 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
25107 25107 SRR25605432 SRX21332628 SRS18578260 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep3 GSM7702835   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702835 GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq GSM7702835 r1 GSM7702835 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_GFP_pos_S4_L001_R2_001.fastq.gz 2707_GFP_pos_S4_L001_R1_001.fastq.gz 2707_GFP_pos_S4_L001_I2_001.fastq.gz 2707_GFP_pos_S4_L001_I1_001.fastq.gz fastq fastq fastq fastq 21603309774.0 156545723.0 GSM7702835 r1 0:10 1:10 2:28 3:90 A:3960451458;C:3105338977;G:3480072824;T:3541218595;N:2033216 10 10 28 90 3960451458 3105338977 3480072824 3541218595 2033216 SRX21332628 SRS18578260 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94286   0.14175   0.78395   0.51541   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25108 25108 SRR25605433 SRX21332628 SRS18578260 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep3 GSM7702835   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702835 GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq GSM7702835 r1 GSM7702835 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_GFP_pos_S4_L002_I1_001.fastq.gz 2707_GFP_pos_S4_L002_I2_001.fastq.gz 2707_GFP_pos_S4_L002_R1_001.fastq.gz 2707_GFP_pos_S4_L002_R2_001.fastq.gz fastq fastq fastq fastq 22413465270.0 162416415.0 GSM7702835 r2 0:10 1:10 2:28 3:90 A:4104405257;C:3220235633;G:3625448968;T:3667329471;N:58021 10 10 28 90 4104405257 3220235633 3625448968 3667329471 58021 SRX21332628 SRS18578260 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94239   0.14234   0.78338   0.50616   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25109 25109 SRR25822232 SRX21332628 SRS18578260 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep3 GSM7702835   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702835 GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq GSM7702835 r1 GSM7702835 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_GFP_pos_S4_L001_R2_002.fastq.gz 2707_GFP_pos_S4_L001_R1_002.fastq.gz 2707_GFP_pos_S4_L001_I2_002.fastq.gz 2707_GFP_pos_S4_L001_I1_002.fastq.gz fastq fastq fastq fastq 21424338264.0 155248828.0 GSM7702835 r3 0:10 1:10 2:28 3:90 A:3928077020;C:3077672525;G:3451667186;T:3513734857;N:1242932 10 10 28 90 3928077020 3077672525 3451667186 3513734857 1242932 SRX21332628 SRS18578260 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.9433   0.14242   0.78328   0.52384   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25110 25110 SRR25822233 SRX21332628 SRS18578260 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep3 GSM7702835   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702835 GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq GSM7702835 r1 GSM7702835 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_GFP_pos_S4_L002_I1_002.fastq.gz 2707_GFP_pos_S4_L002_I2_002.fastq.gz 2707_GFP_pos_S4_L002_R1_002.fastq.gz 2707_GFP_pos_S4_L002_R2_002.fastq.gz fastq fastq fastq fastq 22542479952.0 163351304.0 GSM7702835 r4 0:10 1:10 2:28 3:90 A:4130174287;C:3235362228;G:3643457599;T:3691295761;N:1327485 10 10 28 90 4130174287 3235362228 3643457599 3691295761 1327485 SRX21332628 SRS18578260 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94183   0.14124   0.78301   0.50517   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25111 25111 SRR25605434 SRX21332627 SRS18578259 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep3 GSM7702834   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702834 GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq GSM7702834 r1 GSM7702834 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_pos_Mcherry_S3_L001_R2_001.fastq.gz 2707_pos_Mcherry_S3_L001_R1_001.fastq.gz 2707_pos_Mcherry_S3_L001_I2_001.fastq.gz 2707_pos_Mcherry_S3_L001_I1_001.fastq.gz fastq fastq fastq fastq 20161522758.0 146097991.0 GSM7702834 r1 0:10 1:10 2:28 3:90 A:3649819934;C:2958286158;G:3267504300;T:3271384686;N:1824112 10 10 28 90 3649819934 2958286158 3267504300 3271384686 1824112 SRX21332627 SRS18578259 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94851   0.1483   0.80012   0.52549   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25112 25112 SRR25605435 SRX21332627 SRS18578259 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep3 GSM7702834   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702834 GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq GSM7702834 r1 GSM7702834 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_pos_Mcherry_S3_L002_I1_001.fastq.gz 2707_pos_Mcherry_S3_L002_I2_001.fastq.gz 2707_pos_Mcherry_S3_L002_R1_001.fastq.gz 2707_pos_Mcherry_S3_L002_R2_001.fastq.gz fastq fastq fastq fastq 20708273928.0 150059956.0 GSM7702834 r2 0:10 1:10 2:28 3:90 A:3746088654;C:3037032642;G:3368938151;T:3353289242;N:47351 10 10 28 90 3746088654 3037032642 3368938151 3353289242 47351 SRX21332627 SRS18578259 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94778   0.14581   0.80028   0.52885   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25113 25113 SRR25822230 SRX21332627 SRS18578259 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep3 GSM7702834   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702834 GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq GSM7702834 r1 GSM7702834 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_pos_Mcherry_S3_L001_I1_002.fastq.gz 2707_pos_Mcherry_S3_L001_I2_002.fastq.gz 2707_pos_Mcherry_S3_L001_R1_002.fastq.gz 2707_pos_Mcherry_S3_L001_R2_002.fastq.gz fastq fastq fastq fastq 20078121078.0 145493631.0 GSM7702834 r3 0:10 1:10 2:28 3:90 A:3634984131;C:2943891505;G:3255149272;T:3259243920;N:1157962 10 10 28 90 3634984131 2943891505 3255149272 3259243920 1157962 SRX21332627 SRS18578259 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94884   0.14622   0.80099   0.52572   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25114 25114 SRR25822231 SRX21332627 SRS18578259 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep3 GSM7702834   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702834 GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq GSM7702834 r1 GSM7702834 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_pos_Mcherry_S3_L002_I1_002.fastq.gz 2707_pos_Mcherry_S3_L002_I2_002.fastq.gz 2707_pos_Mcherry_S3_L002_R1_002.fastq.gz 2707_pos_Mcherry_S3_L002_R2_002.fastq.gz fastq fastq fastq fastq 20884392978.0 151336181.0 GSM7702834 r4 0:10 1:10 2:28 3:90 A:3779370721;C:3059502508;G:3396295214;T:3383865877;N:1221970 10 10 28 90 3779370721 3059502508 3396295214 3383865877 1221970 SRX21332627 SRS18578259 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94896   0.14559   0.8002   0.51418   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25115 25115 SRR25605436 SRX21332626 SRS18578258 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep2 GSM7702833   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702833 GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq GSM7702833 r1 GSM7702833 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py|options: allowEarlyFileEnd 1907_GFP_pos_S2_L001_I1_001.fastq.gz 1907_GFP_pos_S2_L001_I2_001.fastq.gz 1907_GFP_pos_S2_L001_R1_001.fastq.gz 1907_GFP_pos_S2_L001_R2_001.fastq.gz fastq fastq fastq fastq 22174775364.0 160686778.0 GSM7702833 r1 0:10 1:10 2:28 3:90 A:4207510387;C:3050740898;G:3362227609;T:3839333241;N:1997885 10 10 28 90 4207510387 3050740898 3362227609 3839333241 1997885 SRX21332626 SRS18578258 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.93287   0.11844   0.81087   0.55264   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25116 25116 SRR25605437 SRX21332626 SRS18578258 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep2 GSM7702833   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702833 GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq GSM7702833 r1 GSM7702833 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py|options: allowEarlyFileEnd 1907_GFP_pos_S2_L002_I1_001.fastq.gz 1907_GFP_pos_S2_L002_I2_001.fastq.gz 1907_GFP_pos_S2_L002_R1_001.fastq.gz 1907_GFP_pos_S2_L002_R2_001.fastq.gz fastq fastq fastq fastq 22047847518.0 159767011.0 GSM7702833 r2 0:10 1:10 2:28 3:90 A:4174013532;C:3033959926;G:3357962867;T:3813042664;N:52001 10 10 28 90 4174013532 3033959926 3357962867 3813042664 52001 SRX21332626 SRS18578258 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.93359   0.11585   0.81087   0.55705   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25117 25117 SRR25822228 SRX21332626 SRS18578258 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep2 GSM7702833   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702833 GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq GSM7702833 r1 GSM7702833 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_GFP_pos_S2_L001_I1_002.fastq.gz 1907_GFP_pos_S2_L001_I2_002.fastq.gz 1907_GFP_pos_S2_L001_R1_002.fastq.gz 1907_GFP_pos_S2_L001_R2_002.fastq.gz fastq fastq fastq fastq 22010894568.0 159499236.0 GSM7702833 r3 0:10 1:10 2:28 3:90 A:4176090595;C:3026940106;G:3336506731;T:3814128890;N:1264918 10 10 28 90 4176090595 3026940106 3336506731 3814128890 1264918 SRX21332626 SRS18578258 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.93457   0.11733   0.81032   0.55203   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25118 25118 SRR25822229 SRX21332626 SRS18578258 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep2 GSM7702833   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702833 GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq GSM7702833 r1 GSM7702833 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_GFP_pos_S2_L002_I1_002.fastq.gz 1907_GFP_pos_S2_L002_I2_002.fastq.gz 1907_GFP_pos_S2_L002_R1_002.fastq.gz 1907_GFP_pos_S2_L002_R2_002.fastq.gz fastq fastq fastq fastq 22227220746.0 161066817.0 GSM7702833 r4 0:10 1:10 2:28 3:90 A:4209198596;C:3055507768;G:3382717459;T:3847294849;N:1294858 10 10 28 90 4209198596 3055507768 3382717459 3847294849 1294858 SRX21332626 SRS18578258 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.93428   0.11629   0.81014   0.56014   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25119 25119 SRR25605438 SRX21332625 SRS18578257 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep2 GSM7702832   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702832 GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq GSM7702832 r1 GSM7702832 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_pos_pos_S1_L001_I1_001.fastq.gz 1907_pos_pos_S1_L001_I2_001.fastq.gz 1907_pos_pos_S1_L001_R1_001.fastq.gz 1907_pos_pos_S1_L001_R2_001.fastq.gz fastq fastq fastq fastq 25141955454.0 182188083.0 GSM7702832 r1 0:10 1:10 2:28 3:90 A:4942067104;C:3446689328;G:3778138998;T:4227670796;N:2361244 10 10 28 90 4942067104 3446689328 3778138998 4227670796 2361244 SRX21332625 SRS18578257 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.90803   0.11273   0.81872   0.54345   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25120 25120 SRR25605439 SRX21332625 SRS18578257 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep2 GSM7702832   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702832 GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq GSM7702832 r1 GSM7702832 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_pos_pos_S1_L002_R2_001.fastq.gz 1907_pos_pos_S1_L002_R1_001.fastq.gz 1907_pos_pos_S1_L002_I2_001.fastq.gz 1907_pos_pos_S1_L002_I1_001.fastq.gz fastq fastq fastq fastq 25433730786.0 184302397.0 GSM7702832 r2 0:10 1:10 2:28 3:90 A:4980326106;C:3488986366;G:3842594871;T:4275245265;N:63122 10 10 28 90 4980326106 3488986366 3842594871 4275245265 63122 SRX21332625 SRS18578257 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.91035   0.11175   0.82016   0.52814   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25121 25121 SRR25822226 SRX21332625 SRS18578257 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep2 GSM7702832   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702832 GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq GSM7702832 r1 GSM7702832 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_pos_pos_S1_L001_R2_002.fastq.gz 1907_pos_pos_S1_L001_R1_002.fastq.gz 1907_pos_pos_S1_L001_I2_002.fastq.gz 1907_pos_pos_S1_L001_I1_002.fastq.gz fastq fastq fastq fastq 24834656088.0 179961276.0 GSM7702832 r3 0:10 1:10 2:28 3:90 A:4878672093;C:3403443000;G:3732878174;T:4180051888;N:1469685 10 10 28 90 4878672093 3403443000 3732878174 4180051888 1469685 SRX21332625 SRS18578257 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.90776   0.11325   0.81852   0.54011   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25122 25122 SRR25822227 SRX21332625 SRS18578257 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep2 GSM7702832   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702832 GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq GSM7702832 r1 GSM7702832 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_pos_pos_S1_L002_I1_002.fastq.gz 1907_pos_pos_S1_L002_I2_002.fastq.gz 1907_pos_pos_S1_L002_R1_002.fastq.gz 1907_pos_pos_S1_L002_R2_002.fastq.gz fastq fastq fastq fastq 25609437216.0 185575632.0 GSM7702832 r4 0:10 1:10 2:28 3:90 A:5015380345;C:3509305882;G:3867598814;T:4308011415;N:1510424 10 10 28 90 5015380345 3509305882 3867598814 4308011415 1510424 SRX21332625 SRS18578257 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.90907   0.11192   0.81994   0.50902   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25123 25123 SRR25605440 SRX21332624 SRS18578256 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep1 GSM7702831   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep1 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702831 GSM7702831: gfp enriched rep1; Danio rerio; RNA Seq GSM7702831 r1 GSM7702831 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py gfp_nre_S1_L001_R2_001.fastq.gz gfp_nre_S1_L001_R1_001.fastq.gz gfp_nre_S1_L001_I2_001.fastq.gz gfp_nre_S1_L001_I1_001.fastq.gz fastq fastq fastq fastq 47873499684.0 346909418.0 GSM7702831 r1 0:10 1:10 2:28 3:90 A:8912593789;C:6786299583;G:7771099171;T:7737013838;N:14841239 10 10 28 90 8912593789 6786299583 7771099171 7737013838 14841239 SRX21332624 SRS18578256 SRA1690580 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.90717   0.15854   0.80501   0.50927   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25124 25124 SRR25605441 SRX21332624 SRS18578256 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep1 GSM7702831   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep1 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702831 GSM7702831: gfp enriched rep1; Danio rerio; RNA Seq GSM7702831 r1 GSM7702831 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py gfp_nre_S1_L002_I1_001.fastq.gz gfp_nre_S1_L002_I2_001.fastq.gz gfp_nre_S1_L002_R1_001.fastq.gz gfp_nre_S1_L002_R2_001.fastq.gz fastq fastq fastq fastq 48659347860.0 352603970.0 GSM7702831 r2 0:10 1:10 2:28 3:90 A:9056524463;C:6888387179;G:7922807308;T:7854042793;N:12595557 10 10 28 90 9056524463 6888387179 7922807308 7854042793 12595557 SRX21332624 SRS18578256 SRA1690580 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.90541   0.15686   0.80543   0.51051   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25125 25125 SRR25605442 SRX21332623 SRS18578255 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep1 GSM7702830   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep1 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702830 GSM7702830: mcherry enriched rep1; Danio rerio; RNA Seq GSM7702830 r1 GSM7702830 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py double_pos_S2_L001_R2_001.fastq.gz double_pos_S2_L001_R1_001.fastq.gz double_pos_S2_L001_I2_001.fastq.gz double_pos_S2_L001_I1_001.fastq.gz fastq fastq fastq fastq 41371188084.0 299791218.0 GSM7702830 r1 0:10 1:10 2:28 3:90 A:7690531012;C:5787287634;G:6514950407;T:6975618202;N:12822365 10 10 28 90 7690531012 5787287634 6514950407 6975618202 12822365 SRX21332623 SRS18578255 SRA1690580 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.93894   0.17677   0.79926   0.51122   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25126 25126 SRR25605443 SRX21332623 SRS18578255 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep1 GSM7702830   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep1 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702830 GSM7702830: mcherry enriched rep1; Danio rerio; RNA Seq GSM7702830 r1 GSM7702830 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py double_pos_S2_L002_I1_001.fastq.gz double_pos_S2_L002_I2_001.fastq.gz double_pos_S2_L002_R1_001.fastq.gz double_pos_S2_L002_R2_001.fastq.gz fastq fastq fastq fastq 42692812980.0 309368210.0 GSM7702830 r2 0:10 1:10 2:28 3:90 A:7933061913;C:5964617781;G:6744802923;T:7189579846;N:11076437 10 10 28 90 7933061913 5964617781 6744802923 7189579846 11076437 SRX21332623 SRS18578255 SRA1690580 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.93887   0.17578   0.79825   0.50169   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
30572 30572 SRR27848813 SRX23511754 SRS20362222 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 7 GSM8061015   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 7 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061015 GSM8061015: Wildtype 7; Danio rerio; RNA Seq GSM8061015 r1 GSM8061015 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT7_1.fq.gz WT7_2.fq.gz fastq fastq 16387213200.0 54624044.0 GSM8061015 r1 0:150 1:150 A:4787207224;C:3312386758;G:3384738324;T:4902574775;N:306119 150 150     4787207224 3312386758 3384738324 4902574775 306119 SRX23511754 SRS20362222 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.92431 0.91825 0.16903 0.16976 0.74067 0.75189 0.50167 0.50261 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30573 30573 SRR27848814 SRX23511753 SRS20362221 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 6 GSM8061014   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 6 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061014 GSM8061014: Wildtype 6; Danio rerio; RNA Seq GSM8061014 r1 GSM8061014 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT6_1.fq.gz WT6_2.fq.gz fastq fastq 19114278900.0 63714263.0 GSM8061014 r1 0:150 1:150 A:5885874877;C:3513555230;G:3610119151;T:6104379853;N:349789 150 150     5885874877 3513555230 3610119151 6104379853 349789 SRX23511753 SRS20362221 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.88104 0.87237 0.33066 0.33508 0.7357 0.7499 0.52706 0.51369 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30574 30574 SRR27848815 SRX23511752 SRS20362220 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 5 GSM8061013   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 5 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061013 GSM8061013: Wildtype 5; Danio rerio; RNA Seq GSM8061013 r1 GSM8061013 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT5_2.fq.gz WT5_1.fq.gz fastq fastq 16120305900.0 53734353.0 GSM8061013 r1 0:150 1:150 A:4774586081;C:3152393582;G:3245217813;T:4947808687;N:299737 150 150     4774586081 3152393582 3245217813 4947808687 299737 SRX23511752 SRS20362220 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.90351 0.89372 0.19598 0.19188 0.74468 0.76037 0.49643 0.5012 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30575 30575 SRR27848816 SRX23511751 SRS20362219 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 4 GSM8061012   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 4 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061012 GSM8061012: Wildtype 4; Danio rerio; RNA Seq GSM8061012 r1 GSM8061012 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT4_1.fq.gz WT4_2.fq.gz fastq fastq 15545813700.0 51819379.0 GSM8061012 r1 0:150 1:150 A:4735339999;C:2883223993;G:2979819364;T:4947148649;N:281695 150 150     4735339999 2883223993 2979819364 4947148649 281695 SRX23511751 SRS20362219 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.88431 0.87409 0.2472 0.24596 0.74675 0.76534 0.50472 0.51348 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30576 30576 SRR27848817 SRX23511750 SRS20362218 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 3 GSM8061011   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 3 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061011 GSM8061011: Wildtype 3; Danio rerio; RNA Seq GSM8061011 r1 GSM8061011 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT3_1.fq.gz WT3_2.fq.gz fastq fastq 17883593700.0 59611979.0 GSM8061011 r1 0:150 1:150 A:5305029339;C:3503937995;G:3594774195;T:5479523425;N:328746 150 150     5305029339 3503937995 3594774195 5479523425 328746 SRX23511750 SRS20362218 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.90376 0.89786 0.22127 0.22019 0.72941 0.74257 0.49283 0.4977 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30577 30577 SRR27848818 SRX23511749 SRS20362217 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 2 GSM8061010   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 2 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061010 GSM8061010: Wildtype 2; Danio rerio; RNA Seq GSM8061010 r1 GSM8061010 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT2_1.fq.gz WT2_2.fq.gz fastq fastq 15921002400.0 53070008.0 GSM8061010 r1 0:150 1:150 A:4801739158;C:2898179014;G:3037454009;T:5183338180;N:292039 150 150     4801739158 2898179014 3037454009 5183338180 292039 SRX23511749 SRS20362217 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.88935 0.87616 0.22376 0.2085 0.75367 0.78123 0.53443 0.51122 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30578 30578 SRR27848819 SRX23511748 SRS20362216 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Wildtype 1 GSM8061009   source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing Wildtype 1 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Wildtype GSM8061009 GSM8061009: Wildtype 1; Danio rerio; RNA Seq GSM8061009 r1 GSM8061009 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py WT1_1.fq.gz WT1_2.fq.gz fastq fastq 15664926900.0 52216423.0 GSM8061009 r1 0:150 1:150 A:4654413024;C:3082161368;G:3150203371;T:4777859952;N:289185 150 150     4654413024 3082161368 3150203371 4777859952 289185 SRX23511748 SRS20362216 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.9012 0.89646 0.22096 0.21863 0.73507 0.7475 0.4816 0.4726 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30579 30579 SRR27848820 SRX23511747 SRS20362215 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 7 GSM8061008   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 7 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061008 GSM8061008: Choroideremia 7; Danio rerio; RNA Seq GSM8061008 r1 GSM8061008 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM7_2.fq.gz CHM7_1.fq.gz fastq fastq 16991281200.0 56637604.0 GSM8061008 r1 0:150 1:150 A:4896856485;C:3497447652;G:3598783228;T:4998138764;N:55071 150 150     4896856485 3497447652 3598783228 4998138764 55071 SRX23511747 SRS20362215 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.926 0.92518 0.16779 0.16551 0.72393 0.73513 0.51723 0.51214 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30580 30580 SRR27848821 SRX23511746 SRS20362214 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 6 GSM8061007   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 6 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061007 GSM8061007: Choroideremia 6; Danio rerio; RNA Seq GSM8061007 r1 GSM8061007 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM6_1.fq.gz CHM6_2.fq.gz fastq fastq 18881901900.0 62939673.0 GSM8061007 r1 0:150 1:150 A:5796692721;C:3348140904;G:3547934333;T:6189072751;N:61191 150 150     5796692721 3348140904 3547934333 6189072751 61191 SRX23511746 SRS20362214 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.86869 0.86484 0.26053 0.2569 0.75057 0.77705 0.66121 0.65975 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30581 30581 SRR27848822 SRX23511745 SRS20362213 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 5 GSM8061006   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 5 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061006 GSM8061006: Choroideremia 5; Danio rerio; RNA Seq GSM8061006 r1 GSM8061006 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM5_2.fq.gz CHM5_1.fq.gz fastq fastq 17802156900.0 59340523.0 GSM8061006 r1 0:150 1:150 A:5198674613;C:3599354426;G:3698229931;T:5305840019;N:57911 150 150     5198674613 3599354426 3698229931 5305840019 57911 SRX23511745 SRS20362213 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.9109 0.91251 0.18901 0.18793 0.72354 0.73456 0.51839 0.52348 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30582 30582 SRR27848823 SRX23511744 SRS20362212 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 4 GSM8061005   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 4 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061005 GSM8061005: Choroideremia 4; Danio rerio; RNA Seq GSM8061005 r1 GSM8061005 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM4_2.fq.gz CHM4_1.fq.gz fastq fastq 15944831400.0 53149438.0 GSM8061005 r1 0:150 1:150 A:4833633886;C:2870981386;G:3055307522;T:5184819306;N:89300 150 150     4833633886 2870981386 3055307522 5184819306 89300 SRX23511744 SRS20362212 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.88929 0.88364 0.25277 0.24996 0.75317 0.77826 0.64914 0.65907 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30583 30583 SRR27848824 SRX23511743 SRS20362211 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 3 GSM8061004   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 3 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061004 GSM8061004: Choroideremia 3; Danio rerio; RNA Seq GSM8061004 r1 GSM8061004 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM3_1.fq.gz CHM3_2.fq.gz fastq fastq 16028608800.0 53428696.0 GSM8061004 r1 0:150 1:150 A:4842495383;C:2966448486;G:3084331699;T:5135033798;N:299434 150 150     4842495383 2966448486 3084331699 5135033798 299434 SRX23511743 SRS20362211 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.89747 0.88445 0.23706 0.23597 0.72904 0.75187 0.5514 0.45471 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30584 30584 SRR27848825 SRX23511742 SRS20362210 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 2 GSM8061003   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 2 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061003 GSM8061003: Choroideremia 2; Danio rerio; RNA Seq GSM8061003 r1 GSM8061003 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM2_1.fq.gz CHM2_2.fq.gz fastq fastq 14968884300.0 49896281.0 GSM8061003 r1 0:150 1:150 A:4575866591;C:2606132581;G:2819446784;T:4967389772;N:48572 150 150     4575866591 2606132581 2819446784 4967389772 48572 SRX23511742 SRS20362210 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.88022 0.87326 0.29312 0.29812 0.7335 0.76228 0.5854 0.57614 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
30585 30585 SRR27848826 SRX23511741 SRS20362209 SRP487850 PRJNA1072679 Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish GSE254948 Transcriptome Analysis Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.       Choroideremia 1 GSM8061002   source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing Choroideremia 1 Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples. Retina   Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   tissue:Retina|genotype:Choroideremia GSM8061002 GSM8061002: Choroideremia 1; Danio rerio; RNA Seq GSM8061002 r1 GSM8061002 1 Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP487850   loader:fastq load.py CHM1_2.fq.gz CHM1_1.fq.gz fastq fastq 15862639500.0 52875465.0 GSM8061002 r1 0:150 1:150 A:4812544148;C:2881706406;G:3014671171;T:5153419977;N:297798 150 150     4812544148 2881706406 3014671171 5153419977 297798 SRX23511741 SRS20362209 SRA1796957 The Francis Crick Institute The Francis Crick Institute 2 0.89157 0.87804 0.24616 0.24284 0.73884 0.76232 0.58251 0.58918 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United Kingdom 2024-02-02 Undetermined Embryo Eye Sensory System
36381 36381 SRR514031 SRX155011 SRS346297 SRP013815 PRJNA168635 Id2a knockdown in zebrafish retina GSE38786 Transcriptome Analysis During vertebrate retinogenesis the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways. Moreover there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non autonomous role for the intrinsic HLH factor Id2a in regulating retinoblast proliferation and differentiation with Id2a deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia. Here we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis. Id2a deficient retinae possess elevated levels of Notch pathway component gene expression while retinae overexpressing id2a possess reduced expression of Notch pathway component genes. Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a deficient retinae. In addition to regulating Notch pathway activity through an RNA Seq and differential gene expression analysis of Id2a deficient retinae we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a. These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis. Overall design: Two biological replicates for both Id2aMM and Id2aMO samples   pubmed:22981606   Zebrafish retina with id2a morpholino treatment replicate 2 GSM949497   source name:Zebrafish retina with id2a morpholino treatment replicate 2|tissue:retina|genotype/variation:id2a knockdown Zebrafish retina with id2a morpholino treatment replicate 2 Filter out all reads with no call ‘N’ and low complexity reads without xxx 4 bases. Take reads that both paired end reads are passed the above condition. Map to EnsEMBL cDNA sequence then calculate RPK100M read counts per kb per 100 million of reads Summarize mapped reads per each cDNA. Determine differentially expressed genes with DESeq Genome build: EnsEMBL version 66 cDNA sequences Supplementary files format and content: tab delimited text files include RPKM values for each Sample DESeq output for differentially expressed genes. Zebrafish retina with id2a morpholino treatment replicate 2   Total RNA was isolated from dissected retinae at 48 hpf using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 microgram of total retinal RNA per condition to generate cDNA libraries by poly A selection.   tissue:retina|genotype/variation:id2a knockdown GSM949497 GSM949497: Zebrafish retina with id2a morpholino treatment replicate 2; Danio rerio; RNA Seq GSM949497 2 GSM949497: Zebrafish retina with id2a morpholino treatment replicate 2 1   GEO Accession:GSM949497 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013815     Uribe201204_id2aKD2.untie_2.fastq.gz fastq 12244707932.0 60617366.0 GSM949497 r1 0:101 1:101 A:3345422426;C:2833723441;G:2860980232;T:3204581833;N:0 101 101     3345422426 2833723441 2860980232 3204581833 0 SRX155011 SRS346297 SRA054377 GEO Department of Biomedical Engineering, Ulsan National Institute of Science and Technology 2 0.8674 0.87016 0.09985 0.10059 0.75442 0.75187 0.47467 0.47364 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   South Korea 2012-06-18 Hatching Embryo Eye Sensory System
36382 36382 SRR514030 SRX155010 SRS346296 SRP013815 PRJNA168635 Id2a knockdown in zebrafish retina GSE38786 Transcriptome Analysis During vertebrate retinogenesis the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways. Moreover there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non autonomous role for the intrinsic HLH factor Id2a in regulating retinoblast proliferation and differentiation with Id2a deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia. Here we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis. Id2a deficient retinae possess elevated levels of Notch pathway component gene expression while retinae overexpressing id2a possess reduced expression of Notch pathway component genes. Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a deficient retinae. In addition to regulating Notch pathway activity through an RNA Seq and differential gene expression analysis of Id2a deficient retinae we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a. These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis. Overall design: Two biological replicates for both Id2aMM and Id2aMO samples   pubmed:22981606   Zebrafish retina with id2a morpholino treatment replicate 1 GSM949496   source name:Zebrafish retina with id2a morpholino treatment replicate 1|tissue:retina|genotype/variation:id2a knockdown Zebrafish retina with id2a morpholino treatment replicate 1 Filter out all reads with no call ‘N’ and low complexity reads without xxx 4 bases. Take reads that both paired end reads are passed the above condition. Map to EnsEMBL cDNA sequence then calculate RPK100M read counts per kb per 100 million of reads Summarize mapped reads per each cDNA. Determine differentially expressed genes with DESeq Genome build: EnsEMBL version 66 cDNA sequences Supplementary files format and content: tab delimited text files include RPKM values for each Sample DESeq output for differentially expressed genes. Zebrafish retina with id2a morpholino treatment replicate 1   Total RNA was isolated from dissected retinae at 48 hpf using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 microgram of total retinal RNA per condition to generate cDNA libraries by poly A selection.   tissue:retina|genotype/variation:id2a knockdown GSM949496 GSM949496: Zebrafish retina with id2a morpholino treatment replicate 1; Danio rerio; RNA Seq GSM949496 2 GSM949496: Zebrafish retina with id2a morpholino treatment replicate 1 1   GEO Accession:GSM949496 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013815     Uribe201204_id2aKD1.untie_1.fastq.gz fastq 9529605934.0 47176267.0 GSM949496 r1 0:101 1:101 A:2628394362;C:2208991321;G:2220322548;T:2471897703;N:0 101 101     2628394362 2208991321 2220322548 2471897703 0 SRX155010 SRS346296 SRA054377 GEO Department of Biomedical Engineering, Ulsan National Institute of Science and Technology 2 0.83877 0.84035 0.0922 0.09318 0.76092 0.75795 0.48081 0.49029 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   South Korea 2012-06-18 Hatching Embryo Eye Sensory System
36383 36383 SRR514029 SRX155009 SRS346295 SRP013815 PRJNA168635 Id2a knockdown in zebrafish retina GSE38786 Transcriptome Analysis During vertebrate retinogenesis the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways. Moreover there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non autonomous role for the intrinsic HLH factor Id2a in regulating retinoblast proliferation and differentiation with Id2a deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia. Here we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis. Id2a deficient retinae possess elevated levels of Notch pathway component gene expression while retinae overexpressing id2a possess reduced expression of Notch pathway component genes. Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a deficient retinae. In addition to regulating Notch pathway activity through an RNA Seq and differential gene expression analysis of Id2a deficient retinae we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a. These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis. Overall design: Two biological replicates for both Id2aMM and Id2aMO samples   pubmed:22981606   Zebrafish retina with Id2aMM morpholino treatment replicate 2 GSM949495   source name:Zebrafish retina with Id2aMM morpholino treatment replicate 2|tissue:retina|genotype/variation:control Zebrafish retina with Id2aMM morpholino treatment replicate 2 Filter out all reads with no call ‘N’ and low complexity reads without xxx 4 bases. Take reads that both paired end reads are passed the above condition. Map to EnsEMBL cDNA sequence then calculate RPK100M read counts per kb per 100 million of reads Summarize mapped reads per each cDNA. Determine differentially expressed genes with DESeq Genome build: EnsEMBL version 66 cDNA sequences Supplementary files format and content: tab delimited text files include RPKM values for each Sample DESeq output for differentially expressed genes. Zebrafish retina with Id2aMM morpholino treatment replicate 2   Total RNA was isolated from dissected retinae at 48 hpf using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 microgram of total retinal RNA per condition to generate cDNA libraries by poly A selection.   tissue:retina|genotype/variation:control GSM949495 GSM949495: Zebrafish retina with Id2aMM morpholino treatment replicate 2; Danio rerio; RNA Seq GSM949495 2 GSM949495: Zebrafish retina with Id2aMM morpholino treatment replicate 2 1   GEO Accession:GSM949495 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013815     Uribe201204_ctrl2.untie_2.fastq.gz fastq 11102513678.0 54962939.0 GSM949495 r1 0:101 1:101 A:3114223438;C:2460129982;G:2471805247;T:3056355011;N:0 101 101     3114223438 2460129982 2471805247 3056355011 0 SRX155009 SRS346295 SRA054377 GEO Department of Biomedical Engineering, Ulsan National Institute of Science and Technology 2 0.86928 0.87394 0.14668 0.14966 0.73462 0.73428 0.47462 0.47615 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   South Korea 2012-06-18 Hatching Embryo Eye Sensory System
36384 36384 SRR514028 SRX155008 SRS346294 SRP013815 PRJNA168635 Id2a knockdown in zebrafish retina GSE38786 Transcriptome Analysis During vertebrate retinogenesis the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways. Moreover there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non autonomous role for the intrinsic HLH factor Id2a in regulating retinoblast proliferation and differentiation with Id2a deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia. Here we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis. Id2a deficient retinae possess elevated levels of Notch pathway component gene expression while retinae overexpressing id2a possess reduced expression of Notch pathway component genes. Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a deficient retinae. In addition to regulating Notch pathway activity through an RNA Seq and differential gene expression analysis of Id2a deficient retinae we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a. These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis. Overall design: Two biological replicates for both Id2aMM and Id2aMO samples   pubmed:22981606   Zebrafish retina with Id2aMM morpholino treatment replicate 1 GSM949494   source name:Zebrafish retina with Id2aMM morpholino treatment replicate 1|tissue:retina|genotype/variation:control Zebrafish retina with Id2aMM morpholino treatment replicate 1 Filter out all reads with no call ‘N’ and low complexity reads without xxx 4 bases. Take reads that both paired end reads are passed the above condition. Map to EnsEMBL cDNA sequence then calculate RPK100M read counts per kb per 100 million of reads Summarize mapped reads per each cDNA. Determine differentially expressed genes with DESeq Genome build: EnsEMBL version 66 cDNA sequences Supplementary files format and content: tab delimited text files include RPKM values for each Sample DESeq output for differentially expressed genes. Zebrafish retina with Id2aMM morpholino treatment replicate 1   Total RNA was isolated from dissected retinae at 48 hpf using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 microgram of total retinal RNA per condition to generate cDNA libraries by poly A selection.   tissue:retina|genotype/variation:control GSM949494 GSM949494: Zebrafish retina with Id2aMM morpholino treatment replicate 1; Danio rerio; RNA Seq GSM949494 2 GSM949494: Zebrafish retina with Id2aMM morpholino treatment replicate 1 1   GEO Accession:GSM949494 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013815     Uribe201204_ctrl1.untie_1.fastq.gz fastq 9965568192.0 49334496.0 GSM949494 r1 0:101 1:101 A:2748582966;C:2261528563;G:2269950332;T:2685506331;N:0 101 101     2748582966 2261528563 2269950332 2685506331 0 SRX155008 SRS346294 SRA054377 GEO Department of Biomedical Engineering, Ulsan National Institute of Science and Technology 2 0.86051 0.86328 0.11721 0.11892 0.74184 0.74075 0.47603 0.47166 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   South Korea 2012-06-18 Hatching Embryo Eye Sensory System
37994 37994 SRR1265763 SRX529157 SRS598854 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Eye Replicate 3 sRNAseq GSM1376646   source name:Eye|tissue:Eye|genetic background:Wild type Singapore strain Eye Replicate 3 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Eye N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. tissue:Eye|genetic background:Wild type Singapore strain GSM1376646 GSM1376646: Eye Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376646   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376646 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZE014_GCCAAT_L005_R1.fastq.gz fastq 299134784.0 3935984.0 GSM1376646 r1 0:76 A:62089027;C:82689882;G:78294122;T:76032871;N:28882 76       62089027 82689882 78294122 76032871 28882 SRX529157 SRS598854 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00078   8e-05   0.99892   0.66406   76   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Eye Sensory System
37995 37995 SRR1265762 SRX529156 SRS598853 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Eye Replicate 2 sRNAseq GSM1376645   source name:Eye|tissue:Eye|genetic background:Wild type Singapore strain Eye Replicate 2 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Eye N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. tissue:Eye|genetic background:Wild type Singapore strain GSM1376645 GSM1376645: Eye Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376645   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376645 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZE013_ACAGTG_L005_R1.fastq.gz fastq 622465080.0 8190330.0 GSM1376645 r1 0:76 A:127621827;C:166524813;G:172833628;T:155425094;N:59718 76       127621827 166524813 172833628 155425094 59718 SRX529156 SRS598853 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00132   7e-05   0.99886   0.66956   76   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Eye Sensory System
37996 37996 SRR1265761 SRX529155 SRS598852 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Eye Replicate 1 sRNAseq GSM1376644   source name:Eye|tissue:Eye|genetic background:Wild type Singapore strain Eye Replicate 1 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Eye N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. tissue:Eye|genetic background:Wild type Singapore strain GSM1376644 GSM1376644: Eye Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376644   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376644 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZE008_TGACCA_L005_R1.fastq.gz fastq 906617148.0 11929173.0 GSM1376644 r1 0:76 A:188700519;C:246755919;G:238402849;T:232669963;N:87898 76       188700519 246755919 238402849 232669963 87898 SRX529155 SRS598852 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00073   4e-05   0.9991   0.61788   76   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Eye Sensory System

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