{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"10x\" and tissue_curation = \"Eye\"", "rows": [[34465, "SRR31769117", "SRX27130830", "SRS23587817", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells day 7 uninjured fish set #3", "GSM8691398", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells day 7 uninjured fish set #3", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7", "GSM8691398", "GSM8691398: adult zebrafish retinal ganglion cells day 7 uninjured fish set #3; Danio rerio; RNA Seq", "GSM8691398 r1", "GSM8691398", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Uninjured-7DPI-3_GRO2357A6_S5_L001_R1_001.fastq.gz Uninjured-7DPI-3_GRO2357A6_S5_L001_R2_001.fastq.gz", "fastq fastq", 63524967830.0, 538347185.0, "GSM8691398 r1", "0:28 1:90", "A:18434935191;C:13740021920;G:14509703351;T:16838781338;N:1526030", 28, 90, null, null, 18434935191, 13740021920, 14509703351, 16838781338, 1526030, "SRX27130830", "SRS23587817", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34466, "SRR31769118", "SRX27130829", "SRS23587816", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells day 7 uninjured fish set #2", "GSM8691397", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells day 7 uninjured fish set #2", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7", "GSM8691397", "GSM8691397: adult zebrafish retinal ganglion cells day 7 uninjured fish set #2; Danio rerio; RNA Seq", "GSM8691397 r1", "GSM8691397", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Uninjured-7DPI-2_GRO2559A7_S11_L001_R1_001.fastq.gz Uninjured-7DPI-2_GRO2559A7_S11_L001_R2_001.fastq.gz", "fastq fastq", 117155938094.0, 992846933.0, "GSM8691397 r1", "0:28 1:90", "A:33056566549;C:26122865037;G:28068647978;T:29904980565;N:2877965", 28, 90, null, null, 33056566549, 26122865037, 28068647978, 29904980565, 2877965, "SRX27130829", "SRS23587816", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34467, "SRR31769119", "SRX27130828", "SRS23587815", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells day 7 uninjured fish set #1", "GSM8691396", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells day 7 uninjured fish set #1", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7", "GSM8691396", "GSM8691396: adult zebrafish retinal ganglion cells day 7 uninjured fish set #1; Danio rerio; RNA Seq", "GSM8691396 r1", "GSM8691396", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Uninjured-7DPI-1_GRO2559A5_S3_L001_R1_001.fastq.gz Uninjured-7DPI-1_GRO2559A5_S3_L001_R2_001.fastq.gz", "fastq fastq", 88479846662.0, 749829209.0, "GSM8691396 r1", "0:28 1:90", "A:24973204142;C:19680603454;G:21127682533;T:22696187157;N:2169376", 28, 90, null, null, 24973204142, 19680603454, 21127682533, 22696187157, 2169376, "SRX27130828", "SRS23587815", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34468, "SRR31769120", "SRX27130827", "SRS23587814", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells 7 xxx post injury fish set #3", "GSM8691395", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells 7 xxx post injury fish set #3", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury", "GSM8691395", "GSM8691395: adult zebrafish retinal ganglion cells 7 xxx post injury fish set #3; Danio rerio; RNA Seq", "GSM8691395 r1", "GSM8691395", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Injured-7DPI-3_GRO2357A5_S9_L001_R1_001.fastq.gz Injured-7DPI-3_GRO2357A5_S9_L001_R2_001.fastq.gz", "fastq fastq", 52866571338.0, 448021791.0, "GSM8691395 r1", "0:28 1:90", "A:15008347140;C:11559305260;G:12319521011;T:13978097023;N:1300904", 28, 90, null, null, 15008347140, 11559305260, 12319521011, 13978097023, 1300904, "SRX27130827", "SRS23587814", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34469, "SRR31769121", "SRX27130826", "SRS23587813", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells 7 xxx post injury fish set #2", "GSM8691394", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells 7 xxx post injury fish set #2", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury", "GSM8691394", "GSM8691394: adult zebrafish retinal ganglion cells 7 xxx post injury fish set #2; Danio rerio; RNA Seq", "GSM8691394 r1", "GSM8691394", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Injured-7DPI-2_GRO2559A8_S13_L001_R1_001.fastq.gz Injured-7DPI-2_GRO2559A8_S13_L001_R2_001.fastq.gz", "fastq fastq", 122844941704.0, 1041058828.0, "GSM8691394 r1", "0:28 1:90", "A:34628566594;C:27526793155;G:30025691872;T:30660901278;N:2988805", 28, 90, null, null, 34628566594, 27526793155, 30025691872, 30660901278, 2988805, "SRX27130826", "SRS23587813", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34470, "SRR31769122", "SRX27130825", "SRS23587812", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells 7 xxx post injury fish set #1", "GSM8691393", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells 7 xxx post injury fish set #1", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury", "GSM8691393", "GSM8691393: adult zebrafish retinal ganglion cells 7 xxx post injury fish set #1; Danio rerio; RNA Seq", "GSM8691393 r1", "GSM8691393", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Injured-7DPI-1_GRO2559A6_S7_L001_R1_001.fastq.gz Injured-7DPI-1_GRO2559A6_S7_L001_R2_001.fastq.gz", "fastq fastq", 120896581754.0, 1024547303.0, "GSM8691393 r1", "0:28 1:90", "A:33711894389;C:26892614943;G:28832438626;T:31456652089;N:2981707", 28, 90, null, null, 33711894389, 26892614943, 28832438626, 31456652089, 2981707, "SRX27130825", "SRS23587812", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34471, "SRR31769123", "SRX27130824", "SRS23587811", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells day 1 uninjured fish set #3", "GSM8691392", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells day 1 uninjured fish set #3", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1", "GSM8691392", "GSM8691392: adult zebrafish retinal ganglion cells day 1 uninjured fish set #3; Danio rerio; RNA Seq", "GSM8691392 r1", "GSM8691392", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Uninjured-1DPI-3_GRO2657A19_S4_L001_R1_001.fastq.gz Uninjured-1DPI-3_GRO2657A19_S4_L001_R2_001.fastq.gz", "fastq fastq", 59387016872.0, 503279804.0, "GSM8691392 r1", "0:28 1:90", "A:17711412598;C:12536566614;G:13563786736;T:15573793585;N:1457339", 28, 90, null, null, 17711412598, 12536566614, 13563786736, 15573793585, 1457339, "SRX27130824", "SRS23587811", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34472, "SRR31769124", "SRX27130823", "SRS23587810", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells day 1 uninjured fish set #2", "GSM8691391", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells day 1 uninjured fish set #2", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1", "GSM8691391", "GSM8691391: adult zebrafish retinal ganglion cells day 1 uninjured fish set #2; Danio rerio; RNA Seq", "GSM8691391 r1", "GSM8691391", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Uninjured-1DPI-2_GRO2553A7_S10_L001_R1_001.fastq.gz Uninjured-1DPI-2_GRO2553A7_S10_L001_R2_001.fastq.gz", "fastq fastq", 106157704906.0, 899641567.0, "GSM8691391 r1", "0:28 1:90", "A:29822848120;C:23694191955;G:25190535492;T:27447524885;N:2604454", 28, 90, null, null, 29822848120, 23694191955, 25190535492, 27447524885, 2604454, "SRX27130823", "SRS23587810", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34473, "SRR31769125", "SRX27130822", "SRS23587809", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells day 1 uninjured fish set #1", "GSM8691390", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells day 1 uninjured fish set #1", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1", "GSM8691390", "GSM8691390: adult zebrafish retinal ganglion cells day 1 uninjured fish set #1; Danio rerio; RNA Seq", "GSM8691390 r1", "GSM8691390", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Uninjured-1DPI-1_GRO2553A5_S2_L001_R1_001.fastq.gz Uninjured-1DPI-1_GRO2553A5_S2_L001_R2_001.fastq.gz", "fastq fastq", 123090850164.0, 1043142798.0, "GSM8691390 r1", "0:28 1:90", "A:34510432265;C:27448485343;G:28965763692;T:32163144642;N:3024222", 28, 90, null, null, 34510432265, 27448485343, 28965763692, 32163144642, 3024222, "SRX27130822", "SRS23587809", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34474, "SRR31769126", "SRX27130821", "SRS23587808", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #4", "GSM8691389", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #4", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury", "GSM8691389", "GSM8691389: adult zebrafish retinal ganglion cells 1 xxx post injury fish set #4; Danio rerio; RNA Seq", "GSM8691389 r1", "GSM8691389", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Injured-1DPI-4_GRO2657A20_S8_L001_R1_001.fastq.gz Injured-1DPI-4_GRO2657A20_S8_L001_R2_001.fastq.gz", "fastq fastq", 72232326244.0, 612138358.0, "GSM8691389 r1", "0:28 1:90", "A:20998820884;C:15527703707;G:16387036598;T:19316988726;N:1776329", 28, 90, null, null, 20998820884, 15527703707, 16387036598, 19316988726, 1776329, "SRX27130821", "SRS23587808", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34475, "SRR31769127", "SRX27130820", "SRS23587807", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #3", "GSM8691388", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #3", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury", "GSM8691388", "GSM8691388: adult zebrafish retinal ganglion cells 1 xxx post injury fish set #3; Danio rerio; RNA Seq", "GSM8691388 r1", "GSM8691388", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Injured-1DPI-3_GRO2357A4_S1_L001_R1_001.fastq.gz Injured-1DPI-3_GRO2357A4_S1_L001_R2_001.fastq.gz", "fastq fastq", 72891590238.0, 617725341.0, "GSM8691388 r1", "0:28 1:90", "A:20358858846;C:16164883435;G:16927165785;T:19438889715;N:1792457", 28, 90, null, null, 20358858846, 16164883435, 16927165785, 19438889715, 1792457, "SRX27130820", "SRS23587807", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34476, "SRR31769128", "SRX27130819", "SRS23587806", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #2", "GSM8691387", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #2", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury", "GSM8691387", "GSM8691387: adult zebrafish retinal ganglion cells 1 xxx post injury fish set #2; Danio rerio; RNA Seq", "GSM8691387 r1", "GSM8691387", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Injured-1DPI-2_GRO2553A8_S12_L001_R1_001.fastq.gz Injured-1DPI-2_GRO2553A8_S12_L001_R2_001.fastq.gz", "fastq fastq", 91792694538.0, 777904191.0, "GSM8691387 r1", "0:28 1:90", "A:25675360853;C:20502226198;G:22024452743;T:23588401816;N:2252928", 28, 90, null, null, 25675360853, 20502226198, 22024452743, 23588401816, 2252928, "SRX27130819", "SRS23587806", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34477, "SRR31769129", "SRX27130818", "SRS23587805", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3 a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #1", "GSM8691386", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #1", "The cellranger count pipeline version 6.1.2 was used for alignment using default arguments producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly for each sample filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next integrated data is re scaled and PCA TSNE and UMAP embeddings are computed using Seurat\u2019s RunPCA RunUMAP and RunTSNE functions. Lastly an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically clusters were removed that had high expression of at least two of the following genes: opn1lw2 opn1mw2 opn1mw1 opn1sw2 opn1lw1 gngt2b gngt2a rho crx pde6c pde6ga opn6a vsx1 glula cabp5a cabp2a gng13b gad1b cd82a gad2 pax6b pax6a cd74a fcer1gl and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury", "GSM8691386", "GSM8691386: adult zebrafish retinal ganglion cells 1 xxx post injury fish set #1; Danio rerio; RNA Seq", "GSM8691386 r1", "GSM8691386", "1", "1 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer's protocol. Briefly single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA amplification enzymatic fragmentation 50 adaptor attachment and sample indexing. On average approximately 7 000 single cells were loaded on each channel and approximately 2 000 4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Injured-1DPI-1_GRO2553A6_S6_L001_R1_001.fastq.gz Injured-1DPI-1_GRO2553A6_S6_L001_R2_001.fastq.gz", "fastq fastq", 82801648902.0, 701708889.0, "GSM8691386 r1", "0:28 1:90", "A:22655489308;C:18871676339;G:19992651055;T:21279810265;N:2021935", 28, 90, null, null, 22655489308, 18871676339, 19992651055, 21279810265, 2021935, "SRX27130818", "SRS23587805", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [50656, "SRR10769144", "SRX7443062", "SRS5887360", "SRP169565", "PRJNA506002", "Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina", "GSE122680", "Transcriptome Analysis", "It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage", null, "pubmed:32467236", null, "48 hpf retina rep", "GSM4233148", null, "source name:Retina|strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:48 hpf", "48 hpf retina rep", "Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We subtract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we subtract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx", "Retina", null, "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer\u2019s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer\u2019s protocol.", null, "strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:48 hpf", "GSM4233148", "GSM4233148: 48 hpf retina rep; Danio rerio; RNA Seq", "GSM4233148", null, "1", "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.", "GEO Accession:GSM4233148", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP169565", null, "intentional duplicate", "48hpf_rep_possorted_genome_bam.bam", "10X Genomics bam file", 31477860150.0, 209852401.0, "GSM4233148 r1", "0:150", "A:9531250692;C:6384514147;G:7053602060;T:8508157890;N:335361", 150, null, null, null, 9531250692, 6384514147, 7053602060, 8508157890, 335361, "SRX7443062", "SRS5887360", "SRA812747", "GEO", "Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS", 1, 0.91107, null, 0.07208, null, 0.83644, null, 0.47681, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-12-26", "Hatching", "Embryo", "Eye", "Sensory System"], [50658, "SRR8206457", "SRX5025782", "SRS4057282", "SRP169565", "PRJNA506002", "Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina", "GSE122680", "Transcriptome Analysis", "It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage", null, "pubmed:32467236", null, "72 hpf retina rep", "GSM3478018", null, "source name:Retina|strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:72 hpf", "72 hpf retina rep", "Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx", "Retina", null, "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer\u2019s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer\u2019s protocol.", null, "strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:72 hpf", "GSM3478018", "GSM3478018: 72 hpf retina rep; Danio rerio; RNA Seq", "GSM3478018", null, "1", "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.", "GEO Accession:GSM3478018", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP169565", null, null, "72hpf_rep_possorted_genome_bam.bam", "10X Genomics bam file", 34981999650.0, 233213331.0, "GSM3478018 r1", "0:150", "A:10674927230;C:6939875303;G:7690258235;T:9676740488;N:198394", 150, null, null, null, 10674927230, 6939875303, 7690258235, 9676740488, 198394, "SRX5025782", "SRS4057282", "SRA812747", "GEO", "Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS", 1, 0.92117, null, 0.11001, null, 0.81395, null, 0.49096, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2018-11-19", "Larval", "Larval", "Eye", "Sensory System"], [50660, "SRR8206455", "SRX5025780", "SRS4057280", "SRP169565", "PRJNA506002", "Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina", "GSE122680", "Transcriptome Analysis", "It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage", null, "pubmed:32467236", null, "72 hpf retina", "GSM3478016", null, "source name:Retina|strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:72 hpf", "72 hpf retina", "Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx", "Retina", null, "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer\u2019s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer\u2019s protocol.", null, "strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:72 hpf", "GSM3478016", "GSM3478016: 72 hpf retina; Danio rerio; RNA Seq", "GSM3478016", null, "1", "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.", "GEO Accession:GSM3478016", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP169565", null, null, "72hpf_possorted_genome_bam.bam", "10X Genomics bam file", 62947056222.0, 416867922.0, "GSM3478016 r1", "0:151", "A:18604638142;C:13175965920;G:12960563931;T:18203901666;N:1986563", 151, null, null, null, 18604638142, 13175965920, 12960563931, 18203901666, 1986563, "SRX5025780", "SRS4057280", "SRA812747", "GEO", "Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS", 1, 0.85367, null, 0.1186, null, 0.80773, null, 0.51136, null, 151, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2018-11-19", "Larval", "Larval", "Eye", "Sensory System"], [50661, "SRR11812054", "SRX5025779", "SRS4057279", "SRP169565", "PRJNA506002", "Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina", "GSE122680", "Transcriptome Analysis", "It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage", null, "pubmed:32467236", null, "48 hpf retina", "GSM3478015", null, "source name:Retina|strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:48 hpf", "48 hpf retina", "Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx", "Retina", null, "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer\u2019s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer\u2019s protocol.", null, "strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:48 hpf", "GSM3478015", "GSM3478015: 48 hpf retina; Danio rerio; RNA Seq", "GSM3478015", null, "1", "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.", "GEO Accession:GSM3478015", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP169565", null, "intentional duplicate", "48hpf_possorted_genome_bam.bam", "10X Genomics bam file", 27828827400.0, 185525516.0, "GSM3478015 r11", "0:150", "A:8568529313;C:5431445717;G:5968188905;T:7860573445;N:90020", 150, null, null, null, 8568529313, 5431445717, 5968188905, 7860573445, 90020, "SRX5025779", "SRS4057279", "SRA812747", "GEO", "Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS", 1, 0.91308, null, 0.11004, null, 0.82213, null, 0.48772, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2018-11-19", "Hatching", "Embryo", "Eye", "Sensory System"], [50662, "SRR8206453", "SRX5025778", "SRS4057278", "SRP169565", "PRJNA506002", "Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina", "GSE122680", "Transcriptome Analysis", "It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage", null, "pubmed:32467236", null, "36 hpf retina", "GSM3478014", null, "source name:Retina|strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:36 hpf", "36 hpf retina", "Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx", "Retina", null, "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer\u2019s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer\u2019s protocol.", null, "strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:36 hpf", "GSM3478014", "GSM3478014: 36 hpf retina; Danio rerio; RNA Seq", "GSM3478014", null, "1", "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.", "GEO Accession:GSM3478014", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP169565", null, null, "36hpf_possorted_genome_bam.bam", "10X Genomics bam file", 55066871015.0, 364681265.0, "GSM3478014 r1", "0:151", "A:16004920970;C:11846723571;G:11830068402;T:15383410377;N:1747695", 151, null, null, null, 16004920970, 11846723571, 11830068402, 15383410377, 1747695, "SRX5025778", "SRS4057278", "SRA812747", "GEO", "Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS", 1, 0.86264, null, 0.06425, null, 0.83834, null, 0.48474, null, 151, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2018-11-19", "Pharyngula", "Embryo", "Eye", "Sensory System"], [50663, "SRR8206452", "SRX5025777", "SRS4057277", "SRP169565", "PRJNA506002", "Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina", "GSE122680", "Transcriptome Analysis", "It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage", null, "pubmed:32467236", null, "24 hpf retina", "GSM3478013", null, "source name:Retina|strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:24 hpf", "24 hpf retina", "Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx", "Retina", null, "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer\u2019s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer\u2019s protocol.", null, "strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:24 hpf", "GSM3478013", "GSM3478013: 24 hpf retina; Danio rerio; RNA Seq", "GSM3478013", null, "1", "We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.", "GEO Accession:GSM3478013", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP169565", null, null, "24hpf_possorted_genome_bam.bam", "10X Genomics bam file", 64649431883.0, 428141933.0, "GSM3478013 r1", "0:151", "A:18206375554;C:14387069686;G:14012075221;T:18041887869;N:2023553", 151, null, null, null, 18206375554, 14387069686, 14012075221, 18041887869, 2023553, "SRX5025777", "SRS4057277", "SRA812747", "GEO", "Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS", 1, 0.88151, null, 0.05606, null, 0.8369, null, 0.50733, null, 151, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2018-11-19", "Pharyngula", "Embryo", "Eye", "Sensory System"], [59292, "SRR11811475", "SRX8362742", "SRS6678633", "SRP262311", "PRJNA633835", "Single cell RNA seq and ATAC seq of zebrafish retina", "GSE150839", "Other", "To study the transcriptomic and chromatin accessibility heterogeneity of zebrafish retinal progenitor cells Overall design: 2 retinal samples from embryonic zebrafish", null, "pubmed:32699896", null, "RNA seq retina atoh7 44hpf", "GSM4559534", null, "source name:retina|strain:Tgatoh7:turboGFP dest1::atoh7:gapRFP|tissue:retina|developmental stage:44 hpf", "RNA seq retina atoh7 44hpf", "Raw datasets of single cell RNA seq were aligned zebrafish genome GRCz10 filtered and counted using the Cell Ranger software v2.1.0 10x Genomics to generate the processed matrix data. Raw data of single cell ATAC seq were aligned zebrafish genome GRCz10 filtered and counted using the Cell Ranger ATAC software v1.1 10x Genomics to generated the processed matrix data. Genome build: GRCz10 Supplementary files format and content: Processed data files are in tar.gz format containing matrix files for further analysis.", "retina", null, "Zebrafish retina at the desired developmental stages were dissected and dissociated using papain for single cell RNA seq. The single nuclei were further extracted by digitonin for single cell ATAC seq. The libraries were constructed using the Chromium Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x genomics PN 120237 or the Chromium Single Cell ATAC Library & Gel Bead Kit 10x genomics following the manufacturer\u2019s protocol", null, "strain:Tgatoh7:turboGFP dest1::atoh7:gapRFP|tissue:retina|developmental stage:44 hpf", "GSM4559534", "GSM4559534: RNA seq retina atoh7 44hpf; Danio rerio; RNA Seq", "GSM4559534", null, "1", "Zebrafish retina at the desired developmental stages were dissected and dissociated using papain for single cell RNA seq. The single nuclei were further extracted by digitonin for single cell ATAC seq. The libraries were constructed using the Chromium Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x genomics PN 120237 or the Chromium Single Cell ATAC Library & Gel Bead Kit 10x genomics following the manufacturer's protocol", "GEO Accession:GSM4559534", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP262311", null, "intentional duplicate|options: max err count 100000000", "atoh7_scRNA_bam.bam", "10X Genomics bam file", 61111212107.0, 414028035.0, "GSM4559534 r1", "0:147.60", "A:18052310869;C:12727112571;G:14225357068;T:16105981406;N:450193", 147, null, null, null, 18052310869, 12727112571, 14225357068, 16105981406, 450193, "SRX8362742", "SRS6678633", "SRA1077074", "GEO", "Institute of Neuroscience, Chinese Academy of Sciences", 1, 0.89647, null, 0.06712, null, 0.85228, null, 0.50102, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-05-19", "Pharyngula", "Embryo", "Eye", "Sensory System"], [59859, "SRR12054798", "SRX8583217", "SRS6874834", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 15", "GSM4627227", null, "source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 15", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina 4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics Pleasanton CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.", "tissue:retina", "GSM4627227", "GSM4627227: Adult Zebrafish 15; Danio rerio; RNA Seq", "GSM4627227", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA", "GEO Accession:GSM4627227", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC15.bam", "10X Genomics bam file", 17489597440.0, 178465280.0, "GSM4627227 r1", "0:98", "A:5144837324;C:3453657332;G:3688751956;T:5199397147;N:2953681", 98, null, null, null, 5144837324, 3453657332, 3688751956, 5199397147, 2953681, "SRX8583217", "SRS6874834", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.88384, null, 0.24019, null, 0.78979, null, 0.51275, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [59860, "SRR12054797", "SRX8583216", "SRS6874833", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 14", "GSM4627226", null, "source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 14", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina 4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics Pleasanton CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.", "tissue:retina", "GSM4627226", "GSM4627226: Adult Zebrafish 14; Danio rerio; RNA Seq", "GSM4627226", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA", "GEO Accession:GSM4627226", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC14.bam", "10X Genomics bam file", 16163588938.0, 164934581.0, "GSM4627226 r1", "0:98", "A:4767424342;C:3189871576;G:3410422503;T:4793151919;N:2718598", 98, null, null, null, 4767424342, 3189871576, 3410422503, 4793151919, 2718598, "SRX8583216", "SRS6874833", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.88242, null, 0.24257, null, 0.78892, null, 0.49263, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [59861, "SRR12054796", "SRX8583215", "SRS6874832", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 13", "GSM4627225", null, "source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 13", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina 4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics Pleasanton CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.", "tissue:retina", "GSM4627225", "GSM4627225: Adult Zebrafish 13; Danio rerio; RNA Seq", "GSM4627225", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA", "GEO Accession:GSM4627225", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC13.bam", "10X Genomics bam file", 14166392450.0, 144555025.0, "GSM4627225 r1", "0:98", "A:4156001799;C:2794969042;G:2979050667;T:4233954883;N:2416059", 98, null, null, null, 4156001799, 2794969042, 2979050667, 4233954883, 2416059, "SRX8583215", "SRS6874832", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.88338, null, 0.24795, null, 0.7893, null, 0.49627, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [59862, "SRR12054795", "SRX8583214", "SRS6874831", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 12", "GSM4627224", null, "source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 12", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina 4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics Pleasanton CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.", "tissue:retina", "GSM4627224", "GSM4627224: Adult Zebrafish 12; Danio rerio; RNA Seq", "GSM4627224", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA", "GEO Accession:GSM4627224", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC12.bam", "10X Genomics bam file", 15484230986.0, 158002357.0, "GSM4627224 r1", "0:98", "A:4556531984;C:3035955488;G:3233886544;T:4655230637;N:2626333", 98, null, null, null, 4556531984, 3035955488, 3233886544, 4655230637, 2626333, "SRX8583214", "SRS6874831", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.88248, null, 0.25141, null, 0.78782, null, 0.49785, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [59863, "SRR12054794", "SRX8583213", "SRS6874830", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 11", "GSM4627223", null, "source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 11", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina 4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics Pleasanton CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.", "tissue:retina", "GSM4627223", "GSM4627223: Adult Zebrafish 11; Danio rerio; RNA Seq", "GSM4627223", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA", "GEO Accession:GSM4627223", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC11.bam", "10X Genomics bam file", 18012879710.0, 183804895.0, "GSM4627223 r1", "0:98", "A:5278772392;C:3561457870;G:3799039640;T:5370568922;N:3040886", 98, null, null, null, 5278772392, 3561457870, 3799039640, 5370568922, 3040886, "SRX8583213", "SRS6874830", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.88456, null, 0.25211, null, 0.7894, null, 0.50115, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [59864, "SRR12054791", "SRX8583210", "SRS6874827", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 8", "GSM4627220", null, "source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 8", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina 4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics Pleasanton CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.", "tissue:retina", "GSM4627220", "GSM4627220: Adult Zebrafish 8; Danio rerio; RNA Seq", "GSM4627220", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA", "GEO Accession:GSM4627220", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC8.bam", "10X Genomics bam file", 14551197976.0, 148481612.0, "GSM4627220 r1", "0:98", "A:4325239722;C:2863430626;G:2994943270;T:4365215038;N:2369320", 98, null, null, null, 4325239722, 2863430626, 2994943270, 4365215038, 2369320, "SRX8583210", "SRS6874827", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.87211, null, 0.29067, null, 0.79431, null, 0.49957, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [59865, "SRR12054790", "SRX8583209", "SRS6874826", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 7", "GSM4627219", null, "source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 7", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina 4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics Pleasanton CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.", "tissue:retina", "GSM4627219", "GSM4627219: Adult Zebrafish 7; Danio rerio; RNA Seq", "GSM4627219", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA", "GEO Accession:GSM4627219", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC7.bam", "10X Genomics bam file", 12894390180.0, 131575410.0, "GSM4627219 r1", "0:98", "A:3809964234;C:2548974567;G:2667179504;T:3866166531;N:2105344", 98, null, null, null, 3809964234, 2548974567, 2667179504, 3866166531, 2105344, "SRX8583209", "SRS6874826", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.87565, null, 0.28214, null, 0.78918, null, 0.51085, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [59866, "SRR12054789", "SRX8583208", "SRS6874825", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 6", "GSM4627218", null, "source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 6", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina 4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics Pleasanton CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.", "tissue:retina", "GSM4627218", "GSM4627218: Adult Zebrafish 6; Danio rerio; RNA Seq", "GSM4627218", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA", "GEO Accession:GSM4627218", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC6.bam", "10X Genomics bam file", 11333584262.0, 115648819.0, "GSM4627218 r1", "0:98", "A:3357618948;C:2223130462;G:2352697999;T:3398318533;N:1818320", 98, null, null, null, 3357618948, 2223130462, 2352697999, 3398318533, 1818320, "SRX8583208", "SRS6874825", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.87718, null, 0.26282, null, 0.7838, null, 0.50701, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [59867, "SRR12054786", "SRX8583205", "SRS6874822", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 3", "GSM4627215", null, "source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 3", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina 4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics Pleasanton CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.", "tissue:retina", "GSM4627215", "GSM4627215: Adult Zebrafish 3; Danio rerio; RNA Seq", "GSM4627215", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA", "GEO Accession:GSM4627215", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC3.bam", "10X Genomics bam file", 22433937540.0, 228917730.0, "GSM4627215 r1", "0:98", "A:6661186629;C:4423555909;G:4672058698;T:6668698022;N:8438282", 98, null, null, null, 6661186629, 4423555909, 4672058698, 6668698022, 8438282, "SRX8583205", "SRS6874822", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.88295, null, 0.30604, null, 0.79228, null, 0.53139, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [59868, "SRR12054785", "SRX8583204", "SRS6874821", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 2", "GSM4627214", null, "source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 2", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina 4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics Pleasanton CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.", "tissue:retina", "GSM4627214", "GSM4627214: Adult Zebrafish 2; Danio rerio; RNA Seq", "GSM4627214", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA", "GEO Accession:GSM4627214", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC2.bam", "10X Genomics bam file", 25334714412.0, 258517494.0, "GSM4627214 r1", "0:98", "A:7365387325;C:5107021128;G:5455973330;T:7396374911;N:9957718", 98, null, null, null, 7365387325, 5107021128, 5455973330, 7396374911, 9957718, "SRX8583204", "SRS6874821", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.90152, null, 0.22907, null, 0.78776, null, 0.50123, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [59869, "SRR12054784", "SRX8583203", "SRS6874820", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 1", "GSM4627213", null, "source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 1", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina 4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics Pleasanton CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES.", "tissue:retina", "GSM4627213", "GSM4627213: Adult Zebrafish 1; Danio rerio; RNA Seq", "GSM4627213", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA", "GEO Accession:GSM4627213", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC1.bam", "10X Genomics bam file", 25693480848.0, 262178376.0, "GSM4627213 r1", "0:98", "A:7491507845;C:5131022895;G:5429848529;T:7631356264;N:9745315", 98, null, null, null, 7491507845, 5131022895, 5429848529, 7631356264, 9745315, "SRX8583203", "SRS6874820", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.90363, null, 0.22835, null, 0.78632, null, 0.48812, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"], [61647, "SRR12899701", "SRX9364745", "SRS7586960", "SRP288616", "PRJNA672101", "Nrl dependent and independent rod photoreceptor development in zebrafish [scRNA Seq]", "GSE160140", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: The retinal single cell suspensions for WT and nrl KO zebrafish were prepared. Each suspension represented a pool of retinal cells from three retinas at the age of 5 month. scRNA seq was performed using the 10X Genomics technology. The retinal cell clusters and the corresponding gene expression patterns were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "nrl KO", "GSM4861219", null, "tissue:Retinal single cell suspension|cell type:Retinal single cell suspension|strain:AB|age:5 mpf KO", "nrl KO", "The scRNA seq data were analyzed using Cell Ranger pipelines to align reads to the reference genome GRCz11 from Ensembl generate feature barcode matrices and perform clustering and gene expression analysis. Seurat Butler et al. 2018 was used for quality control gene expression normalization principal component analysis PCA and cell clustering. In brief cells with a clear outlier number of genes potential multiplets and a high percentage of mitochondrial genes potential dead cells were excluded by \u201cFilterCells\u201d function. A global scaling normalization method \u201cLogNormalize\u201d was employed to normalize the gene expression measurements for each cell. PCA was performed to reduce dimensionality of the dataset. Seurat clustered cells based on their PCA scores. To determine the most contributing PCs a resampling test inspired by the jackStraw procedure was implemented. The significant PCs with a strong enrichment of low p value genes were used to identify the unsupervised cell clusters. t SNE t distributed Stochastic Neighbor Embedding was used to visualize and explore the distribution of cells in a low dimensional space 2D plot. For every single cluster differentially expressed genes up regulated were identified by the likelihood ratio test using \u201cFindAllMarkers\u201d function in Seurat package compared to all other cells. The top 20 differentially expressed genes were selected as marker genes for each cluster. The expression distribution of these marker genes was showed by heatmap and bubble diagram. GO and KEGG enrichment analysis was performed to recognize the main biological functions and the significantly enriched metabolic or signal transduction pathways in differentially expressed genes. Genome build: GRCz11 Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in WT group Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in nrl KO group Supplementary files format and content: Tab delimited text files showing the cell clustering results Supplementary files format and content: Tab delimited text files showing the marker genes for each cell cluster", "Retinal single cell suspension", null, "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", null, "cell type:Retinal single cell suspension|strain:AB|age:5 mpf KO", "GSM4861219", "GSM4861219: nrl KO; Danio rerio; RNA Seq", "GSM4861219", null, "1", "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", "GEO Accession:GSM4861219", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288616", null, null, "nrl-AGTCGCTT_BKDL192540874-1a-AK4445_1.fq.gz nrl-AGTCGCTT_BKDL192540874-1a-AK4445_2.fq.gz", "fastq fastq", 49906125900.0, 166353753.0, "GSM4861219 r1", "0:150 1:150", "A:14865909750;C:8966567919;G:8011176735;T:18062021514;N:449982", 150, 150, null, null, 14865909750, 8966567919, 8011176735, 18062021514, 449982, "SRX9364745", "SRS7586960", "SRA1147910", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.02021, 0.90771, 0.00411, 0.15041, 0.99251, 0.80742, 0.54436, 0.56743, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-10-26", "Adult", "Adult", "Eye", "Sensory System"], [61648, "SRR12899702", "SRX9364745", "SRS7586960", "SRP288616", "PRJNA672101", "Nrl dependent and independent rod photoreceptor development in zebrafish [scRNA Seq]", "GSE160140", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: The retinal single cell suspensions for WT and nrl KO zebrafish were prepared. Each suspension represented a pool of retinal cells from three retinas at the age of 5 month. scRNA seq was performed using the 10X Genomics technology. The retinal cell clusters and the corresponding gene expression patterns were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "nrl KO", "GSM4861219", null, "tissue:Retinal single cell suspension|cell type:Retinal single cell suspension|strain:AB|age:5 mpf KO", "nrl KO", "The scRNA seq data were analyzed using Cell Ranger pipelines to align reads to the reference genome GRCz11 from Ensembl generate feature barcode matrices and perform clustering and gene expression analysis. Seurat Butler et al. 2018 was used for quality control gene expression normalization principal component analysis PCA and cell clustering. In brief cells with a clear outlier number of genes potential multiplets and a high percentage of mitochondrial genes potential dead cells were excluded by \u201cFilterCells\u201d function. A global scaling normalization method \u201cLogNormalize\u201d was employed to normalize the gene expression measurements for each cell. PCA was performed to reduce dimensionality of the dataset. Seurat clustered cells based on their PCA scores. To determine the most contributing PCs a resampling test inspired by the jackStraw procedure was implemented. The significant PCs with a strong enrichment of low p value genes were used to identify the unsupervised cell clusters. t SNE t distributed Stochastic Neighbor Embedding was used to visualize and explore the distribution of cells in a low dimensional space 2D plot. For every single cluster differentially expressed genes up regulated were identified by the likelihood ratio test using \u201cFindAllMarkers\u201d function in Seurat package compared to all other cells. The top 20 differentially expressed genes were selected as marker genes for each cluster. The expression distribution of these marker genes was showed by heatmap and bubble diagram. GO and KEGG enrichment analysis was performed to recognize the main biological functions and the significantly enriched metabolic or signal transduction pathways in differentially expressed genes. Genome build: GRCz11 Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in WT group Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in nrl KO group Supplementary files format and content: Tab delimited text files showing the cell clustering results Supplementary files format and content: Tab delimited text files showing the marker genes for each cell cluster", "Retinal single cell suspension", null, "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", null, "cell type:Retinal single cell suspension|strain:AB|age:5 mpf KO", "GSM4861219", "GSM4861219: nrl KO; Danio rerio; RNA Seq", "GSM4861219", null, "1", "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", "GEO Accession:GSM4861219", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288616", null, null, "nrl-CACGAGAA_BKDL192540874-1a-AK4446_1.fq.gz nrl-CACGAGAA_BKDL192540874-1a-AK4446_2.fq.gz", "fastq fastq", 28499943900.0, 94999813.0, "GSM4861219 r2", "0:150 1:150", "A:8487481226;C:5135100732;G:4580710999;T:10296385881;N:265062", 150, 150, null, null, 8487481226, 5135100732, 4580710999, 10296385881, 265062, "SRX9364745", "SRS7586960", "SRA1147910", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.02019, 0.90836, 0.00419, 0.15121, 0.99273, 0.80706, 0.53819, 0.58197, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-10-26", "Adult", "Adult", "Eye", "Sensory System"], [61649, "SRR12899703", "SRX9364745", "SRS7586960", "SRP288616", "PRJNA672101", "Nrl dependent and independent rod photoreceptor development in zebrafish [scRNA Seq]", "GSE160140", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: The retinal single cell suspensions for WT and nrl KO zebrafish were prepared. Each suspension represented a pool of retinal cells from three retinas at the age of 5 month. scRNA seq was performed using the 10X Genomics technology. The retinal cell clusters and the corresponding gene expression patterns were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "nrl KO", "GSM4861219", null, "tissue:Retinal single cell suspension|cell type:Retinal single cell suspension|strain:AB|age:5 mpf KO", "nrl KO", "The scRNA seq data were analyzed using Cell Ranger pipelines to align reads to the reference genome GRCz11 from Ensembl generate feature barcode matrices and perform clustering and gene expression analysis. Seurat Butler et al. 2018 was used for quality control gene expression normalization principal component analysis PCA and cell clustering. In brief cells with a clear outlier number of genes potential multiplets and a high percentage of mitochondrial genes potential dead cells were excluded by \u201cFilterCells\u201d function. A global scaling normalization method \u201cLogNormalize\u201d was employed to normalize the gene expression measurements for each cell. PCA was performed to reduce dimensionality of the dataset. Seurat clustered cells based on their PCA scores. To determine the most contributing PCs a resampling test inspired by the jackStraw procedure was implemented. The significant PCs with a strong enrichment of low p value genes were used to identify the unsupervised cell clusters. t SNE t distributed Stochastic Neighbor Embedding was used to visualize and explore the distribution of cells in a low dimensional space 2D plot. For every single cluster differentially expressed genes up regulated were identified by the likelihood ratio test using \u201cFindAllMarkers\u201d function in Seurat package compared to all other cells. The top 20 differentially expressed genes were selected as marker genes for each cluster. The expression distribution of these marker genes was showed by heatmap and bubble diagram. GO and KEGG enrichment analysis was performed to recognize the main biological functions and the significantly enriched metabolic or signal transduction pathways in differentially expressed genes. Genome build: GRCz11 Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in WT group Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in nrl KO group Supplementary files format and content: Tab delimited text files showing the cell clustering results Supplementary files format and content: Tab delimited text files showing the marker genes for each cell cluster", "Retinal single cell suspension", null, "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", null, "cell type:Retinal single cell suspension|strain:AB|age:5 mpf KO", "GSM4861219", "GSM4861219: nrl KO; Danio rerio; RNA Seq", "GSM4861219", null, "1", "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", "GEO Accession:GSM4861219", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288616", null, null, "nrl-TCGTCACG_BKDL192540874-1a-AK4447_1.fq.gz nrl-TCGTCACG_BKDL192540874-1a-AK4447_2.fq.gz", "fastq fastq", 34406205600.0, 114687352.0, "GSM4861219 r3", "0:150 1:150", "A:10238014457;C:6196096182;G:5538186725;T:12433588732;N:319504", 150, 150, null, null, 10238014457, 6196096182, 5538186725, 12433588732, 319504, "SRX9364745", "SRS7586960", "SRA1147910", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.01909, 0.90632, 0.00357, 0.14974, 0.9931, 0.80736, 0.53747, 0.582, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-10-26", "Adult", "Adult", "Eye", "Sensory System"], [61650, "SRR12899704", "SRX9364745", "SRS7586960", "SRP288616", "PRJNA672101", "Nrl dependent and independent rod photoreceptor development in zebrafish [scRNA Seq]", "GSE160140", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: The retinal single cell suspensions for WT and nrl KO zebrafish were prepared. Each suspension represented a pool of retinal cells from three retinas at the age of 5 month. scRNA seq was performed using the 10X Genomics technology. The retinal cell clusters and the corresponding gene expression patterns were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "nrl KO", "GSM4861219", null, "tissue:Retinal single cell suspension|cell type:Retinal single cell suspension|strain:AB|age:5 mpf KO", "nrl KO", "The scRNA seq data were analyzed using Cell Ranger pipelines to align reads to the reference genome GRCz11 from Ensembl generate feature barcode matrices and perform clustering and gene expression analysis. Seurat Butler et al. 2018 was used for quality control gene expression normalization principal component analysis PCA and cell clustering. In brief cells with a clear outlier number of genes potential multiplets and a high percentage of mitochondrial genes potential dead cells were excluded by \u201cFilterCells\u201d function. A global scaling normalization method \u201cLogNormalize\u201d was employed to normalize the gene expression measurements for each cell. PCA was performed to reduce dimensionality of the dataset. Seurat clustered cells based on their PCA scores. To determine the most contributing PCs a resampling test inspired by the jackStraw procedure was implemented. The significant PCs with a strong enrichment of low p value genes were used to identify the unsupervised cell clusters. t SNE t distributed Stochastic Neighbor Embedding was used to visualize and explore the distribution of cells in a low dimensional space 2D plot. For every single cluster differentially expressed genes up regulated were identified by the likelihood ratio test using \u201cFindAllMarkers\u201d function in Seurat package compared to all other cells. The top 20 differentially expressed genes were selected as marker genes for each cluster. The expression distribution of these marker genes was showed by heatmap and bubble diagram. GO and KEGG enrichment analysis was performed to recognize the main biological functions and the significantly enriched metabolic or signal transduction pathways in differentially expressed genes. Genome build: GRCz11 Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in WT group Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in nrl KO group Supplementary files format and content: Tab delimited text files showing the cell clustering results Supplementary files format and content: Tab delimited text files showing the marker genes for each cell cluster", "Retinal single cell suspension", null, "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", null, "cell type:Retinal single cell suspension|strain:AB|age:5 mpf KO", "GSM4861219", "GSM4861219: nrl KO; Danio rerio; RNA Seq", "GSM4861219", null, "1", "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", "GEO Accession:GSM4861219", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288616", null, null, "nrl-GTAATTGC_BKDL192540874-1a-AK2351_1.fq.gz nrl-GTAATTGC_BKDL192540874-1a-AK2351_2.fq.gz", "fastq fastq", 29290360200.0, 97634534.0, "GSM4861219 r4", "0:150 1:150", "A:8724008905;C:5269295599;G:4706098740;T:10590684259;N:272697", 150, 150, null, null, 8724008905, 5269295599, 4706098740, 10590684259, 272697, "SRX9364745", "SRS7586960", "SRA1147910", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.01987, 0.90685, 0.00317, 0.14947, 0.99251, 0.80505, 0.53355, 0.58341, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-10-26", "Adult", "Adult", "Eye", "Sensory System"], [61651, "SRR12899697", "SRX9364744", "SRS7586959", "SRP288616", "PRJNA672101", "Nrl dependent and independent rod photoreceptor development in zebrafish [scRNA Seq]", "GSE160140", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: The retinal single cell suspensions for WT and nrl KO zebrafish were prepared. Each suspension represented a pool of retinal cells from three retinas at the age of 5 month. scRNA seq was performed using the 10X Genomics technology. The retinal cell clusters and the corresponding gene expression patterns were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "WT", "GSM4861218", null, "tissue:Retinal single cell suspension|cell type:Retinal single cell suspension|strain:AB|age:5 mpf type", "WT", "The scRNA seq data were analyzed using Cell Ranger pipelines to align reads to the reference genome GRCz11 from Ensembl generate feature barcode matrices and perform clustering and gene expression analysis. Seurat Butler et al. 2018 was used for quality control gene expression normalization principal component analysis PCA and cell clustering. In brief cells with a clear outlier number of genes potential multiplets and a high percentage of mitochondrial genes potential dead cells were excluded by \u201cFilterCells\u201d function. A global scaling normalization method \u201cLogNormalize\u201d was employed to normalize the gene expression measurements for each cell. PCA was performed to reduce dimensionality of the dataset. Seurat clustered cells based on their PCA scores. To determine the most contributing PCs a resampling test inspired by the jackStraw procedure was implemented. The significant PCs with a strong enrichment of low p value genes were used to identify the unsupervised cell clusters. t SNE t distributed Stochastic Neighbor Embedding was used to visualize and explore the distribution of cells in a low dimensional space 2D plot. For every single cluster differentially expressed genes up regulated were identified by the likelihood ratio test using \u201cFindAllMarkers\u201d function in Seurat package compared to all other cells. The top 20 differentially expressed genes were selected as marker genes for each cluster. The expression distribution of these marker genes was showed by heatmap and bubble diagram. GO and KEGG enrichment analysis was performed to recognize the main biological functions and the significantly enriched metabolic or signal transduction pathways in differentially expressed genes. Genome build: GRCz11 Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in WT group Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in nrl KO group Supplementary files format and content: Tab delimited text files showing the cell clustering results Supplementary files format and content: Tab delimited text files showing the marker genes for each cell cluster", "Retinal single cell suspension", null, "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", null, "cell type:Retinal single cell suspension|strain:AB|age:5 mpf type", "GSM4861218", "GSM4861218: WT; Danio rerio; RNA Seq", "GSM4861218", null, "1", "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", "GEO Accession:GSM4861218", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288616", null, null, "WT-ACACTGTT_BKDL192540873-1a-AK4441_1.fq.gz WT-ACACTGTT_BKDL192540873-1a-AK4441_2.fq.gz", "fastq fastq", 39662654400.0, 132208848.0, "GSM4861218 r1", "0:150 1:150", "A:11045522027;C:7598619616;G:9039528129;T:11978732970;N:251658", 150, 150, null, null, 11045522027, 7598619616, 9039528129, 11978732970, 251658, "SRX9364744", "SRS7586959", "SRA1147910", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.0, 0.82252, 0.0, 0.1279, 1.0, 0.82562, null, 0.60079, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-10-26", "Adult", "Adult", "Eye", "Sensory System"], [61652, "SRR12899698", "SRX9364744", "SRS7586959", "SRP288616", "PRJNA672101", "Nrl dependent and independent rod photoreceptor development in zebrafish [scRNA Seq]", "GSE160140", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: The retinal single cell suspensions for WT and nrl KO zebrafish were prepared. Each suspension represented a pool of retinal cells from three retinas at the age of 5 month. scRNA seq was performed using the 10X Genomics technology. The retinal cell clusters and the corresponding gene expression patterns were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "WT", "GSM4861218", null, "tissue:Retinal single cell suspension|cell type:Retinal single cell suspension|strain:AB|age:5 mpf type", "WT", "The scRNA seq data were analyzed using Cell Ranger pipelines to align reads to the reference genome GRCz11 from Ensembl generate feature barcode matrices and perform clustering and gene expression analysis. Seurat Butler et al. 2018 was used for quality control gene expression normalization principal component analysis PCA and cell clustering. In brief cells with a clear outlier number of genes potential multiplets and a high percentage of mitochondrial genes potential dead cells were excluded by \u201cFilterCells\u201d function. A global scaling normalization method \u201cLogNormalize\u201d was employed to normalize the gene expression measurements for each cell. PCA was performed to reduce dimensionality of the dataset. Seurat clustered cells based on their PCA scores. To determine the most contributing PCs a resampling test inspired by the jackStraw procedure was implemented. The significant PCs with a strong enrichment of low p value genes were used to identify the unsupervised cell clusters. t SNE t distributed Stochastic Neighbor Embedding was used to visualize and explore the distribution of cells in a low dimensional space 2D plot. For every single cluster differentially expressed genes up regulated were identified by the likelihood ratio test using \u201cFindAllMarkers\u201d function in Seurat package compared to all other cells. The top 20 differentially expressed genes were selected as marker genes for each cluster. The expression distribution of these marker genes was showed by heatmap and bubble diagram. GO and KEGG enrichment analysis was performed to recognize the main biological functions and the significantly enriched metabolic or signal transduction pathways in differentially expressed genes. Genome build: GRCz11 Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in WT group Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in nrl KO group Supplementary files format and content: Tab delimited text files showing the cell clustering results Supplementary files format and content: Tab delimited text files showing the marker genes for each cell cluster", "Retinal single cell suspension", null, "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", null, "cell type:Retinal single cell suspension|strain:AB|age:5 mpf type", "GSM4861218", "GSM4861218: WT; Danio rerio; RNA Seq", "GSM4861218", null, "1", "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", "GEO Accession:GSM4861218", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288616", null, null, "WT-CAGGATGG_BKDL192540873-1a-AK4442_1.fq.gz WT-CAGGATGG_BKDL192540873-1a-AK4442_2.fq.gz", "fastq fastq", 31348389600.0, 104494632.0, "GSM4861218 r2", "0:150 1:150", "A:8715921134;C:6014807113;G:7149766236;T:9467696558;N:198559", 150, 150, null, null, 8715921134, 6014807113, 7149766236, 9467696558, 198559, "SRX9364744", "SRS7586959", "SRA1147910", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.0, 0.82311, 0.0, 0.12669, 1.0, 0.82749, null, 0.60453, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-10-26", "Adult", "Adult", "Eye", "Sensory System"], [61653, "SRR12899699", "SRX9364744", "SRS7586959", "SRP288616", "PRJNA672101", "Nrl dependent and independent rod photoreceptor development in zebrafish [scRNA Seq]", "GSE160140", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: The retinal single cell suspensions for WT and nrl KO zebrafish were prepared. Each suspension represented a pool of retinal cells from three retinas at the age of 5 month. scRNA seq was performed using the 10X Genomics technology. The retinal cell clusters and the corresponding gene expression patterns were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "WT", "GSM4861218", null, "tissue:Retinal single cell suspension|cell type:Retinal single cell suspension|strain:AB|age:5 mpf type", "WT", "The scRNA seq data were analyzed using Cell Ranger pipelines to align reads to the reference genome GRCz11 from Ensembl generate feature barcode matrices and perform clustering and gene expression analysis. Seurat Butler et al. 2018 was used for quality control gene expression normalization principal component analysis PCA and cell clustering. In brief cells with a clear outlier number of genes potential multiplets and a high percentage of mitochondrial genes potential dead cells were excluded by \u201cFilterCells\u201d function. A global scaling normalization method \u201cLogNormalize\u201d was employed to normalize the gene expression measurements for each cell. PCA was performed to reduce dimensionality of the dataset. Seurat clustered cells based on their PCA scores. To determine the most contributing PCs a resampling test inspired by the jackStraw procedure was implemented. The significant PCs with a strong enrichment of low p value genes were used to identify the unsupervised cell clusters. t SNE t distributed Stochastic Neighbor Embedding was used to visualize and explore the distribution of cells in a low dimensional space 2D plot. For every single cluster differentially expressed genes up regulated were identified by the likelihood ratio test using \u201cFindAllMarkers\u201d function in Seurat package compared to all other cells. The top 20 differentially expressed genes were selected as marker genes for each cluster. The expression distribution of these marker genes was showed by heatmap and bubble diagram. GO and KEGG enrichment analysis was performed to recognize the main biological functions and the significantly enriched metabolic or signal transduction pathways in differentially expressed genes. Genome build: GRCz11 Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in WT group Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in nrl KO group Supplementary files format and content: Tab delimited text files showing the cell clustering results Supplementary files format and content: Tab delimited text files showing the marker genes for each cell cluster", "Retinal single cell suspension", null, "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", null, "cell type:Retinal single cell suspension|strain:AB|age:5 mpf type", "GSM4861218", "GSM4861218: WT; Danio rerio; RNA Seq", "GSM4861218", null, "1", "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", "GEO Accession:GSM4861218", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288616", null, null, "WT-GGCTGAAC_BKDL192540873-1a-AK4443_1.fq.gz WT-GGCTGAAC_BKDL192540873-1a-AK4443_2.fq.gz", "fastq fastq", 40319953800.0, 134399846.0, "GSM4861218 r3", "0:150 1:150", "A:11213499575;C:7749543928;G:9198853498;T:12157801992;N:254807", 150, 150, null, null, 11213499575, 7749543928, 9198853498, 12157801992, 254807, "SRX9364744", "SRS7586959", "SRA1147910", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.0, 0.82103, 0.0, 0.12593, 1.0, 0.82219, null, 0.59917, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-10-26", "Adult", "Adult", "Eye", "Sensory System"], [61654, "SRR12899700", "SRX9364744", "SRS7586959", "SRP288616", "PRJNA672101", "Nrl dependent and independent rod photoreceptor development in zebrafish [scRNA Seq]", "GSE160140", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: The retinal single cell suspensions for WT and nrl KO zebrafish were prepared. Each suspension represented a pool of retinal cells from three retinas at the age of 5 month. scRNA seq was performed using the 10X Genomics technology. The retinal cell clusters and the corresponding gene expression patterns were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "WT", "GSM4861218", null, "tissue:Retinal single cell suspension|cell type:Retinal single cell suspension|strain:AB|age:5 mpf type", "WT", "The scRNA seq data were analyzed using Cell Ranger pipelines to align reads to the reference genome GRCz11 from Ensembl generate feature barcode matrices and perform clustering and gene expression analysis. Seurat Butler et al. 2018 was used for quality control gene expression normalization principal component analysis PCA and cell clustering. In brief cells with a clear outlier number of genes potential multiplets and a high percentage of mitochondrial genes potential dead cells were excluded by \u201cFilterCells\u201d function. A global scaling normalization method \u201cLogNormalize\u201d was employed to normalize the gene expression measurements for each cell. PCA was performed to reduce dimensionality of the dataset. Seurat clustered cells based on their PCA scores. To determine the most contributing PCs a resampling test inspired by the jackStraw procedure was implemented. The significant PCs with a strong enrichment of low p value genes were used to identify the unsupervised cell clusters. t SNE t distributed Stochastic Neighbor Embedding was used to visualize and explore the distribution of cells in a low dimensional space 2D plot. For every single cluster differentially expressed genes up regulated were identified by the likelihood ratio test using \u201cFindAllMarkers\u201d function in Seurat package compared to all other cells. The top 20 differentially expressed genes were selected as marker genes for each cluster. The expression distribution of these marker genes was showed by heatmap and bubble diagram. GO and KEGG enrichment analysis was performed to recognize the main biological functions and the significantly enriched metabolic or signal transduction pathways in differentially expressed genes. Genome build: GRCz11 Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in WT group Supplementary files format and content: Tab delimited text files with raw gene counts for every gene and cell in nrl KO group Supplementary files format and content: Tab delimited text files showing the cell clustering results Supplementary files format and content: Tab delimited text files showing the marker genes for each cell cluster", "Retinal single cell suspension", null, "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", null, "cell type:Retinal single cell suspension|strain:AB|age:5 mpf type", "GSM4861218", "GSM4861218: WT; Danio rerio; RNA Seq", "GSM4861218", null, "1", "Three retinas from WT and nrl KO zebrafsih were dissociated. The single cell suspensions were examined to ensure compliance with the requirements and then loaded onto the 10x Genomics Chromium Single Cell system using the three prime Reagent Kits v3 chemistry. Approximately 10 000 live cells were loaded per sample. Single cell GEM generation barcoding and libraries preparation were performed according to the user guides.", "GEO Accession:GSM4861218", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288616", null, null, "WT-TTTACCCA_BKDL192540873-1a-AK4444_1.fq.gz WT-TTTACCCA_BKDL192540873-1a-AK4444_2.fq.gz", "fastq fastq", 31557387300.0, 105191291.0, "GSM4861218 r4", "0:150 1:150", "A:8779167981;C:6070335814;G:7200941655;T:9506741847;N:200003", 150, 150, null, null, 8779167981, 6070335814, 7200941655, 9506741847, 200003, "SRX9364744", "SRS7586959", "SRA1147910", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.0, 0.82059, 0.0, 0.12768, 1.0, 0.82363, null, 0.5393, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-10-26", "Adult", "Adult", "Eye", "Sensory System"], [64414, "SRR14702158", "SRX11040181", "SRS9109179", "SRP322166", "PRJNA734313", "Single cell profiling of photoreceptor cells in adult zebrafish", "GSE175929", "Other", "Vertebrate vision is mediated by two kinds of photoreceptors rods and cones responsible for dim and bright light vision respectively. Gene expression differences among cone subtypes remain poorly understood compared with rods. We generated single cell transcriptome data using a droplet based approach to reveal the extent of gene expression diversity among adult zebrafish photoreceptor subtypes. Populations of photoreceptor cells were enriched by using the transgenic zebrafish lines Tgrho:EGFPja2Tg and Tggnat2:EGFPja23Tg which express GFP in rods and all cone subtypes respectively. By analyzing the single cell transcriptomes we found that in addition to the four canonical zebrafish cone types ultraviolet blue green and red there exist subpopulations of green and red cones in the ventral retina that express red shifted opsin paralogs opn1mw4 and opn1lw1. This work lays a foundation for future studies aimed at understanding how molecular differences among cone subtypes affect photoreceptor function. Overall design: GFP positive cells collected from two transgenic zebrafish Tgrho:EGFPja2Tg and Tggnat2:EGFPja23Tg were combined into one sample. A small percentage of GFP negative cells was also included in the sample.", null, "pubmed:34462505", null, "retinal cells", "GSM5351368", null, "tissue:retinal cells|age:adult|transgene:Tgrho:egfpja2Tg|transgene:Tggnat2:egfpja23Tg", "retinal cells", "FASTQ files were generated from the raw BCL files using Illumina\u2019s bcl2fastq conversion program. Sample demultiplexing with the mkfastq function from Cell Ranger softwareversion 3.1.0 10X Genomics. Sample alignment with the count function from Cell Ranger software version 6.0.0 10X Genomics. Paired end reads were mapped to the zebrafish genome GRCz11 using Cell Ranger software version 6.0.0 10X Genomics. Mapped reads were quantified using the Cell Ranger software with a custom annotation v432 dr adult eye.gtf included as processed file. The GFP transcript sequence was added manually to the reference assembly as an extra chromosome. Data were analyzed using the Seurat R package v4.0.0. We retained all cells that expressed >500 genes and we considered all genes expressed in at least five cells. Cells with greater than 30% mitochondrial gene content or >40 000 unique molecular identifiers were removed from the analysis. For the remaining cells a gene expression matrix was normalized to total cellular read counts using the Seurat SCTransform function. The 3 000 most variable genes identified by the SCTransform function were used for Principal Component Analysis. The top 30 principal components were selected for subsequent analysis. Graph based clustering was performed to obtain a set of transcriptionally distinct clusters. At this point in the analysis we deliberately set parameters to \"over cluster\" the data to avoid combining distinct cell types and to identify sub populations of low quality cells for removal. To retain high quality photoreceptors and bipolar cells only we subjected our data to multiple rounds of clustering filtering and selection. In the first round we retained those clusters characterized either by the presence of one or more of the following opsin genes or phototransduction genes rho opn1sw1 opn1sw2 opn1mw1 opn1mw2 opn1mw3 opn1mw4 opn1lw1 opn1lw2 gnat1 or gnat2 or bipolar specific genes e.g. gnao1b vsx1 cabp2a cabp5a and cabp5b among the top 20 most differentially expressed genes as identified by the FindAllMarkers function in Seurat. We also removed clusters consisting of low quality cells with low total gene counts 500 1 000 genes/cell compared with high quality photoreceptor clusters 1 000 3 000 genes/cell for rods and 1 000 4 000 genes/cell for cones. In the second round of clustering and selection we removed clusters that showed co expression of photoreceptor genes and M\u00fcller glial genes icn fxyd6l mt2 rlbp1a and glula. We also removed one cluster showing co expression of photoreceptor and bipolar genes and with low total gene counts. In the final round of clustering and selection we removed a rod subpopulation with low total gene counts and retained 2 186 high quality cells. Genome build: GRCz11 Supplementary files format and content: The Gene transfer format GTF containing information about gene structure used for counting the transcripts in the data Supplementary files format and content: Seurat object for scRNA seq data", "retinal cells", null, "Retinas of five mpf adult zebrafish were were harvested at around zeitgeber time 3 ZT 3. The dissected retinas were dissociated with a papain dissociation solution followed by further incubation with 10% FBS in DMEM and DNaseI. post the trituration the samples were resuspended in sorting buffer 20 mM HEPES and 0.04% bovine serum albumin in Calcium and magnesium free HBSS pH 7.4. Four retinas from two individuals were combined for Tgrho:EGFP fish while six retinas from three individuals were combined for Tggnat2:EGFP fish. The filtered samples were incubated in a solution of propidium iodide and Hoechst 33342. GFP positive cells were isolated via fluorescence activated cell sorting FACS. Dead cells were then removed based on propidium iodide positivity. Intact rods and cones were then selected based on the presence of both blue Hoechst 33342 and green fluorescence GFP. About 35 000 viable intact GFP positive cells PI GFP+ Hoechst+ and 1 500 GFP negative cells PI GFP Hoechst+ were collected from Tggnat2:EGFP fish while 10 000 GFP viable intact GFP positive cells and 1 500 GFP negative cells were collected from Tgrho:EGFP fish. These isolated cells were collected into the sorting buffer in one tube. Approximately 6 000 single cells were loaded into a 10X Chromium Single Cell Chip. Single cell libraries were made with Chromium 3\u2019 v3 platform following the manufacturer\u2019s protocol. RNA libraries were prepared for sequencing using standard Illumina protocols.", null, "age:adult|transgene:Tgrho:egfpja2Tg|transgene:Tggnat2:egfpja23Tg", "GSM5351368", "GSM5351368: retinal cells; Danio rerio; RNA Seq", "GSM5351368", null, "1", "Retinas of five mpf adult zebrafish were were harvested at around zeitgeber time 3 ZT 3. The dissected retinas were dissociated with a papain dissociation solution followed by further incubation with 10% FBS in DMEM and DNaseI. post the trituration the samples were resuspended in sorting buffer 20 mM HEPES and 0.04% bovine serum albumin in Calcium and magnesium free HBSS pH 7.4. Four retinas from two individuals were combined for Tgrho:EGFP fish while six retinas from three individuals were combined for Tggnat2:EGFP fish. The filtered samples were incubated in a solution of propidium iodide and Hoechst 33342. GFP positive cells were isolated via fluorescence activated cell sorting FACS. Dead cells were then removed based on propidium iodide positivity. Intact rods and cones were then selected based on the presence of both blue Hoechst 33342 and green fluorescence GFP. About 35 000 viable intact GFP positive cells PI GFP+ Hoechst+ and 1 500 GFP negative cells PI GFP Hoechst+ were collected from Tggnat2:EGFP fish while 10 000 GFP viable intact GFP positive cells and 1 500 GFP negative cells were collected from Tgrho:EGFP fish. These isolated cells were collected into the sorting buffer in one tube. Approximately 6 000 single cells were loaded into a 10X Chromium Single Cell Chip. Single cell libraries were made with Chromium three prime v3 platform following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM5351368", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP322166", null, null, "Cone_S5_L003_R1_001.fastq.gz Cone_S5_L003_R2_001.fastq.gz", "fastq fastq", 68659489710.0, 544916585.0, "GSM5351368 r1", "0:28 1:98", "A:19580055351;C:15466801940;G:15266233048;T:18341055919;N:5343452", 28, 98, null, null, 19580055351, 15466801940, 15266233048, 18341055919, 5343452, "SRX11040181", "SRS9109179", "SRA1239213", "GEO", "Pathology and Immunology, Washington University School of Medicine", 2, 0.0102, 0.85996, 0.00306, 0.14003, 0.98977, 0.84595, 0.44136, 0.62184, 28, 98, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-06-01", "Adult", "Adult", "Eye", "Sensory System"], [69645, "SRR19084407", "SRX15154229", "SRS12896750", "SRP373610", "PRJNA835051", "The regeneration responsive careg element monitors activation of M\u00fcller glia post MNU induced damage in the zebrafish retina", "GSE202212", "Transcriptome Analysis", "We found that the zebrafish non coding element careg which is induced in regenerating fins and heart also participates in retina regeneration. Its activation persisted mostly in M\u00fcller glia from the onset to the termination of retina restoration. To assess the involvement of the careg:EGFP reporter during retina regeneration we used a chemical injury model with MNU treatment. To identify the molecular profile of these cells we performed a single cell RNA sequencing scRNA seq experiment of retinas dissected from adult careg:EGFP zebrafish at 3 7 and 10 dpMNU. Our control retinas were dissected from fish at 3 days post treatment with heat inactivated MNU Overall design: Adult careg:EGFP transgenic zebrafish retinas post MNU induced injury were isolated for scRNA sequencing", null, "pubmed:37138703", null, "10dpMNU 2", "GSM6106359", null, "source name:retina|tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L|geo loc name:missing|collection date:missing", "10dpMNU 2", "Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.2.0 The GFP transcript sequence was added manually to the reference assembly. Further processing was performed using Seurat v4 in R. Assembly: GRCz11 Supplementary files format and content: gene barcode expression matrix", "retina", null, "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 10X Genomics.", null, "tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L", "GSM6106359", "GSM6106359: 10dpMNU 2; Danio rerio; RNA Seq", "GSM6106359 r1", "GSM6106359", "1", "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP373610", null, "assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped", "10dp2_possorted_genome_bam.bam", "10X Genomics bam file", 54359767157.0, 600605770.0, "GSM6106359 r1", "0:90.51", "A:17183149218;C:10280467884;G:13561914128;T:13318350579;N:15885348", 90, null, null, null, 17183149218, 10280467884, 13561914128, 13318350579, 15885348, "SRX15154229", "SRS12896750", "SRA1420445", "University of Fribourg", "University of Fribourg", 1, 0.86617, null, 0.34213, null, 0.86312, null, 0.64043, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2022-05-04", "Adult", "Adult", "Eye", "Sensory System"], [69646, "SRR19084408", "SRX15154228", "SRS12896749", "SRP373610", "PRJNA835051", "The regeneration responsive careg element monitors activation of M\u00fcller glia post MNU induced damage in the zebrafish retina", "GSE202212", "Transcriptome Analysis", "We found that the zebrafish non coding element careg which is induced in regenerating fins and heart also participates in retina regeneration. Its activation persisted mostly in M\u00fcller glia from the onset to the termination of retina restoration. To assess the involvement of the careg:EGFP reporter during retina regeneration we used a chemical injury model with MNU treatment. To identify the molecular profile of these cells we performed a single cell RNA sequencing scRNA seq experiment of retinas dissected from adult careg:EGFP zebrafish at 3 7 and 10 dpMNU. Our control retinas were dissected from fish at 3 days post treatment with heat inactivated MNU Overall design: Adult careg:EGFP transgenic zebrafish retinas post MNU induced injury were isolated for scRNA sequencing", null, "pubmed:37138703", null, "10dpMNU 1", "GSM6106358", null, "source name:retina|tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L|geo loc name:missing|collection date:missing", "10dpMNU 1", "Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.2.0 The GFP transcript sequence was added manually to the reference assembly. Further processing was performed using Seurat v4 in R. Assembly: GRCz11 Supplementary files format and content: gene barcode expression matrix", "retina", null, "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 10X Genomics.", null, "tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L", "GSM6106358", "GSM6106358: 10dpMNU 1; Danio rerio; RNA Seq", "GSM6106358 r1", "GSM6106358", "1", "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP373610", null, "assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped", "10dp1_possorted_genome_bam.bam", "10X Genomics bam file", 49157136786.0, 543237322.0, "GSM6106358 r1", "0:90.49", "A:14388514140;C:10285005448;G:11549735765;T:12919526731;N:14354702", 90, null, null, null, 14388514140, 10285005448, 11549735765, 12919526731, 14354702, "SRX15154228", "SRS12896749", "SRA1420445", "University of Fribourg", "University of Fribourg", 1, 0.88102, null, 0.31782, null, 0.79571, null, 0.6372, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2022-05-04", "Adult", "Adult", "Eye", "Sensory System"], [69647, "SRR19084409", "SRX15154227", "SRS12896748", "SRP373610", "PRJNA835051", "The regeneration responsive careg element monitors activation of M\u00fcller glia post MNU induced damage in the zebrafish retina", "GSE202212", "Transcriptome Analysis", "We found that the zebrafish non coding element careg which is induced in regenerating fins and heart also participates in retina regeneration. Its activation persisted mostly in M\u00fcller glia from the onset to the termination of retina restoration. To assess the involvement of the careg:EGFP reporter during retina regeneration we used a chemical injury model with MNU treatment. To identify the molecular profile of these cells we performed a single cell RNA sequencing scRNA seq experiment of retinas dissected from adult careg:EGFP zebrafish at 3 7 and 10 dpMNU. Our control retinas were dissected from fish at 3 days post treatment with heat inactivated MNU Overall design: Adult careg:EGFP transgenic zebrafish retinas post MNU induced injury were isolated for scRNA sequencing", null, "pubmed:37138703", null, "7dpMNU 2", "GSM6106357", null, "source name:retina|tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L|geo loc name:missing|collection date:missing", "7dpMNU 2", "Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.2.0 The GFP transcript sequence was added manually to the reference assembly. Further processing was performed using Seurat v4 in R. Assembly: GRCz11 Supplementary files format and content: gene barcode expression matrix", "retina", null, "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 10X Genomics.", null, "tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L", "GSM6106357", "GSM6106357: 7dpMNU 2; Danio rerio; RNA Seq", "GSM6106357 r1", "GSM6106357", "1", "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP373610", null, "assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped", "7dp2_possorted_genome_bam.bam", "10X Genomics bam file", 51097903854.0, 564773099.0, "GSM6106357 r1", "0:90.48", "A:16865813537;C:9568375873;G:11541078798;T:13107697081;N:14938565", 90, null, null, null, 16865813537, 9568375873, 11541078798, 13107697081, 14938565, "SRX15154227", "SRS12896748", "SRA1420445", "University of Fribourg", "University of Fribourg", 1, 0.88078, null, 0.36957, null, 0.83493, null, 0.66026, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2022-05-04", "Adult", "Adult", "Eye", "Sensory System"], [69648, "SRR19084410", "SRX15154226", "SRS12896747", "SRP373610", "PRJNA835051", "The regeneration responsive careg element monitors activation of M\u00fcller glia post MNU induced damage in the zebrafish retina", "GSE202212", "Transcriptome Analysis", "We found that the zebrafish non coding element careg which is induced in regenerating fins and heart also participates in retina regeneration. Its activation persisted mostly in M\u00fcller glia from the onset to the termination of retina restoration. To assess the involvement of the careg:EGFP reporter during retina regeneration we used a chemical injury model with MNU treatment. To identify the molecular profile of these cells we performed a single cell RNA sequencing scRNA seq experiment of retinas dissected from adult careg:EGFP zebrafish at 3 7 and 10 dpMNU. Our control retinas were dissected from fish at 3 days post treatment with heat inactivated MNU Overall design: Adult careg:EGFP transgenic zebrafish retinas post MNU induced injury were isolated for scRNA sequencing", null, "pubmed:37138703", null, "7dpMNU 1", "GSM6106356", null, "source name:retina|tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L|geo loc name:missing|collection date:missing", "7dpMNU 1", "Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.2.0 The GFP transcript sequence was added manually to the reference assembly. Further processing was performed using Seurat v4 in R. Assembly: GRCz11 Supplementary files format and content: gene barcode expression matrix", "retina", null, "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 10X Genomics.", null, "tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L", "GSM6106356", "GSM6106356: 7dpMNU 1; Danio rerio; RNA Seq", "GSM6106356 r1", "GSM6106356", "1", "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP373610", null, "assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped", "7dp1_possorted_genome_bam.bam", "10X Genomics bam file", 49933869130.0, 551758467.0, "GSM6106356 r1", "0:90.50", "A:14541918290;C:10501492165;G:11630509992;T:13245294913;N:14653770", 90, null, null, null, 14541918290, 10501492165, 11630509992, 13245294913, 14653770, "SRX15154226", "SRS12896747", "SRA1420445", "University of Fribourg", "University of Fribourg", 1, 0.89836, null, 0.32967, null, 0.79504, null, 0.53681, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2022-05-04", "Adult", "Adult", "Eye", "Sensory System"], [69649, "SRR19084411", "SRX15154225", "SRS12896746", "SRP373610", "PRJNA835051", "The regeneration responsive careg element monitors activation of M\u00fcller glia post MNU induced damage in the zebrafish retina", "GSE202212", "Transcriptome Analysis", "We found that the zebrafish non coding element careg which is induced in regenerating fins and heart also participates in retina regeneration. Its activation persisted mostly in M\u00fcller glia from the onset to the termination of retina restoration. To assess the involvement of the careg:EGFP reporter during retina regeneration we used a chemical injury model with MNU treatment. To identify the molecular profile of these cells we performed a single cell RNA sequencing scRNA seq experiment of retinas dissected from adult careg:EGFP zebrafish at 3 7 and 10 dpMNU. Our control retinas were dissected from fish at 3 days post treatment with heat inactivated MNU Overall design: Adult careg:EGFP transgenic zebrafish retinas post MNU induced injury were isolated for scRNA sequencing", null, "pubmed:37138703", null, "3dpMNU 2", "GSM6106355", null, "source name:retina|tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L|geo loc name:missing|collection date:missing", "3dpMNU 2", "Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.2.0 The GFP transcript sequence was added manually to the reference assembly. Further processing was performed using Seurat v4 in R. Assembly: GRCz11 Supplementary files format and content: gene barcode expression matrix", "retina", null, "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 10X Genomics.", null, "tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L", "GSM6106355", "GSM6106355: 3dpMNU 2; Danio rerio; RNA Seq", "GSM6106355 r1", "GSM6106355", "1", "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP373610", null, "assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped", "3dp2_possorted_genome_bam.bam", "10X Genomics bam file", 47804143445.0, 528253804.0, "GSM6106355 r1", "0:90.49", "A:14174450101;C:9743573685;G:10481602026;T:13390478656;N:14038977", 90, null, null, null, 14174450101, 9743573685, 10481602026, 13390478656, 14038977, "SRX15154225", "SRS12896746", "SRA1420445", "University of Fribourg", "University of Fribourg", 1, 0.89901, null, 0.32665, null, 0.78362, null, 0.60733, null, 89, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2022-05-04", "Adult", "Adult", "Eye", "Sensory System"], [69650, "SRR19084412", "SRX15154224", "SRS12896745", "SRP373610", "PRJNA835051", "The regeneration responsive careg element monitors activation of M\u00fcller glia post MNU induced damage in the zebrafish retina", "GSE202212", "Transcriptome Analysis", "We found that the zebrafish non coding element careg which is induced in regenerating fins and heart also participates in retina regeneration. Its activation persisted mostly in M\u00fcller glia from the onset to the termination of retina restoration. To assess the involvement of the careg:EGFP reporter during retina regeneration we used a chemical injury model with MNU treatment. To identify the molecular profile of these cells we performed a single cell RNA sequencing scRNA seq experiment of retinas dissected from adult careg:EGFP zebrafish at 3 7 and 10 dpMNU. Our control retinas were dissected from fish at 3 days post treatment with heat inactivated MNU Overall design: Adult careg:EGFP transgenic zebrafish retinas post MNU induced injury were isolated for scRNA sequencing", null, "pubmed:37138703", null, "3dpMNU 1", "GSM6106354", null, "source name:retina|tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L|geo loc name:missing|collection date:missing", "3dpMNU 1", "Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.2.0 The GFP transcript sequence was added manually to the reference assembly. Further processing was performed using Seurat v4 in R. Assembly: GRCz11 Supplementary files format and content: gene barcode expression matrix", "retina", null, "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 10X Genomics.", null, "tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with MNU 150mg/L", "GSM6106354", "GSM6106354: 3dpMNU 1; Danio rerio; RNA Seq", "GSM6106354 r1", "GSM6106354", "1", "Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. 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