metadata: run_metadata: 66 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation

66 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation_coarse = "Sensory System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
34465	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.			adult zebrafish retinal ganglion cells day 7 uninjured fish set #3	GSM8691398	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34466	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.			adult zebrafish retinal ganglion cells day 7 uninjured fish set #2	GSM8691397	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34467	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.			adult zebrafish retinal ganglion cells day 7 uninjured fish set #1	GSM8691396	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34468	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.			adult zebrafish retinal ganglion cells 7 xxx post injury fish set #3	GSM8691395	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34469	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.			adult zebrafish retinal ganglion cells 7 xxx post injury fish set #2	GSM8691394	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34470	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.			adult zebrafish retinal ganglion cells 7 xxx post injury fish set #1	GSM8691393	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34471	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.			adult zebrafish retinal ganglion cells day 1 uninjured fish set #3	GSM8691392	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34472	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.			adult zebrafish retinal ganglion cells day 1 uninjured fish set #2	GSM8691391	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34473	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.			adult zebrafish retinal ganglion cells day 1 uninjured fish set #1	GSM8691390	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34474	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.			adult zebrafish retinal ganglion cells 1 xxx post injury fish set #4	GSM8691389	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34475	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.			adult zebrafish retinal ganglion cells 1 xxx post injury fish set #3	GSM8691388	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34476	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.			adult zebrafish retinal ganglion cells 1 xxx post injury fish set #2	GSM8691387	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
34477	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.			adult zebrafish retinal ganglion cells 1 xxx post injury fish set #1	GSM8691386	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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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.	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP552478		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	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												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-18	Adult	Adult	Eye	Sensory System
50656	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		pubmed:32467236	48 hpf retina rep	GSM4233148	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		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 40μm 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.		strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:48 hpf	GSM4233148	GSM4233148: 48 hpf retina rep; Danio rerio; RNA Seq	GSM4233148		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 40μm 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	SRP169565	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		9531250692	6384514147	7053602060	8508157890	335361	SRX7443062	SRS5887360	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.91107		0.07208		0.83644		0.47681		150		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-26	Hatching	Embryo	Eye	Sensory System
50658	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		pubmed:32467236	72 hpf retina rep	GSM3478018	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		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 40μm 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.		strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:72 hpf	GSM3478018	GSM3478018: 72 hpf retina rep; Danio rerio; RNA Seq	GSM3478018		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 40μm 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	SRP169565		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		10674927230	6939875303	7690258235	9676740488	198394	SRX5025782	SRS4057282	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.92117		0.11001		0.81395		0.49096		150		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-11-19	Larval	Larval	Eye	Sensory System
50660	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		pubmed:32467236	72 hpf retina	GSM3478016	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		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 40μm 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.		strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:72 hpf	GSM3478016	GSM3478016: 72 hpf retina; Danio rerio; RNA Seq	GSM3478016		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 40μm 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	SRP169565		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		18604638142	13175965920	12960563931	18203901666	1986563	SRX5025780	SRS4057280	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.85367		0.1186		0.80773		0.51136		151		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-11-19	Larval	Larval	Eye	Sensory System
50661	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		pubmed:32467236	48 hpf retina	GSM3478015	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		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 40μm 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.		strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:48 hpf	GSM3478015	GSM3478015: 48 hpf retina; Danio rerio; RNA Seq	GSM3478015		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 40μm 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	SRP169565	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		8568529313	5431445717	5968188905	7860573445	90020	SRX5025779	SRS4057279	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.91308		0.11004		0.82213		0.48772		150		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-11-19	Hatching	Embryo	Eye	Sensory System
50662	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		pubmed:32467236	36 hpf retina	GSM3478014	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		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 40μm 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.		strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:36 hpf	GSM3478014	GSM3478014: 36 hpf retina; Danio rerio; RNA Seq	GSM3478014		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 40μm 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	SRP169565		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		16004920970	11846723571	11830068402	15383410377	1747695	SRX5025778	SRS4057278	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.86264		0.06425		0.83834		0.48474		151		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-11-19	Pharyngula	Embryo	Eye	Sensory System
50663	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		pubmed:32467236	24 hpf retina	GSM3478013	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		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 40μm 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.		strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:24 hpf	GSM3478013	GSM3478013: 24 hpf retina; Danio rerio; RNA Seq	GSM3478013		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 40μm 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	SRP169565		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		18206375554	14387069686	14012075221	18041887869	2023553	SRX5025777	SRS4057277	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.88151		0.05606		0.8369		0.50733		151		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-11-19	Pharyngula	Embryo	Eye	Sensory System
50723	50723	SRR8270602	SRX5087288	SRS4099391	SRP171998	PRJNA507898	Single cell RNA Seq reveals Fgf signaling dynamics during sensory hair cell regeneration	GSE123241	Transcriptome Analysis	Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells zebrafish ear and lateral line hair cells regenerate from poorly characterized proliferating support cells. Equally ill defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single cell RNA Sequencing scRNA Seq of lateral line sensory organs and uncovered five different support cell types including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self renew and new groups of genes required for hair cell differentiation. scRNA Seq analyses of fgf3 mutants in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 3 different samples: wild type fgf3 mutants and fgf3 siblings.		pubmed:30681411;pubmed:31488837	fgf3 mutant	GSM3498554	source name:neuromast\|age:5dpf\|tissue:neuromast\|genotype:fgf3 / \|strain:fgf3^t26212; ETkrt4:EGFPSqGw57A; Tgpou4f3:GAP GFPs356t screened for mutants	fgf3 mutant	Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.	neuromast		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|genotype:fgf3 / \|strain:fgf3^t26212;ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t screened for mutants	GSM3498554	GSM3498554: fgf3 mutant; Danio rerio; RNA Seq	GSM3498554		1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq	GEO Accession:GSM3498554	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP171998		possorted_genome_bam_fgf3_mut.bam	10X Genomics bam file	16974126576.0	171455824.0	GSM3498554 r1	0:99	A:5250835858;C:3266700009;G:3497115040;T:4840312852;N:119162817	99		5250835858	3266700009	3497115040	4840312852	119162817	SRX5087288	SRS4099391	SRA817952	GEO	Stowers Institute	1	0.89941		0.21879		0.80805		0.48702		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2018-12-02	Larval	Larval	Lateral Line	Sensory System
50724	50724	SRR8270601	SRX5087287	SRS4099390	SRP171998	PRJNA507898	Single cell RNA Seq reveals Fgf signaling dynamics during sensory hair cell regeneration	GSE123241	Transcriptome Analysis	Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells zebrafish ear and lateral line hair cells regenerate from poorly characterized proliferating support cells. Equally ill defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single cell RNA Sequencing scRNA Seq of lateral line sensory organs and uncovered five different support cell types including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self renew and new groups of genes required for hair cell differentiation. scRNA Seq analyses of fgf3 mutants in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 3 different samples: wild type fgf3 mutants and fgf3 siblings.		pubmed:30681411;pubmed:31488837	fgf3 sibling	GSM3498553	source name:neuromast\|age:5dpf\|tissue:neuromast\|genotype:fgf3+/ \|strain:fgf3^t26212; ETkrt4:EGFPSqGw57A; Tgpou4f3:GAP GFPs356t	fgf3 sibling	Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.	neuromast		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|genotype:fgf3+/ \|strain:fgf3^t26212;ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t	GSM3498553	GSM3498553: fgf3 sibling; Danio rerio; RNA Seq	GSM3498553		1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq	GEO Accession:GSM3498553	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP171998		possorted_genome_bam_fgf3_sib.bam	10X Genomics bam file	15833733894.0	159936706.0	GSM3498553 r1	0:99	A:4876827108;C:3036857735;G:3248946665;T:4560644612;N:110457774	99		4876827108	3036857735	3248946665	4560644612	110457774	SRX5087287	SRS4099390	SRA817952	GEO	Stowers Institute	1	0.89735		0.21699		0.80409		0.4894		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2018-12-02	Larval	Larval	Lateral Line	Sensory System
50725	50725	SRR8270600	SRX5087286	SRS4099389	SRP171998	PRJNA507898	Single cell RNA Seq reveals Fgf signaling dynamics during sensory hair cell regeneration	GSE123241	Transcriptome Analysis	Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells zebrafish ear and lateral line hair cells regenerate from poorly characterized proliferating support cells. Equally ill defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single cell RNA Sequencing scRNA Seq of lateral line sensory organs and uncovered five different support cell types including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self renew and new groups of genes required for hair cell differentiation. scRNA Seq analyses of fgf3 mutants in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 3 different samples: wild type fgf3 mutants and fgf3 siblings.		pubmed:30681411;pubmed:31488837	WT	GSM3498552	source name:neuromast\|age:5dpf\|tissue:neuromast\|genotype:WT\|strain:ETkrt4:EGFPSqGw57A; Tgpou4f3:GAP GFPs356t	WT	Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.	neuromast		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|genotype:WT\|strain:ETkrt4:EGFPSqGw57A;Tgpou4f3:GAP GFPs356t	GSM3498552	GSM3498552: WT; Danio rerio; RNA Seq	GSM3498552		1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq	GEO Accession:GSM3498552	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP171998		possorted_genome_bam_WT.bam	10X Genomics bam file	32918660478.0	332511722.0	GSM3498552 r1	0:99	A:10031241232;C:6365493396;G:6804558002;T:9674542542;N:42825306	99		10031241232	6365493396	6804558002	9674542542	42825306	SRX5087286	SRS4099389	SRA817952	GEO	Stowers Institute	1	0.90685		0.26503		0.79368		0.47639		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2018-12-02	Larval	Larval	Lateral Line	Sensory System
56605	56605	SRR11031290	SRX7683557	SRS6110537	SRP247442	PRJNA605021	Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2	GSE144827	Transcriptome Analysis	This dataset consists of single cell RNA seq 10X data of neuromast cells from zebrafish larvae. Posterior lateral line neuromast cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs and from Tg[Etkrt4:EGFPsqgw57A] larvae expressing EGFP in supporting cells. Overall design: A single cell RNA seq experiment of isolated neuromast cells from zebrafish larvae was performed using 10X Genomics technology to generate single cell transcriptomic profiles of supporting cells and hair cells.		pubmed:32109392	hair cells	GSM4298909	source name:zebrafish neuromast cells\|genotype:Tg[myo6b:actb1 EGFP]\|source tissue:neuromast\|developmental day:7 dpf	hair cells	The 10X Genomics core computational software Cellranger v.2.1.1 was used for alignment and processing of next generation sequencing reads of the scRNA seq data as recommended https://support.10xgenomics.com/single cell gene expression/software/overview/welcome. Genome build: GRCz11 Supplementary files format and content: Raw UMI count matrix feature x cell barcode from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format cell barcodes as tab delimited text file and feature names as tab delimited text file.	zebrafish neuromast cells	none	Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 PN #120237 from 10x Genomics. Libraries were sequenced on the HiSeq4000 Illumina with 150bp paired end sequencing. RNA Seq 10X Genomics	Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution.	genotype:Tg[myo6b:actb1 EGFP]\|source tissue:neuromast\|developmental day:7 dpf	GSM4298909	GSM4298909: hair cells; Danio rerio; RNA Seq	GSM4298909		1	Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 PN #120237 from 10x Genomics. Libraries were sequenced on the HiSeq4000 Illumina with 150bp paired end sequencing. RNA Seq 10X Genomics	GEO Accession:GSM4298909	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP247442		hair_cells_R2.fastq.gz hair_cells_R1.fastq.gz	fastq fastq	89474157378.0	505503714.0	GSM4298909 r1	0:26 1:151	A:25071099481;C:19794086212;G:19845960995;T:24749018204;N:13992486	26	151	25071099481	19794086212	19845960995	24749018204	13992486	SRX7683557	SRS6110537	SRA1038640	GEO	Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München	2	0.00294	0.9352	0.00072	0.07461	0.99358	0.81487	0.46744	0.43177	26	151	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2020-02-05	Larval	Larval	Lateral Line	Sensory System
56606	56606	SRR11031289	SRX7683556	SRS6110536	SRP247442	PRJNA605021	Epithelial planar bipolarity emerges from Notch mediated asymmetric inhibition of Emx2	GSE144827	Transcriptome Analysis	This dataset consists of single cell RNA seq 10X data of neuromast cells from zebrafish larvae. Posterior lateral line neuromast cells were isolated by fluorescence activated cell sorting FACS from the dissociated trunks of Tg[myo6b:actb1 EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair cell progenitors UHCPs and from Tg[Etkrt4:EGFPsqgw57A] larvae expressing EGFP in supporting cells. Overall design: A single cell RNA seq experiment of isolated neuromast cells from zebrafish larvae was performed using 10X Genomics technology to generate single cell transcriptomic profiles of supporting cells and hair cells.		pubmed:32109392	supporting cells	GSM4298908	source name:zebrafish neuromast cells\|genotype:Tg[Etkrt4:EGFPsqgw57A]\|source tissue:neuromast\|developmental day:7 dpf	supporting cells	The 10X Genomics core computational software Cellranger v.2.1.1 was used for alignment and processing of next generation sequencing reads of the scRNA seq data as recommended https://support.10xgenomics.com/single cell gene expression/software/overview/welcome. Genome build: GRCz11 Supplementary files format and content: Raw UMI count matrix feature x cell barcode from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format cell barcodes as tab delimited text file and feature names as tab delimited text file.	zebrafish neuromast cells	none	Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 PN #120237 from 10x Genomics. Libraries were sequenced on the HiSeq4000 Illumina with 150bp paired end sequencing. RNA Seq 10X Genomics	Standardized conditions at 28.5°C in the 0 3 x Danieau’s solution.	genotype:Tg[Etkrt4:EGFPsqgw57A]\|source tissue:neuromast\|developmental day:7 dpf	GSM4298908	GSM4298908: supporting cells; Danio rerio; RNA Seq	GSM4298908		1	Enzymatic dissociation of larval trunks and isolation of green fluorescent protein expressing cells by FAC sorting. Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 PN #120237 from 10x Genomics. Libraries were sequenced on the HiSeq4000 Illumina with 150bp paired end sequencing. RNA Seq 10X Genomics	GEO Accession:GSM4298908	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP247442		support_cells_R2.fastq.gz support_cells_R1.fastq.gz	fastq fastq	209506251249.0	1183651137.0	GSM4298908 r1	0:26 1:151	A:59676591457;C:46803384480;G:47908589489;T:55084749523;N:32936300	26	151	59676591457	46803384480	47908589489	55084749523	32936300	SRX7683556	SRS6110536	SRA1038640	GEO	Research Unit Sensory Biology and Organogenesis, Helmholtz Zentrum München	2	0.00206	0.92892	0.00042	0.04303	0.99508	0.86354	0.40312	0.45704	26	151	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2020-02-05	Larval	Larval	Lateral Line	Sensory System
59292	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		pubmed:32699896	RNA seq retina atoh7 44hpf	GSM4559534	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		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		strain:Tgatoh7:turboGFP dest1::atoh7:gapRFP\|tissue:retina\|developmental stage:44 hpf	GSM4559534	GSM4559534: RNA seq retina atoh7 44hpf; Danio rerio; RNA Seq	GSM4559534		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	SRP262311	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		18052310869	12727112571	14225357068	16105981406	450193	SRX8362742	SRS6678633	SRA1077074	GEO	Institute of Neuroscience, Chinese Academy of Sciences	1	0.89647		0.06712		0.85228		0.50102		150		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2020-05-19	Pharyngula	Embryo	Eye	Sensory System
59859	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.		pubmed:33357413	Adult Zebrafish 15	GSM4627227	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 “cellranger count” 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°C 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 30µm 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’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s 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		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C 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 30µm 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	SRP268010	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		5144837324	3453657332	3688751956	5199397147	2953681	SRX8583217	SRS6874834	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.88384		0.24019		0.78979		0.51275		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System
59860	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.		pubmed:33357413	Adult Zebrafish 14	GSM4627226	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 “cellranger count” 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°C 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 30µm 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’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s 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		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C 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 30µm 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	SRP268010	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		4767424342	3189871576	3410422503	4793151919	2718598	SRX8583216	SRS6874833	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.88242		0.24257		0.78892		0.49263		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System
59861	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.		pubmed:33357413	Adult Zebrafish 13	GSM4627225	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 “cellranger count” 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°C 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 30µm 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’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s 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		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C 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 30µm 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	SRP268010	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		4156001799	2794969042	2979050667	4233954883	2416059	SRX8583215	SRS6874832	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.88338		0.24795		0.7893		0.49627		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System
59862	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.		pubmed:33357413	Adult Zebrafish 12	GSM4627224	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 “cellranger count” 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°C 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 30µm 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’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s 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		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C 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 30µm 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	SRP268010	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		4556531984	3035955488	3233886544	4655230637	2626333	SRX8583214	SRS6874831	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.88248		0.25141		0.78782		0.49785		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System
59863	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.		pubmed:33357413	Adult Zebrafish 11	GSM4627223	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 “cellranger count” 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°C 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 30µm 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’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s 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		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C 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 30µm 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	SRP268010	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		5278772392	3561457870	3799039640	5370568922	3040886	SRX8583213	SRS6874830	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.88456		0.25211		0.7894		0.50115		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System
59864	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.		pubmed:33357413	Adult Zebrafish 8	GSM4627220	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 “cellranger count” 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°C 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 30µm 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’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s 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		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C 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 30µm 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	SRP268010	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		4325239722	2863430626	2994943270	4365215038	2369320	SRX8583210	SRS6874827	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.87211		0.29067		0.79431		0.49957		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System
59865	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.		pubmed:33357413	Adult Zebrafish 7	GSM4627219	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 “cellranger count” 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°C 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 30µm 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’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s 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		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C 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 30µm 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	SRP268010	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		3809964234	2548974567	2667179504	3866166531	2105344	SRX8583209	SRS6874826	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.87565		0.28214		0.78918		0.51085		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System
59866	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.		pubmed:33357413	Adult Zebrafish 6	GSM4627218	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 “cellranger count” 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°C 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 30µm 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’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s 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		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C 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 30µm 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	SRP268010	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		3357618948	2223130462	2352697999	3398318533	1818320	SRX8583208	SRS6874825	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.87718		0.26282		0.7838		0.50701		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System
59867	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.		pubmed:33357413	Adult Zebrafish 3	GSM4627215	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 “cellranger count” 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°C 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 30µm 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’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s 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		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C 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 30µm 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	SRP268010	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		6661186629	4423555909	4672058698	6668698022	8438282	SRX8583205	SRS6874822	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.88295		0.30604		0.79228		0.53139		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System
59868	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.		pubmed:33357413	Adult Zebrafish 2	GSM4627214	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 “cellranger count” 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°C 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 30µm 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’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s 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		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C 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 30µm 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	SRP268010	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		7365387325	5107021128	5455973330	7396374911	9957718	SRX8583204	SRS6874821	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.90152		0.22907		0.78776		0.50123		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System
59869	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.		pubmed:33357413	Adult Zebrafish 1	GSM4627213	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 “cellranger count” 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°C 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 30µm 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’ v2 platform 10X Genomics Pleasanton CA	Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s 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		1	Retinas were digested in papain 20U/ml in ox Ames at 28°C 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 30µm 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	SRP268010	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		7491507845	5131022895	5429848529	7631356264	9745315	SRX8583203	SRS6874820	SRA1089100	GEO	Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley	1	0.90363		0.22835		0.78632		0.48812		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Multi-stage	Multi-stage	Eye	Sensory System
61647	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	nrl KO	GSM4861219	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 “FilterCells” function. A global scaling normalization method “LogNormalize” 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 “FindAllMarkers” 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…	Retinal single cell suspension		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.		cell type:Retinal single cell suspension\|strain:AB\|age:5 mpf KO	GSM4861219	GSM4861219: nrl KO; Danio rerio; RNA Seq	GSM4861219		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	SRP288616		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	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	China	2020-10-26	Adult	Adult	Eye	Sensory System
61648	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	nrl KO	GSM4861219	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 “FilterCells” function. A global scaling normalization method “LogNormalize” 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 “FindAllMarkers” 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…	Retinal single cell suspension		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.		cell type:Retinal single cell suspension\|strain:AB\|age:5 mpf KO	GSM4861219	GSM4861219: nrl KO; Danio rerio; RNA Seq	GSM4861219		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	SRP288616		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	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	China	2020-10-26	Adult	Adult	Eye	Sensory System
61649	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	nrl KO	GSM4861219	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 “FilterCells” function. A global scaling normalization method “LogNormalize” 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 “FindAllMarkers” 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…	Retinal single cell suspension		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.		cell type:Retinal single cell suspension\|strain:AB\|age:5 mpf KO	GSM4861219	GSM4861219: nrl KO; Danio rerio; RNA Seq	GSM4861219		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	SRP288616		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	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	China	2020-10-26	Adult	Adult	Eye	Sensory System
61650	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	nrl KO	GSM4861219	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 “FilterCells” function. A global scaling normalization method “LogNormalize” 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 “FindAllMarkers” 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…	Retinal single cell suspension		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.		cell type:Retinal single cell suspension\|strain:AB\|age:5 mpf KO	GSM4861219	GSM4861219: nrl KO; Danio rerio; RNA Seq	GSM4861219		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	SRP288616		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	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	China	2020-10-26	Adult	Adult	Eye	Sensory System
61651	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	WT	GSM4861218	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 “FilterCells” function. A global scaling normalization method “LogNormalize” 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 “FindAllMarkers” 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…	Retinal single cell suspension		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.		cell type:Retinal single cell suspension\|strain:AB\|age:5 mpf type	GSM4861218	GSM4861218: WT; Danio rerio; RNA Seq	GSM4861218		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	SRP288616		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	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		0.60079	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2020-10-26	Adult	Adult	Eye	Sensory System
61652	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	WT	GSM4861218	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 “FilterCells” function. A global scaling normalization method “LogNormalize” 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 “FindAllMarkers” 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…	Retinal single cell suspension		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.		cell type:Retinal single cell suspension\|strain:AB\|age:5 mpf type	GSM4861218	GSM4861218: WT; Danio rerio; RNA Seq	GSM4861218		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	SRP288616		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	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		0.60453	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2020-10-26	Adult	Adult	Eye	Sensory System
61653	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	WT	GSM4861218	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 “FilterCells” function. A global scaling normalization method “LogNormalize” 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 “FindAllMarkers” 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…	Retinal single cell suspension		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.		cell type:Retinal single cell suspension\|strain:AB\|age:5 mpf type	GSM4861218	GSM4861218: WT; Danio rerio; RNA Seq	GSM4861218		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	SRP288616		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	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		0.59917	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2020-10-26	Adult	Adult	Eye	Sensory System
61654	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	WT	GSM4861218	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 “FilterCells” function. A global scaling normalization method “LogNormalize” 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 “FindAllMarkers” 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…	Retinal single cell suspension		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.		cell type:Retinal single cell suspension\|strain:AB\|age:5 mpf type	GSM4861218	GSM4861218: WT; Danio rerio; RNA Seq	GSM4861218		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	SRP288616		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	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		0.5393	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2020-10-26	Adult	Adult	Eye	Sensory System
64414	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.		pubmed:34462505	retinal cells	GSM5351368	tissue:retinal cells\|age:adult\|transgene:Tgrho:egfpja2Tg\|transgene:Tggnat2:egfpja23Tg	retinal cells	FASTQ files were generated from the raw BCL files using Illumina’s 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 …	retinal cells		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’ v3 platform following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard Illumina protocols.		age:adult\|transgene:Tgrho:egfpja2Tg\|transgene:Tggnat2:egfpja23Tg	GSM5351368	GSM5351368: retinal cells; Danio rerio; RNA Seq	GSM5351368		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	SRP322166		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	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	United States	2021-06-01	Adult	Adult	Eye	Sensory System
67897	67897	SRR17413278	SRX13584925	SRS11474973	SRP353328	PRJNA793867	A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish	GSE192947	Other	Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.		pubmed:36212030	Day7 DTR Saccule scRNAseq	GSM5769451	tissue:Regenerating adult zebrafish saccule\|strain:myo6b:hDTR\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:0.05 ng/ul Diphtheria Toxin	Day7 DTR Saccule scRNAseq	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format.	Regenerating adult zebrafish saccule		For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		strain:myo6b:hDTR\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:0.05 ng/ul Diphtheria Toxin	GSM5769451	GSM5769451: Day7 DTR Saccule scRNAseq; Danio rerio; RNA Seq	GSM5769451 r1	GSM5769451	1	For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP353328	assembly:danRer11\|intentional duplicate	Day7_DTR_S.bam	10X Genomics bam file	2977382681.0	32718491.0	GSM5769451 r1	0:91	A:897353356;C:606781567;G:635522033;T:834175973;N:3549752	91		897353356	606781567	635522033	834175973	3549752	SRX13584925	SRS11474973	SRA1351664	Shawn Burgess, NHGRI, NIH	Shawn Burgess, NHGRI, NIH	1	0.90368		0.24681		0.80545		0.63964		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_droplet	10x	United States	2022-01-03	Adult	Adult	Ear	Sensory System
67899	67899	SRR17413280	SRX13584923	SRS11474971	SRP353328	PRJNA793867	A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish	GSE192947	Other	Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.		pubmed:36212030	Day5 DTR Saccule scRNAseq	GSM5769449	tissue:Regenerating adult zebrafish saccule\|strain:myo6b:hDTR\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:0.05 ng/ul Diphtheria Toxin	Day5 DTR Saccule scRNAseq	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format.	Regenerating adult zebrafish saccule		For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		strain:myo6b:hDTR\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:0.05 ng/ul Diphtheria Toxin	GSM5769449	GSM5769449: Day5 DTR Saccule scRNAseq; Danio rerio; RNA Seq	GSM5769449 r1	GSM5769449	1	For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP353328	assembly:danRer11\|intentional duplicate	Day5_DTR_S.bam	10X Genomics bam file	2743635167.0	30149837.0	GSM5769449 r1	0:91	A:824173714;C:546471747;G:619313829;T:750434697;N:3241180	91		824173714	546471747	619313829	750434697	3241180	SRX13584923	SRS11474971	SRA1351664	Shawn Burgess, NHGRI, NIH	Shawn Burgess, NHGRI, NIH	1	0.89351		0.24046		0.79547		0.55401		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_droplet	10x	United States	2022-01-03	Adult	Adult	Ear	Sensory System
67901	67901	SRR17413282	SRX13584921	SRS11474969	SRP353328	PRJNA793867	A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish	GSE192947	Other	Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.		pubmed:36212030	Day4 DTR Saccule scRNAseq	GSM5769447	tissue:Regenerating adult zebrafish saccule\|strain:myo6b:hDTR\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:0.05 ng/ul Diphtheria Toxin	Day4 DTR Saccule scRNAseq	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format.	Regenerating adult zebrafish saccule		For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		strain:myo6b:hDTR\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:0.05 ng/ul Diphtheria Toxin	GSM5769447	GSM5769447: Day4 DTR Saccule scRNAseq; Danio rerio; RNA Seq	GSM5769447 r1	GSM5769447	1	For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP353328	assembly:danRer11\|intentional duplicate	Day4_DTR_S.bam	10X Genomics bam file	2212530229.0	24313519.0	GSM5769447 r1	0:91	A:662453123;C:446920712;G:485929921;T:614604891;N:2621582	91		662453123	446920712	485929921	614604891	2621582	SRX13584921	SRS11474969	SRA1351664	Shawn Burgess, NHGRI, NIH	Shawn Burgess, NHGRI, NIH	1	0.90066		0.25447		0.80255		0.6844		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_droplet	10x	United States	2022-01-03	Adult	Adult	Ear	Sensory System
67903	67903	SRR17413284	SRX13584919	SRS11474967	SRP353328	PRJNA793867	A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish	GSE192947	Other	Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.		pubmed:36212030	Untreated DTR Saccule scRNAseq	GSM5769445	tissue:Untreated DTR saccule\|strain:myo6b:hDTR\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:N1	Untreated DTR Saccule scRNAseq	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format.	Untreated DTR saccule		For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		strain:myo6b:hDTR\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:N1	GSM5769445	GSM5769445: Untreated DTR Saccule scRNAseq; Danio rerio; RNA Seq	GSM5769445 r1	GSM5769445	1	For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP353328	assembly:danRer11\|intentional duplicate	DTR_S.bam	10X Genomics bam file	2688090860.0	29539460.0	GSM5769445 r1	0:91	A:809804738;C:543094593;G:588432755;T:743564790;N:3193984	91		809804738	543094593	588432755	743564790	3193984	SRX13584919	SRS11474967	SRA1351664	Shawn Burgess, NHGRI, NIH	Shawn Burgess, NHGRI, NIH	1	0.91096		0.22811		0.82672		0.70832		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_droplet	10x	United States	2022-01-03	Adult	Adult	Ear	Sensory System
67905	67905	SRR17413286	SRX13584917	SRS11474965	SRP353328	PRJNA793867	A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish	GSE192947	Other	Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.		pubmed:36212030	Day4 WT Saccule scRNAseq	GSM5769443	tissue:Day 4 post DT wild type saccule\|strain:TAB 5\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:0.05 ng/ul Diphtheria Toxin	Day4 WT Saccule scRNAseq	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format.	Day 4 post DT wild type saccule		For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		strain:TAB 5\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:0.05 ng/ul Diphtheria Toxin	GSM5769443	GSM5769443: Day4 WT Saccule scRNAseq; Danio rerio; RNA Seq	GSM5769443 r1	GSM5769443	1	For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP353328	assembly:danRer11\|intentional duplicate	Day4_WT_S.bam	10X Genomics bam file	2443716548.0	26854028.0	GSM5769443 r1	0:91	A:723842022;C:489011349;G:542403323;T:685572222;N:2887632	91		723842022	489011349	542403323	685572222	2887632	SRX13584917	SRS11474965	SRA1351664	Shawn Burgess, NHGRI, NIH	Shawn Burgess, NHGRI, NIH	1	0.90861		0.21636		0.82193		0.70068		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_droplet	10x	United States	2022-01-03	Adult	Adult	Ear	Sensory System
67907	67907	SRR17413288	SRX13584915	SRS11474963	SRP353328	PRJNA793867	A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish	GSE192947	Other	Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.		pubmed:36212030	Untreated WT Saccule scRNAseq	GSM5769441	tissue:Untreated wild type saccule\|strain:TAB 5\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:N1	Untreated WT Saccule scRNAseq	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format.	Untreated wild type saccule		For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		strain:TAB 5\|embryo age:6 mpf 10 mpf adult zebrafish\|treatment:N1	GSM5769441	GSM5769441: Untreated WT Saccule scRNAseq; Danio rerio; RNA Seq	GSM5769441 r1	GSM5769441	1	For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP353328	assembly:danRer11\|intentional duplicate	WT_S.bam	10X Genomics bam file	2371392114.0	26059254.0	GSM5769441 r1	0:91	A:717065741;C:489303110;G:485561048;T:676653943;N:2808272	91		717065741	489303110	485561048	676653943	2808272	SRX13584915	SRS11474963	SRA1351664	Shawn Burgess, NHGRI, NIH	Shawn Burgess, NHGRI, NIH	1	0.92038		0.23016		0.82771		0.61794		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_droplet	10x	United States	2022-01-03	Adult	Adult	Ear	Sensory System
68516	68516	SRR17900890	SRX14059608	SRS11892528	SRP358576	PRJNA803902	High resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration	GSE196211	Transcriptome Analysis	NOT PROVIDED; REQUESTED Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 7 different samples: homeo 0min post neomycin 30min 1hr 3hr 5hr 10hr		pubmed:35316618	10hr post neomycin	GSM5862805	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:10hr post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	10hr post neomycin	Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.	neuromast		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|treatment/time point:10hr post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	GSM5862805	GSM5862805: 10hr post neomycin; Danio rerio; RNA Seq	GSM5862805 r1	GSM5862805	1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	10hr_possorted_genome_bam.bam	10X Genomics bam file	11755529379.0	118742721.0	GSM5862805 r1	0:99	A:3815855652;C:2300159508;G:2649552225;T:2989724050;N:237944	99		3815855652	2300159508	2649552225	2989724050	237944	SRX14059608	SRS11892528	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.88584		0.18938		0.81968		0.57795		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68517	68517	SRR17900891	SRX14059607	SRS11892527	SRP358576	PRJNA803902	High resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration	GSE196211	Transcriptome Analysis	NOT PROVIDED; REQUESTED Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 7 different samples: homeo 0min post neomycin 30min 1hr 3hr 5hr 10hr		pubmed:35316618	5hr post neomycin	GSM5862804	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:5hr post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	5hr post neomycin	Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.	neuromast		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|treatment/time point:5hr post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	GSM5862804	GSM5862804: 5hr post neomycin; Danio rerio; RNA Seq	GSM5862804 r1	GSM5862804	1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	5hr_possorted_genome_bam.bam	10X Genomics bam file	10868082885.0	109778615.0	GSM5862804 r1	0:99	A:3267489116;C:2251000050;G:2404850523;T:2944522797;N:220399	99		3267489116	2251000050	2404850523	2944522797	220399	SRX14059607	SRS11892527	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.93721		0.18379		0.81852		0.54714		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68518	68518	SRR17900892	SRX14059606	SRS11892526	SRP358576	PRJNA803902	High resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration	GSE196211	Transcriptome Analysis	NOT PROVIDED; REQUESTED Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 7 different samples: homeo 0min post neomycin 30min 1hr 3hr 5hr 10hr		pubmed:35316618	3hr post neomycin	GSM5862803	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:3hr post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	3hr post neomycin	Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.	neuromast		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|treatment/time point:3hr post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	GSM5862803	GSM5862803: 3hr post neomycin; Danio rerio; RNA Seq	GSM5862803 r1	GSM5862803	1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	3hr_possorted_genome_bam.bam	10X Genomics bam file	30818123028.0	311294172.0	GSM5862803 r1	0:99	A:9348916523;C:6246488965;G:6684733854;T:8511548264;N:26435422	99		9348916523	6246488965	6684733854	8511548264	26435422	SRX14059606	SRS11892526	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.92667		0.21879		0.80736		0.52626		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68519	68519	SRR17900893	SRX14059605	SRS11892525	SRP358576	PRJNA803902	High resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration	GSE196211	Transcriptome Analysis	NOT PROVIDED; REQUESTED Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 7 different samples: homeo 0min post neomycin 30min 1hr 3hr 5hr 10hr		pubmed:35316618	1hr post neomycin	GSM5862802	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:1hr post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	1hr post neomycin	Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.	neuromast		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|treatment/time point:1hr post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	GSM5862802	GSM5862802: 1hr post neomycin; Danio rerio; RNA Seq	GSM5862802 r1	GSM5862802	1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	1hr_possorted_genome_bam.bam	10X Genomics bam file	17016505902.0	171883898.0	GSM5862802 r1	0:99	A:5220935048;C:3448280771;G:3717726451;T:4625338927;N:4224705	99		5220935048	3448280771	3717726451	4625338927	4224705	SRX14059605	SRS11892525	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.92365		0.21642		0.83339		0.55101		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68520	68520	SRR17900894	SRX14059604	SRS11892524	SRP358576	PRJNA803902	High resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration	GSE196211	Transcriptome Analysis	NOT PROVIDED; REQUESTED Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 7 different samples: homeo 0min post neomycin 30min 1hr 3hr 5hr 10hr		pubmed:35316618	30min post neomycin	GSM5862801	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:30min post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	30min post neomycin	Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.	neuromast		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|treatment/time point:30min post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	GSM5862801	GSM5862801: 30min post neomycin; Danio rerio; RNA Seq	GSM5862801 r1	GSM5862801	1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	30min_possorted_genome_bam.bam	10X Genomics bam file	15228653913.0	153824787.0	GSM5862801 r1	0:99	A:4774203586;C:3007224980;G:3233337864;T:4213847766;N:39717	99		4774203586	3007224980	3233337864	4213847766	39717	SRX14059604	SRS11892524	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.92255		0.24454		0.83128		0.55089		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68521	68521	SRR17900895	SRX14059603	SRS11892523	SRP358576	PRJNA803902	High resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration	GSE196211	Transcriptome Analysis	NOT PROVIDED; REQUESTED Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 7 different samples: homeo 0min post neomycin 30min 1hr 3hr 5hr 10hr		pubmed:35316618	0min post neomycin	GSM5862800	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:0min post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	0min post neomycin	Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.	neuromast		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|treatment/time point:0min post neomycin\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	GSM5862800	GSM5862800: 0min post neomycin; Danio rerio; RNA Seq	GSM5862800 r1	GSM5862800	1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	0min_possorted_genome_bam.bam	10X Genomics bam file	16733371941.0	169023959.0	GSM5862800 r1	0:99	A:5247307437;C:3263851520;G:3538128507;T:4684038782;N:45695	99		5247307437	3263851520	3538128507	4684038782	45695	SRX14059603	SRS11892523	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.91636		0.24042		0.82875		0.54973		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
68522	68522	SRR17900896	SRX14059602	SRS11892522	SRP358576	PRJNA803902	High resolution single cell transcriptome analysis of zebrafish sensory hair cell regeneration	GSE196211	Transcriptome Analysis	NOT PROVIDED; REQUESTED Overall design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 7 different samples: homeo 0min post neomycin 30min 1hr 3hr 5hr 10hr		pubmed:35316618	homeo	GSM5862799	source name:neuromast\|age:5dpf\|tissue:neuromast\|treatment/time point:homeo\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	homeo	Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Genome build: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.	neuromast		Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		age:5dpf\|tissue:neuromast\|treatment/time point:homeo\|strain:Tgmyo6b:H2B mScarlet I/Et20:GFP	GSM5862799	GSM5862799: homeo; Danio rerio; RNA Seq	GSM5862799 r1	GSM5862799	1	Presumptive neuromast cells GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v2 chemistry Droplet based scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP358576	assembly:danRer10\|intentional duplicate	homeo_possorted_genome_bam.bam	10X Genomics bam file	15150832686.0	153038714.0	GSM5862799 r1	0:99	A:4484040403;C:3115374217;G:3333967460;T:4132413883;N:85036723	99		4484040403	3115374217	3333967460	4132413883	85036723	SRX14059602	SRS11892522	SRA1367859	Piotrowski Lab, Stowers Institute for Medical Research	Piotrowski Lab, Stowers Institute for Medical Research	1	0.93926		0.18875		0.80762		0.50625		99		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-02-06	Larval	Larval	Lateral Line	Sensory System
69645	69645	SRR19084407	SRX15154229	SRS12896750	SRP373610	PRJNA835051	The regeneration responsive careg element monitors activation of Müller 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 Müller 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		pubmed:37138703	10dpMNU 2	GSM6106359	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		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’ Library and Gel Bead Kit v3 10X Genomics.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP373610	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		17183149218	10280467884	13561914128	13318350579	15885348	SRX15154229	SRS12896750	SRA1420445	University of Fribourg	University of Fribourg	1	0.86617		0.34213		0.86312		0.64043		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2022-05-04	Adult	Adult	Eye	Sensory System
69646	69646	SRR19084408	SRX15154228	SRS12896749	SRP373610	PRJNA835051	The regeneration responsive careg element monitors activation of Müller 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 Müller 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		pubmed:37138703	10dpMNU 1	GSM6106358	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		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’ Library and Gel Bead Kit v3 10X Genomics.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP373610	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		14388514140	10285005448	11549735765	12919526731	14354702	SRX15154228	SRS12896749	SRA1420445	University of Fribourg	University of Fribourg	1	0.88102		0.31782		0.79571		0.6372		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2022-05-04	Adult	Adult	Eye	Sensory System
69647	69647	SRR19084409	SRX15154227	SRS12896748	SRP373610	PRJNA835051	The regeneration responsive careg element monitors activation of Müller 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 Müller 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		pubmed:37138703	7dpMNU 2	GSM6106357	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		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’ Library and Gel Bead Kit v3 10X Genomics.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP373610	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		16865813537	9568375873	11541078798	13107697081	14938565	SRX15154227	SRS12896748	SRA1420445	University of Fribourg	University of Fribourg	1	0.88078		0.36957		0.83493		0.66026		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2022-05-04	Adult	Adult	Eye	Sensory System
69648	69648	SRR19084410	SRX15154226	SRS12896747	SRP373610	PRJNA835051	The regeneration responsive careg element monitors activation of Müller 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 Müller 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		pubmed:37138703	7dpMNU 1	GSM6106356	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		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’ Library and Gel Bead Kit v3 10X Genomics.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP373610	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		14541918290	10501492165	11630509992	13245294913	14653770	SRX15154226	SRS12896747	SRA1420445	University of Fribourg	University of Fribourg	1	0.89836		0.32967		0.79504		0.53681		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2022-05-04	Adult	Adult	Eye	Sensory System
69649	69649	SRR19084411	SRX15154225	SRS12896746	SRP373610	PRJNA835051	The regeneration responsive careg element monitors activation of Müller 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 Müller 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		pubmed:37138703	3dpMNU 2	GSM6106355	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		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’ Library and Gel Bead Kit v3 10X Genomics.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP373610	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		14174450101	9743573685	10481602026	13390478656	14038977	SRX15154225	SRS12896746	SRA1420445	University of Fribourg	University of Fribourg	1	0.89901		0.32665		0.78362		0.60733		89		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2022-05-04	Adult	Adult	Eye	Sensory System
69650	69650	SRR19084412	SRX15154224	SRS12896745	SRP373610	PRJNA835051	The regeneration responsive careg element monitors activation of Müller 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 Müller 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		pubmed:37138703	3dpMNU 1	GSM6106354	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		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’ Library and Gel Bead Kit v3 10X Genomics.		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. Libraries for scRNA seq were prepared using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP373610	assembly:GRCz11\|intentional duplicate\|dangling references:treat as unmapped	3dp1_possorted_genome_bam.bam	10X Genomics bam file	51272764697.0	566478602.0	GSM6106354 r1	0:90.51	A:14704198694;C:10962905971;G:12742686582;T:12848062367;N:14911083	90		14704198694	10962905971	12742686582	12848062367	14911083	SRX15154224	SRS12896745	SRA1420445	University of Fribourg	University of Fribourg	1	0.88519		0.29735		0.82749		0.56205		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2022-05-04	Adult	Adult	Eye	Sensory System
69651	69651	SRR19084413	SRX15154223	SRS12896744	SRP373610	PRJNA835051	The regeneration responsive careg element monitors activation of Müller 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 Müller 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		pubmed:37138703	uninjured 2	GSM6106353	source name:retina\|tissue:adult retina\|strain:Tgcareg:EGFP\|treatment:1h treatment with heat inactivated MNU\|geo loc name:missing\|collection date:missing	uninjured 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		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’ Library and Gel Bead Kit v3 10X Genomics.		tissue:adult retina\|strain:Tgcareg:EGFP\|treatment:1h treatment with heat inactivated MNU	GSM6106353	GSM6106353: uninjured 2; Danio rerio; RNA Seq	GSM6106353 r1	GSM6106353	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP373610	assembly:GRCz11\|intentional duplicate\|dangling references:treat as unmapped	ctrl2_possorted_genome_bam.bam	10X Genomics bam file	57621646933.0	636766824.0	GSM6106353 r1	0:90.49	A:17885101259;C:11398086500;G:13905144263;T:14416474331;N:16840580	90		17885101259	11398086500	13905144263	14416474331	16840580	SRX15154223	SRS12896744	SRA1420445	University of Fribourg	University of Fribourg	1	0.86467		0.39517		0.87028		0.69195		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2022-05-04	Adult	Adult	Eye	Sensory System
69652	69652	SRR19084414	SRX15154222	SRS12896743	SRP373610	PRJNA835051	The regeneration responsive careg element monitors activation of Müller 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 Müller 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		pubmed:37138703	uninjured 1	GSM6106352	source name:retina\|tissue:adult retina\|strain:Tgcareg:EGFP\|treatment:1h treatment with heat inactivated MNU\|geo loc name:missing\|collection date:missing	uninjured 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		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’ Library and Gel Bead Kit v3 10X Genomics.		tissue:adult retina\|strain:Tgcareg:EGFP\|treatment:1h treatment with heat inactivated MNU	GSM6106352	GSM6106352: uninjured 1; Danio rerio; RNA Seq	GSM6106352 r1	GSM6106352	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP373610	assembly:GRCz11\|intentional duplicate\|dangling references:treat as unmapped	ctrl1_possorted_genome_bam.bam	10X Genomics bam file	43888459732.0	485067105.0	GSM6106352 r1	0:90.48	A:13055406117;C:8931800171;G:9711907132;T:12176465725;N:12880587	90		13055406117	8931800171	9711907132	12176465725	12880587	SRX15154222	SRS12896743	SRA1420445	University of Fribourg	University of Fribourg	1	0.88385		0.35485		0.8089		0.55076		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2022-05-04	Adult	Adult	Eye	Sensory System

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