metadata: run_metadata: 601 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue

601 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation = "Brain"

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.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
28725	28725	SRR26623262	SRX22323921	SRS19374450	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Lineage tracing rep1 cirbpb scars	GSM7875190	source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 cirbpb scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875190	GSM7875190: Lineage tracing rep1 cirbpb scars; Danio rerio; OTHER	GSM7875190 r1	GSM7875190	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP469552	loader:fastq load.py	lin1_cirbpb_scar_R1.fastq.gz lin1_cirbpb_scar_R2.fastq.gz	fastq fastq	157576336.0	949552.0	GSM7875190 r1												SRX22323921	SRS19374450	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00141	0.78069	0.00053	0.00877	0.99857	0.97822	0.33536	0.05199	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28726	28726	SRR26623263	SRX22323920	SRS19374449	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Lineage tracing rep1 cfl1 scars	GSM7875189	source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 cfl1 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875189	GSM7875189: Lineage tracing rep1 cfl1 scars; Danio rerio; OTHER	GSM7875189 r1	GSM7875189	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP469552	loader:fastq load.py	lin1_cfl1_scar_R2.fastq.gz lin1_cfl1_scar_R1.fastq.gz	fastq fastq	381453696.0	2184402.0	GSM7875189 r1												SRX22323920	SRS19374449	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.0002	0.91626	0.00014	0.00132	0.99987	0.99726	0.16666	0.56363	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28727	28727	SRR26623264	SRX22323919	SRS19374448	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Lineage tracing rep1 actb2 scars	GSM7875188	source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 actb2 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875188	GSM7875188: Lineage tracing rep1 actb2 scars; Danio rerio; OTHER	GSM7875188 r1	GSM7875188	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP469552	loader:fastq load.py	lin1_actb2_scar_R1.fastq.gz lin1_actb2_scar_R2.fastq.gz	fastq fastq	491682118.0	2851156.0	GSM7875188 r1												SRX22323919	SRS19374448	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00051	0.41901	0.00032	0.0029	0.99945	0.99182	0.57575	0.007	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28728	28728	SRR26623265	SRX22323918	SRS19374446	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Lineage tracing rep1 actb1 scars	GSM7875187	source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 actb1 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875187	GSM7875187: Lineage tracing rep1 actb1 scars; Danio rerio; OTHER	GSM7875187 r1	GSM7875187	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP469552	loader:fastq load.py	lin1_actb1_scar_R1.fastq.gz lin1_actb1_scar_R2.fastq.gz	fastq fastq	390405832.0	2283319.0	GSM7875187 r1												SRX22323918	SRS19374446	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00038	0.73548	0.00017	0.00057	0.99963	0.99571	0.29729	0.00243	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28729	28729	SRR26623266	SRX22323917	SRS19374447	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Brain 23 telencephalon Notch inhibition scSLAMseq	GSM7875186	source name:adult brain\|tissue:adult brain\|tissue region:telencephalon\|cell type:mixed tissue dissociation\|genotype:wildtype\|treatment:Notch inhibition DAPT\|geo loc name:missing\|collection date:missing	Brain 23 telencephalon Notch inhibition scSLAMseq	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq	adult brain	Notch inhibiton: zebrafish were incubated in a water bath containing system water with 50 µM DAPT Gamma Secretase Inhibitor Sigma Aldrich for 48 hours.	The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions …		tissue:adult brain\|tissue region:telencephalon\|cell type:mixed tissue dissociation\|genotype:wildtype\|treatment:Notch inhibition DAPT	GSM7875186	GSM7875186: Brain 23 telencephalon Notch inhibition scSLAMseq; Danio rerio; OTHER	GSM7875186 r1	GSM7875186	1	The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions …		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469552	loader:fastq load.py	b23_ni_tre_R1.fastq.gz b23_ni_tre_R2.fastq.gz	fastq fastq	62392458570.0	271271559.0	GSM7875186 r1	0:28 1:202	A:18682905645;C:13783082970;G:14751373116;T:15161083446;N:14013393	28	202			18682905645	13783082970	14751373116	15161083446	14013393	SRX22323917	SRS19374447	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.01404	0.82351	0.00466	0.1026	0.99129	0.86774	0.36033	0.67345	28	202	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28730	28730	SRR26623267	SRX22323916	SRS19374445	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Brain 22 telencephalon control scSLAMseq	GSM7875185	source name:adult brain\|tissue:adult brain\|tissue region:telencephalon\|cell type:mixed tissue dissociation\|genotype:wildtype\|treatment:Control DMSO\|geo loc name:missing\|collection date:missing	Brain 22 telencephalon control scSLAMseq	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq	adult brain	Control for Notch inhibition: zebrafish were incubated in a water bath containing system water with 1:200 diluted DMSO for 48 hours.	The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions …		tissue:adult brain\|tissue region:telencephalon\|cell type:mixed tissue dissociation\|genotype:wildtype\|treatment:Control DMSO	GSM7875185	GSM7875185: Brain 22 telencephalon control scSLAMseq; Danio rerio; OTHER	GSM7875185 r1	GSM7875185	1	The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions …		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469552	loader:fastq load.py	b22_ni_con_R1.fastq.gz b22_ni_con_R2.fastq.gz	fastq fastq	59793114490.0	259970063.0	GSM7875185 r1	0:28 1:202	A:18600519530;C:12714987967;G:14147370465;T:14316863915;N:13372613	28	202			18600519530	12714987967	14147370465	14316863915	13372613	SRX22323916	SRS19374445	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.01402	0.79448	0.00498	0.11405	0.99074	0.8518	0.39874	0.67082	28	202	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28754	28754	SRR26623291	SRX22323897	SRS19374426	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Lineage tracing rep2 ube2e1 scars	GSM7875196	source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep2 ube2e1 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875196	GSM7875196: Lineage tracing rep2 ube2e1 scars; Danio rerio; OTHER	GSM7875196 r1	GSM7875196	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469552	loader:fastq load.py	lin2_ube2e1_scar_R1.fastq.gz lin2_ube2e1_scar_R2.fastq.gz	fastq fastq	213092161.0	1190459.0	GSM7875196 r1												SRX22323897	SRS19374426	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00752	0.90776	0.00286	0.01739	0.99346	0.95444	0.46002	0.96817	28	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28755	28755	SRR26623292	SRX22323896	SRS19374425	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Lineage tracing rep2 rpl39 scars	GSM7875195	source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep2 rpl39 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875195	GSM7875195: Lineage tracing rep2 rpl39 scars; Danio rerio; OTHER	GSM7875195 r1	GSM7875195	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469552	loader:fastq load.py	lin2_rpl39_scar_R2.fastq.gz lin2_rpl39_scar_R1.fastq.gz	fastq fastq	1023403502.0	5717338.0	GSM7875195 r1												SRX22323896	SRS19374425	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00086	0.83744	0.0003	0.00337	0.99845	0.97057	0.26605	0.40241	28	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28756	28756	SRR26623293	SRX22323895	SRS19374424	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Lineage tracing rep2 cirbpb scars	GSM7875194	source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep2 cirbpb scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875194	GSM7875194: Lineage tracing rep2 cirbpb scars; Danio rerio; OTHER	GSM7875194 r1	GSM7875194	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469552	loader:fastq load.py	lin2_cirbpb_scar_R1.fastq.gz lin2_cirbpb_scar_R2.fastq.gz	fastq fastq	276120388.0	1542572.0	GSM7875194 r1												SRX22323895	SRS19374424	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00206	0.80328	0.00078	0.00662	0.9975	0.98039	0.55421	0.0258	28	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28757	28757	SRR26623294	SRX22323894	SRS19374423	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Lineage tracing rep2 cfl1 scars	GSM7875193	source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep2 cfl1 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875193	GSM7875193: Lineage tracing rep2 cfl1 scars; Danio rerio; OTHER	GSM7875193 r1	GSM7875193	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469552	loader:fastq load.py	lin2_cfl1_scar_R1.fastq.gz lin2_cfl1_scar_R2.fastq.gz	fastq fastq	791318009.0	4420771.0	GSM7875193 r1												SRX22323894	SRS19374423	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00067	0.46079	0.00055	0.16353	0.99965	0.99332	0.52631	0.44939	28	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28758	28758	SRR26623295	SRX22323893	SRS19374421	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Lineage tracing rep1 ube2e1 scars	GSM7875192	source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 ube2e1 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875192	GSM7875192: Lineage tracing rep1 ube2e1 scars; Danio rerio; OTHER	GSM7875192 r1	GSM7875192	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP469552	loader:fastq load.py	lin1_ube2e1_scar_R1.fastq.gz lin1_ube2e1_scar_R2.fastq.gz	fastq fastq	99407618.0	601781.0	GSM7875192 r1												SRX22323893	SRS19374421	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00657	0.84532	0.00205	0.03049	0.99537	0.95286	0.43306	0.19203	28	150	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28759	28759	SRR26623296	SRX22323892	SRS19374422	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956	Lineage tracing rep1 rpl39 scars	GSM7875191	source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 rpl39 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875191	GSM7875191: Lineage tracing rep1 rpl39 scars; Danio rerio; OTHER	GSM7875191 r1	GSM7875191	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP469552	loader:fastq load.py	lin1_rpl39_scar_R1.fastq.gz lin1_rpl39_scar_R2.fastq.gz	fastq fastq	401898718.0	2276836.0	GSM7875191 r1												SRX22323892	SRS19374422	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00037	0.2642	0.00015	0.00086	0.99922	0.99026	0.23076	0.42455	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
34508	34508	SRR32041235	SRX27390499	SRS23823272	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI]+VC 3 group	Cr+VC 3	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 14\|health state:health\|sample type:tissue\|lep:Cr+VC 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300476	EHK0300476	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202		Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz	fastq fastq	6579236402.0	21785551.0	Cr+VC 3.R1.raw.fastq.gz	0:151 1:151	A:1950296368;C:1342383640;G:1373591474;T:1912893257;N:71663	151	151			1950296368	1342383640	1373591474	1912893257	71663	SRX27390499	SRS23823272	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34509	34509	SRR32041236	SRX27390498	SRS23823271	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI]+VC 2 group	Cr+VC 2	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 14\|health state:health\|sample type:tissue\|lep:Cr+VC 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300475	EHK0300475	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202		Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz	fastq fastq	7431192898.0	24606599.0	Cr+VC 2.R1.raw.fastq.gz	0:151 1:151	A:2185434880;C:1533450452;G:1567401090;T:2144825061;N:81415	151	151			2185434880	1533450452	1567401090	2144825061	81415	SRX27390498	SRS23823271	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34510	34510	SRR32041237	SRX27390497	SRS23823270	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI]+VC 1 group	Cr+VC 1	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 14\|health state:health\|sample type:tissue\|lep:Cr+VC 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300474	EHK0300474	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202		Cr+VC-1.R1.raw.fastq.gz Cr+VC-1.R2.raw.fastq.gz	fastq fastq	6385666180.0	21144590.0	Cr+VC 1.R1.raw.fastq.gz	0:151 1:151	A:1864936934;C:1329491594;G:1363211111;T:1827956599;N:69942	151	151			1864936934	1329491594	1363211111	1827956599	69942	SRX27390497	SRS23823270	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34511	34511	SRR32041238	SRX27390496	SRS23823269	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI] 3 group	Cr 3	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 13\|health state:health\|sample type:tissue\|lep:Cr 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300473	EHK0300473	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202		Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz	fastq fastq	6339933716.0	20993158.0	Cr 3.R1.raw.fastq.gz	0:151 1:151	A:1873178321;C:1296125569;G:1333622723;T:1836939106;N:67997	151	151			1873178321	1296125569	1333622723	1836939106	67997	SRX27390496	SRS23823269	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34512	34512	SRR32041239	SRX27390495	SRS23823268	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI] 2 group	Cr 2	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 13\|health state:health\|sample type:tissue\|lep:Cr 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300472	EHK0300472	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202		Cr-2.R1.raw.fastq.gz Cr-2.R2.raw.fastq.gz	fastq fastq	6461518010.0	21395755.0	Cr 2.R1.raw.fastq.gz	0:151 1:151	A:1878799067;C:1352321588;G:1386809443;T:1843520259;N:67653	151	151			1878799067	1352321588	1386809443	1843520259	67653	SRX27390495	SRS23823268	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34513	34513	SRR32041240	SRX27390494	SRS23823267	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI] 1 group	Cr 1	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 13\|health state:health\|sample type:tissue\|lep:Cr 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300471	EHK0300471	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202		Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz	fastq fastq	7143701582.0	23654641.0	Cr 1.R1.raw.fastq.gz	0:151 1:151	A:1955056767;C:1615392059;G:1650478323;T:1922695182;N:79251	151	151			1955056767	1615392059	1650478323	1922695182	79251	SRX27390494	SRS23823267	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34514	34514	SRR32041241	SRX27390493	SRS23823266	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			control 3 group	Con 3	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 12\|health state:health\|sample type:tissue\|lep:Con 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300470	EHK0300470	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202		Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz	fastq fastq	6474159730.0	21437615.0	Con 3.R1.raw.fastq.gz	0:151 1:151	A:1937289968;C:1298659806;G:1337603954;T:1900535989;N:70013	151	151			1937289968	1298659806	1337603954	1900535989	70013	SRX27390493	SRS23823266	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34515	34515	SRR32041242	SRX27390492	SRS23823265	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			control 2 group	Con 2	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 12\|health state:health\|sample type:tissue\|lep:Con 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300469	EHK0300469	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202		Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz	fastq fastq	8372440828.0	27723314.0	Con 2.R1.raw.fastq.gz	0:151 1:151	A:2235968446;C:1933538809;G:1977416201;T:2225425413;N:91959	151	151			2235968446	1933538809	1977416201	2225425413	91959	SRX27390492	SRS23823265	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34516	34516	SRR32041243	SRX27390491	SRS23823264	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			control 1 group	Con 1	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 12\|health state:health\|sample type:tissue\|lep:Con 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300468	EHK0300468	normal			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202		Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz	fastq fastq	6527063486.0	21612793.0	Con 1.R1.raw.fastq.gz	0:151 1:151	A:1939230604;C:1326702799;G:1357063348;T:1903995450;N:71285	151	151			1939230604	1326702799	1357063348	1903995450	71285	SRX27390491	SRS23823264	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
35830	35830	SRR33092387	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM3_S4_L001_I1_001.fastq.gz DM3_S4_L001_I2_001.fastq.gz DM3_S4_L001_R1_001.fastq.gz DM3_S4_L001_R2_001.fastq.gz	fastq fastq fastq fastq	11107731642.0	80490809.0	GSM8902567 r1	0:10 1:10 2:28 3:90	A:2157723967;C:1504121492;G:1825572140;T:1756490239;N:264972	10	10	28	90	2157723967	1504121492	1825572140	1756490239	264972	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35831	35831	SRR33092396	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM1_S8_L001_I1_001.fastq.gz DM1_S8_L001_R1_001.fastq.gz DM1_S8_L001_R2_001.fastq.gz	fastq fastq fastq	8767935982.0	69038866.0	GSM8902567 r9	0:8 1:28 2:91	A:1900494869;C:1290834687;G:1472019387;T:1618958908;N:228955	8	28	91		1900494869	1290834687	1472019387	1618958908	228955	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35832	35832	SRR33092397	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM6_S5_L002_I1_001.fastq.gz DM6_S5_L002_I2_001.fastq.gz DM6_S5_L002_R1_001.fastq.gz DM6_S5_L002_R2_001.fastq.gz	fastq fastq fastq fastq	9191569902.0	66605579.0	GSM8902567 r8	0:10 1:10 2:28 3:90	A:1725225973;C:1333554410;G:1502913160;T:1432625042;N:183525	10	10	28	90	1725225973	1333554410	1502913160	1432625042	183525	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35833	35833	SRR33092398	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM6_S5_L001_I1_001.fastq.gz DM6_S5_L001_I2_001.fastq.gz DM6_S5_L001_R1_001.fastq.gz DM6_S5_L001_R2_001.fastq.gz	fastq fastq fastq fastq	9182505648.0	66539896.0	GSM8902567 r7	0:10 1:10 2:28 3:90	A:1723464701;C:1332487233;G:1501026049;T:1431438610;N:174047	10	10	28	90	1723464701	1332487233	1501026049	1431438610	174047	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35834	35834	SRR33092399	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM5_S4_L002_I1_001.fastq.gz DM5_S4_L002_I2_001.fastq.gz DM5_S4_L002_R1_001.fastq.gz DM5_S4_L002_R2_001.fastq.gz	fastq fastq fastq fastq	8580819162.0	62179849.0	GSM8902567 r6	0:10 1:10 2:28 3:90	A:1587762735;C:1253245062;G:1408923693;T:1346083547;N:171373	10	10	28	90	1587762735	1253245062	1408923693	1346083547	171373	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35835	35835	SRR33092400	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM5_S4_L001_I1_001.fastq.gz DM5_S4_L001_I2_001.fastq.gz DM5_S4_L001_R1_001.fastq.gz DM5_S4_L001_R2_001.fastq.gz	fastq fastq fastq fastq	8573531934.0	62127043.0	GSM8902567 r5	0:10 1:10 2:28 3:90	A:1586630090;C:1252294774;G:1407253665;T:1345091343;N:163998	10	10	28	90	1586630090	1252294774	1407253665	1345091343	163998	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35836	35836	SRR33092401	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM4_S5_L002_I1_001.fastq.gz DM4_S5_L002_I2_001.fastq.gz DM4_S5_L002_R1_001.fastq.gz DM4_S5_L002_R2_001.fastq.gz	fastq fastq fastq fastq	11397415308.0	82589966.0	GSM8902567 r4	0:10 1:10 2:28 3:90	A:2216636094;C:1527643231;G:1900622198;T:1787851155;N:344262	10	10	28	90	2216636094	1527643231	1900622198	1787851155	344262	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35837	35837	SRR33092402	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM4_S5_L001_I1_001.fastq.gz DM4_S5_L001_I2_001.fastq.gz DM4_S5_L001_R1_001.fastq.gz DM4_S5_L001_R2_001.fastq.gz	fastq fastq fastq fastq	11531255988.0	83559826.0	GSM8902567 r3	0:10 1:10 2:28 3:90	A:2239272402;C:1547657194;G:1925092927;T:1808081258;N:280559	10	10	28	90	2239272402	1547657194	1925092927	1808081258	280559	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35838	35838	SRR33092403	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM3_S4_L002_I1_001.fastq.gz DM3_S4_L002_I2_001.fastq.gz DM3_S4_L002_R1_001.fastq.gz DM3_S4_L002_R2_001.fastq.gz	fastq fastq fastq fastq	10988645094.0	79627863.0	GSM8902567 r2	0:10 1:10 2:28 3:90	A:2137568981;C:1486116359;G:1804028894;T:1738462802;N:330634	10	10	28	90	2137568981	1486116359	1804028894	1738462802	330634	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35839	35839	SRR33092404	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM2_S9_L002_I1_001.fastq.gz DM2_S9_L002_R1_001.fastq.gz DM2_S9_L002_R2_001.fastq.gz	fastq fastq fastq	8482264214.0	66789482.0	GSM8902567 r12	0:8 1:28 2:91	A:1871553275;C:1241403117;G:1416606054;T:1548058897;N:221519	8	28	91		1871553275	1241403117	1416606054	1548058897	221519	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35840	35840	SRR33092405	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM2_S9_L001_I1_001.fastq.gz DM2_S9_L001_R1_001.fastq.gz DM2_S9_L001_R2_001.fastq.gz	fastq fastq fastq	8526585309.0	67138467.0	GSM8902567 r11	0:8 1:28 2:91	A:1882385546;C:1247436899;G:1424000842;T:1555556923;N:220287	8	28	91		1882385546	1247436899	1424000842	1555556923	220287	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35841	35841	SRR33092406	SRX28356288	SRS24685480	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Pachymeninges scRNA seq	GSM8902567	source name:Pachymeninges\|tissue:Pachymeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Pachymeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Pachymeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Pachymeninges	GSM8902567	GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq	GSM8902567 r1	GSM8902567	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	DM1_S8_L002_I1_001.fastq.gz DM1_S8_L002_R1_001.fastq.gz DM1_S8_L002_R2_001.fastq.gz	fastq fastq fastq	8727095068.0	68717284.0	GSM8902567 r10	0:8 1:28 2:91	A:1890991056;C:1285158535;G:1465221643;T:1611675024;N:226586	8	28	91		1890991056	1285158535	1465221643	1611675024	226586	SRX28356288	SRS24685480	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35842	35842	SRR33092388	SRX28356287	SRS24685479	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Leptomeninges scRNA seq	GSM8902566	source name:Leptomeninges\|tissue:Leptomeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Leptomeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Leptomeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Leptomeninges	GSM8902566	GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq	GSM8902566 r1	GSM8902566	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	LP5_S3_L001_I1_001.fastq.gz LP5_S3_L001_I2_001.fastq.gz LP5_S3_L001_R1_001.fastq.gz LP5_S3_L001_R2_001.fastq.gz	fastq fastq fastq fastq	15568833630.0	112817635.0	GSM8902566 r3	0:10 1:10 2:28 3:90	A:3095918108;C:2067214324;G:2193944375;T:2796211477;N:298866	10	10	28	90	3095918108	2067214324	2193944375	2796211477	298866	SRX28356287	SRS24685479	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35843	35843	SRR33092389	SRX28356287	SRS24685479	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Leptomeninges scRNA seq	GSM8902566	source name:Leptomeninges\|tissue:Leptomeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Leptomeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Leptomeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Leptomeninges	GSM8902566	GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq	GSM8902566 r1	GSM8902566	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	LP4_S2_L002_I1_001.fastq.gz LP4_S2_L002_I2_001.fastq.gz LP4_S2_L002_R1_001.fastq.gz LP4_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	9285387684.0	67285418.0	GSM8902566 r2	0:10 1:10 2:28 3:90	A:1865276237;C:1235101824;G:1340998802;T:1614123547;N:187210	10	10	28	90	1865276237	1235101824	1340998802	1614123547	187210	SRX28356287	SRS24685479	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35844	35844	SRR33092390	SRX28356287	SRS24685479	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Leptomeninges scRNA seq	GSM8902566	source name:Leptomeninges\|tissue:Leptomeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Leptomeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Leptomeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Leptomeninges	GSM8902566	GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq	GSM8902566 r1	GSM8902566	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	LP3_S15_L002_I1_001.fastq.gz LP3_S15_L002_R1_001.fastq.gz LP3_S15_L002_R2_001.fastq.gz	fastq fastq fastq	9389706646.0	73934698.0	GSM8902566 r8	0:8 1:28 2:91	A:2272647309;C:1189928271;G:1407239573;T:1858001350;N:241015	8	28	91		2272647309	1189928271	1407239573	1858001350	241015	SRX28356287	SRS24685479	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35845	35845	SRR33092391	SRX28356287	SRS24685479	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Leptomeninges scRNA seq	GSM8902566	source name:Leptomeninges\|tissue:Leptomeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Leptomeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Leptomeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Leptomeninges	GSM8902566	GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq	GSM8902566 r1	GSM8902566	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	LP3_S15_L001_I1_001.fastq.gz LP3_S15_L001_R1_001.fastq.gz LP3_S15_L001_R2_001.fastq.gz	fastq fastq fastq	9430875982.0	74258866.0	GSM8902566 r7	0:8 1:28 2:91	A:2283581426;C:1194788838;G:1413526478;T:1865417297;N:242767	8	28	91		2283581426	1194788838	1413526478	1865417297	242767	SRX28356287	SRS24685479	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35846	35846	SRR33092392	SRX28356287	SRS24685479	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Leptomeninges scRNA seq	GSM8902566	source name:Leptomeninges\|tissue:Leptomeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Leptomeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Leptomeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Leptomeninges	GSM8902566	GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq	GSM8902566 r1	GSM8902566	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	LP2_S14_L002_I1_001.fastq.gz LP2_S14_L002_R1_001.fastq.gz LP2_S14_L002_R2_001.fastq.gz	fastq fastq fastq	8600113229.0	67717427.0	GSM8902566 r6	0:8 1:28 2:91	A:2031057495;C:1116227631;G:1301307083;T:1713473857;N:219791	8	28	91		2031057495	1116227631	1301307083	1713473857	219791	SRX28356287	SRS24685479	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35847	35847	SRR33092393	SRX28356287	SRS24685479	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Leptomeninges scRNA seq	GSM8902566	source name:Leptomeninges\|tissue:Leptomeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Leptomeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Leptomeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Leptomeninges	GSM8902566	GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq	GSM8902566 r1	GSM8902566	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	LP2_S14_L001_I1_001.fastq.gz LP2_S14_L001_R1_001.fastq.gz LP2_S14_L001_R2_001.fastq.gz	fastq fastq fastq	8637039114.0	68008182.0	GSM8902566 r5	0:8 1:28 2:91	A:2040552249;C:1120589408;G:1306950110;T:1720431887;N:220908	8	28	91		2040552249	1120589408	1306950110	1720431887	220908	SRX28356287	SRS24685479	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35848	35848	SRR33092394	SRX28356287	SRS24685479	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Leptomeninges scRNA seq	GSM8902566	source name:Leptomeninges\|tissue:Leptomeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Leptomeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Leptomeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Leptomeninges	GSM8902566	GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq	GSM8902566 r1	GSM8902566	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	LP5_S3_L002_I1_001.fastq.gz LP5_S3_L002_I2_001.fastq.gz LP5_S3_L002_R1_001.fastq.gz LP5_S3_L002_R2_001.fastq.gz	fastq fastq fastq fastq	15558164850.0	112740325.0	GSM8902566 r4	0:10 1:10 2:28 3:90	A:3093961545;C:2065582935;G:2192533724;T:2794237154;N:313892	10	10	28	90	3093961545	2065582935	2192533724	2794237154	313892	SRX28356287	SRS24685479	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
35849	35849	SRR33092395	SRX28356287	SRS24685479	SRP578043	PRJNA1249042	Anatomical and Molecular Characterization of the Zebrafish Meninges	GSE294335	Transcriptome Analysis	The meninges are a set of connective tissue layers that surround the central nervous system protecting the brain from mechanical shock supporting its buoyancy guarding it from infection and injury and maintaining brain homeostasis. Despite their critical role the molecular identity developmental origins and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here we show that the zebrafish a genetically and experimentally accessible vertebrate possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology electron microscopy and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics we define the molecular identities of meningeal cell populations including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges provide a foundational description for future zebrafish meningeal research and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing			Zebrafish Adult Leptomeninges scRNA seq	GSM8902566	source name:Leptomeninges\|tissue:Leptomeninges\|geo loc name:missing\|collection date:missing	Zebrafish Adult Leptomeninges scRNA seq	cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files	Leptomeninges		Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		tissue:Leptomeninges	GSM8902566	GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq	GSM8902566 r1	GSM8902566	1	Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females 13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP578043	loader:fastq load.py	LP4_S2_L001_I1_001.fastq.gz LP4_S2_L001_I2_001.fastq.gz LP4_S2_L001_R1_001.fastq.gz LP4_S2_L001_R2_001.fastq.gz	fastq fastq fastq fastq	9290858970.0	67325065.0	GSM8902566 r1	0:10 1:10 2:28 3:90	A:1866460292;C:1235842442;G:1341443403;T:1615329817;N:179896	10	10	28	90	1866460292	1235842442	1341443403	1615329817	179896	SRX28356287	SRS24685479	SRA2109616	Weinstein Lab, NICHD, NIH	Weinstein Lab, NICHD, NIH												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-04-10	Adult	Adult	Brain	Nervous System
43990	43990	SRR6811825	SRX3768865	SRS3023383	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.		pubmed:29644996	Brain 3 scar	GSM3032168	source name:Brain\|strain/background:Zebrabow M\|tissue:Brain\|developmental stage:Adult	Brain 3 scar	Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim…	Brain		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Brain\|developmental stage:Adult	GSM3032168	GSM3032168: Brain 3 scar; Danio rerio; OTHER	GSM3032168		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM3032168	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343		B7_scar_R2.fastq.gz B7_scar_R1.fastq.gz	fastq fastq	1359725968.0	10965532.0	GSM3032168 r1	0:26 1:98	A:397239266;C:429529094;G:288126336;T:244165622;N:665650	26	98			397239266	429529094	288126336	244165622	665650	SRX3768865	SRS3023383	SRA623333	GEO	Max Delbrück Center	2	0.00032	0.00295	0.00026	0.0003	0.99991	0.99642	0.3	0.64327	26	98	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2018-03-06	Adult	Adult	Brain	Nervous System
43996	43996	SRR6811819	SRX3768859	SRS3023375	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.		pubmed:29644996	Brain 3 mRNA	GSM3032162	source name:Brain\|strain/background:Zebrabow M\|tissue:Brain\|developmental stage:Adult	Brain 3 mRNA	Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.	Brain		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Brain\|developmental stage:Adult	GSM3032162	GSM3032162: Brain 3 mRNA; Danio rerio; RNA Seq	GSM3032162		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM3032162	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP121343		B7_wt_R2.fastq.gz B7_wt_R1.fastq.gz	fastq fastq	35200219264.0	283872736.0	GSM3032162 r1	0:26 1:98	A:10338159874;C:7412176847;G:7655217994;T:9778922063;N:15742486	26	98			10338159874	7412176847	7655217994	9778922063	15742486	SRX3768859	SRS3023375	SRA623333	GEO	Max Delbrück Center	2	0.00528	0.88902	0.00406	0.20497	0.99573	0.78595	0.42436	0.62912	26	98	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2018-03-06	Adult	Adult	Brain	Nervous System
44003	44003	SRR6211489	SRX3320764	SRS2626337	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.		pubmed:29644996	Brain 1 mRNA	GSM2830059	source name:Brain\|strain/background:Zebrabow M\|tissue:Brain\|developmental stage:Adult	Brain 1 mRNA	Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.	Brain		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Brain\|developmental stage:Adult	GSM2830059	GSM2830059: Brain 1 mRNA; Danio rerio; RNA Seq	GSM2830059		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830059	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiniSeq	SRP121343		B5_wt_R1.fastq.gz B5_wt_R2.fastq.gz	fastq fastq	4538898000.0	36023000.0	GSM2830059 r1	0:26 1:100	A:1403578459;C:926366830;G:979609921;T:1228675807;N:666983	26	100			1403578459	926366830	979609921	1228675807	666983	SRX3320764	SRS2626337	SRA623333	GEO	Max Delbrück Center	2	0.0031	0.90951	0.00167	0.32324	0.99582	0.82834	0.46718	0.66863	26	100	T	B	sc-like readlen	illumina	miseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Brain	Nervous System
44011	44011	SRR6211481	SRX3320756	SRS2626330	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.		pubmed:29644996	Brain 1 scar	GSM2830052	source name:Brain\|strain/background:Zebrabow M\|tissue:Brain\|developmental stage:Adult	Brain 1 scar	Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim…	Brain		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Brain\|developmental stage:Adult	GSM2830052	GSM2830052: Brain 1 scar; Danio rerio; OTHER	GSM2830052		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830052	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343		B5_scar_R1.fastq.gz B5_scar_R2.fastq.gz	fastq fastq	438883452.0	3483202.0	GSM2830052 r1	0:26 1:100	A:125829044;C:139532010;G:100613706;T:72846911;N:61781	26	100			125829044	139532010	100613706	72846911	61781	SRX3320756	SRS2626330	SRA623333	GEO	Max Delbrück Center	2	0.00072	0.0013	0.00069	0.00011	0.99991	0.99878	0.75	0.36879	26	100	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Brain	Nervous System
45059	45059	SRR6497183	SRX3586252	SRS2608612	SRP131047	PRJNA429936	10X genomics analysis of adult and larval habenula from the gng8 GFP transgenic line	GSE109158	Transcriptome Analysis	The identification of cell types and marker genes is critical for dissecting neural development and function but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly despite brain growth and functional maturation cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: For larval dataset multiple gng8 GFP labeled zebrafish brains were dissociated and habenular cells FAC sorted into PBS+1%BSA and immediately loaded into 10X chromium for cell capture. For adult dataset 5 6 habenulae were cleanly dissected out dissociated filtered in PBS+BSA and immediately captured in droplets with 10x platform. Both libraries were then constructed using standard instrutions of the 10x plaform.	parent bioproject:PRJNA414719	pubmed:29576475	HabenulaR2	GSM2818523	source name:adult habenula\|developmental stage:Adult\|tissue:Brain\|tissue subtype:adult habenula	HabenulaR2	Raw requencing data was converted to matrizes of expression conts using cell ranger software provided by 10x genomics. Briefly raw BCL files from Illumina nExtseq were demultiplexed into compressed Fastqs for each channel using "cellranger mkfastq" FASTQ files were then provided as input to “cellranger count” which partitioned the reads into their cell of origin based on the 14bp cell barcode on the left read aligned reads to a zebrafish reference transcriptome and quantified transcript counts for each annotated gene within every cell. Here the 10bp unique molecular identifier UMI on the left read was used to collapse PCR duplicates and accurately quantify the number of transcript molecules captured for each gene in every cell. Supplementary files format and content: text file with tab delimiters	adult habenula		polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/		developmental stage:Adult\|tissue:Brain\|tissue subtype:adult habenula	GSM2818523	GSM2818523: HabenulaR2; Danio rerio; RNA Seq	GSM2818523 2		1	polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/	GEO Accession:GSM2818523	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP131047	dangling references:treat as unmapped	AdultR2_possorted_genome_bam.bam	10X Genomics bam file	47424636672.0	483924864.0	GSM2818523 r11	0:98	A:13883773158;C:9254138795;G:10071286557;T:14206806013;N:8632149	98				13883773158	9254138795	10071286557	14206806013	8632149	SRX3586252	SRS2608612	SRA650466	GEO	Schier Lab, Molecular and Cellular Biology, Harvard University	1	0.89145		0.21966		0.80417		0.4925		98		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2017-10-18	Adult	Adult	Brain	Nervous System
45060	45060	SRR6497182	SRX3586251	SRS2608614	SRP131047	PRJNA429936	10X genomics analysis of adult and larval habenula from the gng8 GFP transgenic line	GSE109158	Transcriptome Analysis	The identification of cell types and marker genes is critical for dissecting neural development and function but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly despite brain growth and functional maturation cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: For larval dataset multiple gng8 GFP labeled zebrafish brains were dissociated and habenular cells FAC sorted into PBS+1%BSA and immediately loaded into 10X chromium for cell capture. For adult dataset 5 6 habenulae were cleanly dissected out dissociated filtered in PBS+BSA and immediately captured in droplets with 10x platform. Both libraries were then constructed using standard instrutions of the 10x plaform.	parent bioproject:PRJNA414719	pubmed:29576475	HabenulaR1	GSM2818522	source name:adult habenula\|developmental stage:Adult\|tissue:Brain\|tissue subtype:adult habenula	HabenulaR1	Raw requencing data was converted to matrizes of expression conts using cell ranger software provided by 10x genomics. Briefly raw BCL files from Illumina nExtseq were demultiplexed into compressed Fastqs for each channel using "cellranger mkfastq" FASTQ files were then provided as input to “cellranger count” which partitioned the reads into their cell of origin based on the 14bp cell barcode on the left read aligned reads to a zebrafish reference transcriptome and quantified transcript counts for each annotated gene within every cell. Here the 10bp unique molecular identifier UMI on the left read was used to collapse PCR duplicates and accurately quantify the number of transcript molecules captured for each gene in every cell. Supplementary files format and content: text file with tab delimiters	adult habenula		polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/		developmental stage:Adult\|tissue:Brain\|tissue subtype:adult habenula	GSM2818522	GSM2818522: HabenulaR1; Danio rerio; RNA Seq	GSM2818522 2		1	polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/	GEO Accession:GSM2818522	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP131047		AdultR1_possorted_genome_bam.bam dr82_jeffspike.fasta	10X Genomics bam file fasta	34221168849.0	580019811.0	GSM2818522 r11	0:59	A:10793327710;C:6125333298;G:6353453321;T:10947283926;N:1770594	59				10793327710	6125333298	6353453321	10947283926	1770594	SRX3586251	SRS2608614	SRA650466	GEO	Schier Lab, Molecular and Cellular Biology, Harvard University	1	0.84773		0.23824		0.816		0.51567		59		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2017-10-18	Adult	Adult	Brain	Nervous System
48774	48774	SRR7297839	SRX4200373	SRS3410607	SRP150365	PRJNA475784	Phenotypic landscape of schizophrenia associated genes defines candidates and their shared functions	GSE115427	Transcriptome Analysis	Znf536 mutant and wild types were profiled to discover cell type landscape modulated by the transcription factor. Overall design: 10x libraries of single cell transcriptomes		pubmed:30929901	znf mut 10x	GSM3187949	source name:zebrafish brain\|tissue:Forebrain\|developmental stage:6dpf\|genotype/variation:znf mutant	znf mut 10x	Raw sequencing data was converted to matrices of expression using the cell ranger software provide by 10x genomics. Raw BCL files from Illumina nextseq were demultiplexed into paired end gzip compressed FASTQ files using cellranger mkgastq. Both FASTQs were then provided as input to cell ranger count which partitioned reads into cell of origin based on a 16 bp barcode on the left read. Reads were aligned to a zebrafish reference transcriptomeENSEMBL Zv10 release 82 reference transcriptome and transcript counts quantified for each annotated gene. 10bp UMI on th eleft read was used to collapse PCR duplicates. Genome build: GRCz10 Supplementary files format and content: CSV files for transcriptome data were generated using the cellranger pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for gene.	zebrafish brain		Single cell suspensions were processsed according to manufacturer's instructions by 10X chromium 10x chromium		tissue:Forebrain\|developmental stage:6dpf\|genotype/variation:znf mutant	GSM3187949	GSM3187949: znf mut 10x; Danio rerio; RNA Seq	GSM3187949		1	Single cell suspensions were processsed according to manufacturer's instructions by 10X chromium 10x chromium	GEO Accession:GSM3187949	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP150365		mut_possorted_genome_bam.bam	10X Genomics bam file	16531944740.0	285033530.0	GSM3187949 r1	0:58	A:5037043538;C:3032099047;G:3558921957;T:4900111360;N:3768838	58				5037043538	3032099047	3558921957	4900111360	3768838	SRX4200373	SRS3410607	SRA720602	GEO	Schier Lab, Molecular and Cellular Biology, Harvard University	1	0.88667		0.33708		0.83102		0.50699		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2018-06-12	Larval	Larval	Brain	Nervous System
48775	48775	SRR7297838	SRX4200372	SRS3410606	SRP150365	PRJNA475784	Phenotypic landscape of schizophrenia associated genes defines candidates and their shared functions	GSE115427	Transcriptome Analysis	Znf536 mutant and wild types were profiled to discover cell type landscape modulated by the transcription factor. Overall design: 10x libraries of single cell transcriptomes		pubmed:30929901	znf wt 10x	GSM3187948	source name:zebrafish brain\|tissue:Forebrain\|developmental stage:6dpf\|genotype/variation:znf wild type	znf wt 10x	Raw sequencing data was converted to matrices of expression using the cell ranger software provide by 10x genomics. Raw BCL files from Illumina nextseq were demultiplexed into paired end gzip compressed FASTQ files using cellranger mkgastq. Both FASTQs were then provided as input to cell ranger count which partitioned reads into cell of origin based on a 16 bp barcode on the left read. Reads were aligned to a zebrafish reference transcriptomeENSEMBL Zv10 release 82 reference transcriptome and transcript counts quantified for each annotated gene. 10bp UMI on th eleft read was used to collapse PCR duplicates. Genome build: GRCz10 Supplementary files format and content: CSV files for transcriptome data were generated using the cellranger pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for gene.	zebrafish brain		Single cell suspensions were processsed according to manufacturer's instructions by 10X chromium 10x chromium		tissue:Forebrain\|developmental stage:6dpf\|genotype/variation:znf wild type	GSM3187948	GSM3187948: znf wt 10x; Danio rerio; RNA Seq	GSM3187948		1	Single cell suspensions were processsed according to manufacturer's instructions by 10X chromium 10x chromium	GEO Accession:GSM3187948	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP150365		wt_possorted_genome_bam.bam	10X Genomics bam file	10334856266.0	178187177.0	GSM3187948 r1	0:58	A:3176662073;C:1883843325;G:2216500039;T:3055499601;N:2351228	58				3176662073	1883843325	2216500039	3055499601	2351228	SRX4200372	SRS3410606	SRA720602	GEO	Schier Lab, Molecular and Cellular Biology, Harvard University	1	0.89165		0.36096		0.83372		0.49416		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2018-06-12	Larval	Larval	Brain	Nervous System
49093	49093	SRR7723466	SRX4579978	SRS3674265	SRP157997	PRJNA486153	Single cell analyses of Amyloid beta42 and Interleukin 4 on neural stem cell plasticity I	GSE118577	Transcriptome Analysis	The neural stem cell NSC reservoir can be harnessed for stem cell based regenerative therapies. Zebrafish remarkably regenerate their brain by inducing NSC plasticity in a Amyloid ß 42 Aß42 induced experimental Alzheimer's disease AD model. Interleukin 4 IL 4 is also critical for AD induced NSC proliferation. However the mechanisms of this response have remained unknown. Using single cell transcriptomics in the adult zebrafish brain we identify distinct subtypes of NSCs and neurons and differentially regulated pathways and their gene ontologies and investigate how cell cell communication is altered through ligand receptor pairs in AD conditions. Our results propose the existence of heterogeneous and spatially organized stem cell populations that react distinctly to amyloid toxicity. This resource article provides an extensive database for the molecular basis of NSC plasticity in the AD model of the adult zebrafish brain. Further analyses of stem cell heterogeneity and neuro regenerative ability at single cell resolution could yield drug targets for mobilizing NSCs for endogenous neuro regeneration in humans. Overall design: Single cell analyses of zebrafish telencephalon by 10X Genomics		pubmed:31018142;pubmed:34685728;pubmed:35681503	PBS Control	GSM3334110	tissue:Telencephalon\|treatment:PBS Control	PBS Control	The fastq files were aligned to zebrafish transcript Ensembl Version 91by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Genome build: danRer10 Supplementary files format and content: tab delimited file with gene names in rows and cell names and counts in columns.	Telencephalon	Fish were injected PBS by CVMI.	Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol	Fish were kept at 28 °C water system with 14/10 hours light/dark cycles	treatment:PBS Control	GSM3334110	GSM3334110: PBS Control; Danio rerio; RNA Seq	GSM3334110 2		1	Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol	GEO Accession:GSM3334110	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP157997	dangling references:treat as unmapped	PBS_possorted_genome_bam.bam	10X Genomics bam file	6292411773.0	110393189.0	GSM3334110 r11	0:57	A:1933363206;C:1158155764;G:1296886350;T:1901320452;N:2686001	57				1933363206	1158155764	1296886350	1901320452	2686001	SRX4579978	SRS3674265	SRA759092	GEO	AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association	1	0.87993		0.28191		0.77861		0.50645		57		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2018-08-15	Undetermined	Adult	Brain	Nervous System
49094	49094	SRR7723465	SRX4579977	SRS3672878	SRP157997	PRJNA486153	Single cell analyses of Amyloid beta42 and Interleukin 4 on neural stem cell plasticity I	GSE118577	Transcriptome Analysis	The neural stem cell NSC reservoir can be harnessed for stem cell based regenerative therapies. Zebrafish remarkably regenerate their brain by inducing NSC plasticity in a Amyloid ß 42 Aß42 induced experimental Alzheimer's disease AD model. Interleukin 4 IL 4 is also critical for AD induced NSC proliferation. However the mechanisms of this response have remained unknown. Using single cell transcriptomics in the adult zebrafish brain we identify distinct subtypes of NSCs and neurons and differentially regulated pathways and their gene ontologies and investigate how cell cell communication is altered through ligand receptor pairs in AD conditions. Our results propose the existence of heterogeneous and spatially organized stem cell populations that react distinctly to amyloid toxicity. This resource article provides an extensive database for the molecular basis of NSC plasticity in the AD model of the adult zebrafish brain. Further analyses of stem cell heterogeneity and neuro regenerative ability at single cell resolution could yield drug targets for mobilizing NSCs for endogenous neuro regeneration in humans. Overall design: Single cell analyses of zebrafish telencephalon by 10X Genomics		pubmed:31018142;pubmed:34685728;pubmed:35681503	interleukin 4	GSM3333764	tissue:Telencephalon\|treatment:interleukin 4	interleukin 4	The fastq files were aligned to zebrafish transcript Ensembl Version 91by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Genome build: danRer10 Supplementary files format and content: tab delimited file with gene names in rows and cell names and counts in columns.	Telencephalon	Fish were injected interleukin 4 by CVMI.	Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol	Fish were kept at 28 °C water system with 14/10 hours light/dark cycles	treatment:interleukin 4	GSM3333764	GSM3333764: interleukin 4; Danio rerio; RNA Seq	GSM3333764 2		1	Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol	GEO Accession:GSM3333764	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP157997	dangling references:treat as unmapped	IL4_possorted_genome_bam.bam	10X Genomics bam file	7136552532.0	125202676.0	GSM3333764 r11	0:57	A:2212558326;C:1297976520;G:1461158205;T:2161803665;N:3055816	57				2212558326	1297976520	1461158205	2161803665	3055816	SRX4579977	SRS3672878	SRA759092	GEO	AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association	1	0.87473		0.30099		0.77828		0.49122		57		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2018-08-15	Undetermined	Adult	Brain	Nervous System
49095	49095	SRR7697065	SRX4555360	SRS3672366	SRP157997	PRJNA486153	Single cell analyses of Amyloid beta42 and Interleukin 4 on neural stem cell plasticity I	GSE118577	Transcriptome Analysis	The neural stem cell NSC reservoir can be harnessed for stem cell based regenerative therapies. Zebrafish remarkably regenerate their brain by inducing NSC plasticity in a Amyloid ß 42 Aß42 induced experimental Alzheimer's disease AD model. Interleukin 4 IL 4 is also critical for AD induced NSC proliferation. However the mechanisms of this response have remained unknown. Using single cell transcriptomics in the adult zebrafish brain we identify distinct subtypes of NSCs and neurons and differentially regulated pathways and their gene ontologies and investigate how cell cell communication is altered through ligand receptor pairs in AD conditions. Our results propose the existence of heterogeneous and spatially organized stem cell populations that react distinctly to amyloid toxicity. This resource article provides an extensive database for the molecular basis of NSC plasticity in the AD model of the adult zebrafish brain. Further analyses of stem cell heterogeneity and neuro regenerative ability at single cell resolution could yield drug targets for mobilizing NSCs for endogenous neuro regeneration in humans. Overall design: Single cell analyses of zebrafish telencephalon by 10X Genomics		pubmed:31018142;pubmed:34685728;pubmed:35681503	amyloid beta 42	GSM3333461	tissue:Telencephalon\|treatment:amyloid beta 42	amyloid beta 42	The fastq files were aligned to zebrafish transcript Ensembl Version 91by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Genome build: danRer10 Supplementary files format and content: tab delimited file with gene names in rows and cell names and counts in columns.	Telencephalon	Fish were injected amyloid beta 42 by CVMI.	Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol	Fish were kept at 28 °C water system with 14/10 hours light/dark cycles	treatment:amyloid beta 42	GSM3333461	GSM3333461: amyloid beta 42; Danio rerio; RNA Seq	GSM3333461		1	Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol	GEO Accession:GSM3333461	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP157997	dangling references:treat as unmapped	AB42_possorted_genome_bam.bam	10X Genomics bam file	4538914104.0	79630072.0	GSM3333461 r1	0:57	A:1398743208;C:825411025;G:924551078;T:1388288174;N:1920619	57				1398743208	825411025	924551078	1388288174	1920619	SRX4555360	SRS3672366	SRA759092	GEO	AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association	1	0.88003		0.26711		0.78336		0.50584		57		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2018-08-15	Undetermined	Adult	Brain	Nervous System
49096	49096	SRR7698982	SRX4557276	SRS3674267	SRP158038	PRJNA486182	Single cell analyses of Amyloid beta42 and Interleukin 4 on neural stem cell plasticity IV	GSE118599	Other	Neural stem cells NSCs constitute the reservoir for new cells and might be harnessed for stem cell based regenerative therapies. Zebrafish has remarkable ability to regenerate its brain by inducing NSC plasticity upon Alzheimer's pathology. We recently identified that NSCs enhance their proliferation and neurogenic outcome in an Amyloid beta42 based Aß42 experimental Alzheimer's disease model in zebrafish brain and Interleukin 4 IL4 is a critical molecule for inducing NSC proliferation in AD conditions. However the mechanisms by which Aß42 and IL4 affect NSCs remained unknown. Using single cell transcriptomics we determined distinct subtypes of NSCs and neurons in adult zebrafish brain identified differentially expressed genes post Aß42 and IL4 treatments analyzed the gene ontology and pathways that are affected by Aß42 and IL4 and investigated how cell cell communication is altered through secreted molecules and their receptors. Our results constitute the most extensive resource in the Alzheimer's disease model of adult zebrafish brain are likely to provide unique insights into how Aß42/IL4 affects NSC plasticity and yield in novel drug targets for mobilizing neural stem cells for endogenous neuro regeneration. Overall design: Single cell analyses of zebrafish telencephalon by 10X Genomics		pubmed:31905199	serotonin	GSM3334111	tissue:Telencephalon\|treatment:serotonin	serotonin	The fastq files were aligned to zebrafish transcript Ensembl Version 91by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Genome build: danRer10 Supplementary files format and content: tab delimited file with gene names in rows and cell names and counts in columns.	Telencephalon	Fish were injected serotonin by CVMI.	Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol	Fish were kept at 28 °C water system with 14/10 hours light/dark cycles	treatment:serotonin	GSM3334111	GSM3334111: serotonin; Danio rerio; RNA Seq	GSM3334111		1	Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol	GEO Accession:GSM3334111	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP158038	dangling references:treat as unmapped	SRT_possorted_genome_bam.bam	10X Genomics bam file	6880682724.0	120713732.0	GSM3334111 r1	0:57	A:2102623379;C:1264130463;G:1410616586;T:2100393658;N:2918638	57				2102623379	1264130463	1410616586	2100393658	2918638	SRX4557276	SRS3674267	SRA759542	GEO	AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association	1	0.87735		0.27987		0.78346		0.49332		57		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2018-08-15	Undetermined	Adult	Brain	Nervous System
53147	53147	SRR9685040	SRX6444484	SRS5098421	SRP214637	PRJNA554650	Zebrafish whole brain single cell RNA seq of nr1d1:VNP fish	GSE134288	Other	we report a transgenic zebrafish line using destabilized fluorescent protein Venus NLS PEST VNP driven by the promoter of a key circadian clock gene nr1d1. This system allows us to monitor the development of single cell circadian rhythm in live zebrafish larva in a cell type specific manner. To identify the cell types expressing nr1d1:VNP in the whole brain we conducted single cell RNA seq scRNA seq of 15 000 cells dissociated from the brain of Tgnr1d1:VNP larval fish at 6.5dpf. Among them 6514 cells were identified with number of genes > 500 and used for the following analysis. 26 cells clusters were classified from scRNAseq and manually annotated by comparing the marker genes with the adult zebrfiash whole brain single cell RNA seq data. The mRNA of nr1d1:VNP was enriched in photoreceptors in pineal gland granule cells and purkinje cells in cerebellum habenula cells as well as non neuron cell. Overall design: To identify the cell types expressing nr1d1:VNP in the whole brain we conducted single cell RNA seq scRNA seq of 15 000 cells dissociated from the brain of Tgnr1d1:VNP larval fish at 6.5dpf using 10X genomics.		pubmed:32168317	whole brain single cell RNA seq of nr1d1:VNP fish	GSM3941431	source name:Zebrafish brain\|age:6.5dpf\|genotype:nr1d1:VNP\|tissue:brain\|brain region:pineal	whole brain single cell RNA seq of nr1d1:VNP fish	Raw sequencing data was converted to matrices of expression counts using the cellranger software provided by 10X Chromium system. Reads were aligned to a zebrafish reference transcriptome ENSEMBL Zv11 release 95. The gene expression matrix were then loaded into Seurat package in R for clustering. Cells with less than 500 genes or percentage of mitochondiral genes>0.02 were excluded. Genome build: Zv11 Supplementary files format and content: processed data is a matrix each row represent one gene while each column represent one cell.	Zebrafish brain	The fish were untreated.	6.5 dpf larval heads were dissected on dissection medium DMEF/F12 with 2% 100X penicillin streptomycin and pineal region were enriched by pipetting the pineal into the tube. Dissociation of the brain cells following the protocol from Miguel A. Lopez Ramirez et al. www.jove.com 2016. Briefly Add 300ul papain solution to the dissected tissue digest the tissue at 37 in water heater for 15 minute pipetting during digest. Then stop the digestion by adding 1.2ml of washing solution. Washing the cells twice using washing solution. In the end sterilize the cells using 40um pore size filter. Stain cells using trypan blue and count the living cells using a hemocytometer. The library were constructed following the instruction of 10X Chromium system.	Embryos were produced by natural spawning in the morning and raised in egg water containing methylene blue 0.3 ppm in a light controlled incubator under 12h/12h LD cycles at 28 oC. ZT0 is defined as the time when the lights are turned on 9 A.M..	age:6.5dpf\|genotype:nr1d1:VNP\|tissue:brain\|brain region:pineal	GSM3941431	GSM3941431: whole brain single cell RNA seq of nr1d1:VNP fish; Danio rerio; RNA Seq	GSM3941431		1	6.5 dpf larval heads were dissected on dissection medium DMEF/F12 with 2% 100X penicillin streptomycin and pineal region were enriched by pipetting the pineal into the tube. Dissociation of the brain cells following the protocol from Miguel A. Lopez Ramirez et al. www.jove.com 2016. Briefly Add 300ul papain solution to the dissected tissue digest the tissue at 37 in water heater for 15 minute pipetting during digest. Then stop the digestion by adding 1.2ml of washing solution. Washing the cells twice using washing solution. In the end sterilize the cells using 40um pore size filter. Stain cells using trypan blue and count the living cells using a hemocytometer. The library were constructed following the instruction of 10X Chromium system.	GEO Accession:GSM3941431	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina Genome Analyzer IIx	SRP214637		pineal_S1_L001_R1_001.fastq.gz pineal_S1_L001_R2_001.fastq.gz	fastq fastq	40509923100.0	135033077.0	GSM3941431 r1	0:150 1:150	A:12010442156;C:5708633132;G:6678955522;T:16110568611;N:1323679	150	150			12010442156	5708633132	6678955522	16110568611	1323679	SRX6444484	SRS5098421	SRA921010	GEO	Institute of Neuroscience	2	0.39852	0.8845	0.05199	0.15658	0.96644	0.78774	0.42222	0.51714	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	early_illumina	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-07-15	Larval	Larval	Brain	Nervous System
55640	55640	SRR10586526	SRX7266919	SRS5761461	SRP234691	PRJNA593445	A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA Seq]	GSE141427	Transcriptome Analysis	Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf 24hpf and 44hpf zebrafish hindbrains were used for single cell RNA sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity dorso ventral patterning boundary and centre progenitor cells and temporal regulation of neurogenesis. Overall design: 16hpf 24hpf 44hpf hindbrains were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina HiSeq 4000.	parent bioproject:PRJNA593433	pubmed:32094115	44hpf Hindbrain scRNA seq	GSM4202682	source name:Dissected hindbrain and surrounding tissues\|tissue:Dissected hindbrain and surrounding tissues\|Stage:44hpf\|strain:LondonAB\|genotype:wt\|growth:25°C	44hpf Hindbrain scRNA seq	10X’s Cell Ranger software was used to de multiplex Illumina BCL output create fastq files and generate single cell feature counts for each library Three 10X libraries representing the 16hpf 24hpf and 44hpf stages of embryonic development were aggregated using the 10X software “cellranger aggr” function which sub samples reads such that all libraries have the same effective sequencing depth. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file containing aggregated Cell Ranger counts	Dissected hindbrain and surrounding tissues		Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles		tissue:Dissected hindbrain and surrounding tissues\|Stage:44hpf\|strain:LondonAB\|genotype:wt\|growth:25°C	GSM4202682	GSM4202682: 44hpf Hindbrain scRNA seq; Danio rerio; RNA Seq	GSM4202682		1	Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles	GEO Accession:GSM4202682	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP234691	loader:fastq load.py\|options: readTypes=TTB read1PairFiles=MT 10X240118 S1 L006 I1 001.fastq.gz read2PairFiles=MT 10X240118 S1 L006 R1 001.fastq.gz read3PairFiles=MT 10X240118 S1 L006 R2 001.fastq.gz	MT_10X240118_S1_L006_R2_001.fastq.gz MT_10X240118_S1_L006_R1_001.fastq.gz MT_10X240118_S1_L006_I1_001.fastq.gz	fastq fastq fastq	67359962250.0	320761725.0	GSM4202682 r1	0:8 1:101 2:101	A:16212646159;C:11777426351;G:12335518595;T:27032040933;N:2330212	8	101	101		16212646159	11777426351	12335518595	27032040933	2330212	SRX7266919	SRS5761461	SRA1006557	GEO	The Francis Crick Institute	1	0.9195		0.12389		0.82593		0.50909		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2019-12-04	Pharyngula	Embryo	Brain	Nervous System
55641	55641	SRR10586525	SRX7266917	SRS5761460	SRP234691	PRJNA593445	A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA Seq]	GSE141427	Transcriptome Analysis	Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf 24hpf and 44hpf zebrafish hindbrains were used for single cell RNA sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity dorso ventral patterning boundary and centre progenitor cells and temporal regulation of neurogenesis. Overall design: 16hpf 24hpf 44hpf hindbrains were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina HiSeq 4000.	parent bioproject:PRJNA593433	pubmed:32094115	24hpf Hindbrain scRNA seq	GSM4202681	source name:Dissected hindbrain and surrounding tissues\|tissue:Dissected hindbrain and surrounding tissues\|Stage:24hpf\|strain:LondonAB\|genotype:wt\|growth:28.5°C	24hpf Hindbrain scRNA seq	10X’s Cell Ranger software was used to de multiplex Illumina BCL output create fastq files and generate single cell feature counts for each library Three 10X libraries representing the 16hpf 24hpf and 44hpf stages of embryonic development were aggregated using the 10X software “cellranger aggr” function which sub samples reads such that all libraries have the same effective sequencing depth. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file containing aggregated Cell Ranger counts	Dissected hindbrain and surrounding tissues		Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles		tissue:Dissected hindbrain and surrounding tissues\|Stage:24hpf\|strain:LondonAB\|genotype:wt\|growth:28.5°C	GSM4202681	GSM4202681: 24hpf Hindbrain scRNA seq; Danio rerio; RNA Seq	GSM4202681		1	Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles	GEO Accession:GSM4202681	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP234691	loader:fastq load.py\|options: readTypes=TTB read1PairFiles=TAM677A2 S7 L008 I1 001.fastq.gz read2PairFiles=TAM677A2 S7 L008 R1 001.fastq.gz read3PairFiles=TAM677A2 S7 L008 R2 001.fastq.gz	TAM677A2_S7_L008_I1_001.fastq.gz TAM677A2_S7_L008_R1_001.fastq.gz TAM677A2_S7_L008_R2_001.fastq.gz	fastq fastq fastq	71824244730.0	342020213.0	GSM4202681 r1	0:8 1:101 2:101	A:16595981302;C:11865598791;G:12955979417;T:30401981747;N:4703473	8	101	101		16595981302	11865598791	12955979417	30401981747	4703473	SRX7266917	SRS5761460	SRA1006557	GEO	The Francis Crick Institute	1	0.92906		0.11719		0.80982		0.52506		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2019-12-04	Pharyngula	Embryo	Brain	Nervous System
55642	55642	SRR10586524	SRX7266915	SRS5761459	SRP234691	PRJNA593445	A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA Seq]	GSE141427	Transcriptome Analysis	Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf 24hpf and 44hpf zebrafish hindbrains were used for single cell RNA sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity dorso ventral patterning boundary and centre progenitor cells and temporal regulation of neurogenesis. Overall design: 16hpf 24hpf 44hpf hindbrains were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina HiSeq 4000.	parent bioproject:PRJNA593433	pubmed:32094115	16hpf Hindbrain scRNA seq	GSM4202680	source name:Dissected hindbrain and surrounding tissues\|tissue:Dissected hindbrain and surrounding tissues\|Stage:16hpf\|strain:LondonAB\|genotype:wt\|growth:25°C	16hpf Hindbrain scRNA seq	10X’s Cell Ranger software was used to de multiplex Illumina BCL output create fastq files and generate single cell feature counts for each library Three 10X libraries representing the 16hpf 24hpf and 44hpf stages of embryonic development were aggregated using the 10X software “cellranger aggr” function which sub samples reads such that all libraries have the same effective sequencing depth. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file containing aggregated Cell Ranger counts	Dissected hindbrain and surrounding tissues		Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles		tissue:Dissected hindbrain and surrounding tissues\|Stage:16hpf\|strain:LondonAB\|genotype:wt\|growth:25°C	GSM4202680	GSM4202680: 16hpf Hindbrain scRNA seq; Danio rerio; RNA Seq	GSM4202680		1	Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles	GEO Accession:GSM4202680	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP234691	loader:fastq load.py\|options: readTypes=TTB read1PairFiles=TAM677A1 S2 L008 I1 001.fastq.gz read2PairFiles=TAM677A1 S2 L008 R1 001.fastq.gz read3PairFiles=TAM677A1 S2 L008 R2 001.fastq.gz	TAM677A1_S2_L008_R2_001.fastq.gz TAM677A1_S2_L008_R1_001.fastq.gz TAM677A1_S2_L008_I1_001.fastq.gz	fastq fastq fastq	72155333460.0	343596826.0	GSM4202680 r1	0:8 1:101 2:101	A:16535121466;C:12722320120;G:13646437290;T:29245478028;N:5976556	8	101	101		16535121466	12722320120	13646437290	29245478028	5976556	SRX7266915	SRS5761459	SRA1006557	GEO	The Francis Crick Institute	1	0.91053		0.09489		0.848		0.50461		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2019-12-04	Segmentation	Embryo	Brain	Nervous System
59879	59879	SRR12060553	SRX8588729	SRS6880197	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858	Sox10+ 68 70hpf	GSM4629199	tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 68 70hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629199	GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq	GSM4629199		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145	loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=GFPplus S1 L001 R1 001.fastq read2PairFiles=GFPplus S1 L001 R2 001.fastq read3PairFiles=GFPplus S1 L001 I1 001.fastq	GFPplus_S1_L001_I1_001.fastq GFPplus_S1_L001_R1_001.fastq GFPplus_S1_L001_R2_001.fastq	fastq fastq fastq	6274319830.0	39710885.0	GSM4629199 r1	0:26 1:124 2:8	A:1841798453;C:1283501945;G:1425301974;T:1723079104;N:638354	26	124	8		1841798453	1283501945	1425301974	1723079104	638354	SRX8588729	SRS6880197	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.00247	0.91739	0.00057	0.08148	0.99486	0.8098	0.40168	0.49704	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59880	59880	SRR12060554	SRX8588729	SRS6880197	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858	Sox10+ 68 70hpf	GSM4629199	tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 68 70hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629199	GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq	GSM4629199		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145	loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=GFPplus S1 L002 R1 001.fastq read2PairFiles=GFPplus S1 L002 R2 001.fastq read3PairFiles=GFPplus S1 L002 I1 001.fastq			3615497884.0	22882898.0	GSM4629199 r2	0:26 1:124 2:8	A:1062722875;C:724671651;G:825496420;T:1002262450;N:344488	26	124	8		1062722875	724671651	825496420	1002262450	344488	SRX8588729	SRS6880197	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.00228	0.91709	0.00071	0.08087	0.99557	0.80984	0.37288	0.50652	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59881	59881	SRR12060555	SRX8588729	SRS6880197	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858	Sox10+ 68 70hpf	GSM4629199	tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 68 70hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629199	GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq	GSM4629199		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145	loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=GFPplus S1 L003 R1 001.fastq read2PairFiles=GFPplus S1 L003 R2 001.fastq read3PairFiles=GFPplus S1 L003 I1 001.fastq	GFPplus_S1_L003_I1_001.fastq GFPplus_S1_L003_R1_001.fastq GFPplus_S1_L003_R2_001.fastq	fastq fastq fastq	6350185110.0	40191045.0	GSM4629199 r3	0:26 1:124 2:8	A:1852452135;C:1299393173;G:1456328475;T:1740481266;N:1530061	26	124	8		1852452135	1299393173	1456328475	1740481266	1530061	SRX8588729	SRS6880197	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.00235	0.91442	0.00069	0.08011	0.99535	0.80813	0.37864	0.50714	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59882	59882	SRR12060556	SRX8588729	SRS6880197	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858	Sox10+ 68 70hpf	GSM4629199	tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 68 70hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629199	GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq	GSM4629199		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145	loader:fastq load.py\|options: allowEarlyFileEnd platform=Illumina readTypes=BBT read1PairFiles=GFPplus S1 L004 R1 001.fastq read2PairFiles=GFPplus S1 L004 R2 001.fastq read3PairFiles=GFPplus S1 L004 I1 001.fastq			5812557404.0	36788338.0	GSM4629199 r4	0:26 1:124 2:8	A:1702052926;C:1187088636;G:1324270973;T:1598146532;N:998337	26	124	8		1702052926	1187088636	1324270973	1598146532	998337	SRX8588729	SRS6880197	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.00277	0.91719	0.00069	0.08091	0.9945	0.80783	0.39641	0.51387	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59883	59883	SRR12060549	SRX8588728	SRS6880196	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858	Sox10+ 48 50hpf	GSM4629198	tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 48 50hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629198	GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq	GSM4629198		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145	loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=Sox10Enriched 48h S1 L001 R1 001 mod.fastq read2PairFiles=Sox10Enriched 48h S1 L001 R2 001.fastq read3PairFiles=Sox10Enriched 48h S1 L001 I1 001 mod.fastq			1616949090.0	10233855.0	GSM4629198 r1	0:26 1:124 2:8	A:456678394;C:358389976;G:376486936;T:425174329;N:219455	26	124	8		456678394	358389976	376486936	425174329	219455	SRX8588728	SRS6880196	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.01006	0.95005	0.00118	0.07248	0.98175	0.8351	0.41141	0.49367	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59884	59884	SRR12060550	SRX8588728	SRS6880196	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858	Sox10+ 48 50hpf	GSM4629198	tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 48 50hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629198	GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq	GSM4629198		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145	loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=Sox10Enriched 48h S1 L002 R1 001 mod.fastq read2PairFiles=Sox10Enriched 48h S1 L002 R2 001.fastq read3PairFiles=Sox10Enriched 48h S1 L002 I1 001 mod.fastq			1382737000.0	8751500.0	GSM4629198 r2	0:26 1:124 2:8	A:393565729;C:306444540;G:319283385;T:363276484;N:166862	26	124	8		393565729	306444540	319283385	363276484	166862	SRX8588728	SRS6880196	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.01049	0.94963	0.00135	0.07338	0.98192	0.83952	0.3958	0.49146	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59885	59885	SRR12060551	SRX8588728	SRS6880196	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858	Sox10+ 48 50hpf	GSM4629198	tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 48 50hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629198	GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq	GSM4629198		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145	loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=Sox10Enriched 48h S1 L003 R1 001.fastq read2PairFiles=Sox10Enriched 48h S1 L003 R2 001.fastq read3PairFiles=Sox10Enriched 48h S1 L003 I1 001.fastq	Sox10Enriched_48h_S1_L003_I1_001.fastq Sox10Enriched_48h_S1_L003_R1_001.fastq Sox10Enriched_48h_S1_L003_R2_001.fastq	fastq fastq fastq	7027816932.0	44479854.0	GSM4629198 r3	0:26 1:124 2:8	A:1977891064;C:1517642706;G:1691754065;T:1838521085;N:2008012	26	124	8		1977891064	1517642706	1691754065	1838521085	2008012	SRX8588728	SRS6880196	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.01071	0.94964	0.00138	0.06976	0.98123	0.83116	0.39988	0.4831	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59886	59886	SRR12060552	SRX8588728	SRS6880196	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858	Sox10+ 48 50hpf	GSM4629198	tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 48 50hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629198	GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq	GSM4629198		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145	loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=Sox10Enriched 48h S1 L004 R1 001.fastq read2PairFiles=Sox10Enriched 48h S1 L004 R2 001.fastq read3PairFiles=Sox10Enriched 48h S1 L004 I1 001.fastq			6734234423.0	42621737.0	GSM4629198 r4	0:26 1:124.00 2:8	A:1913564054;C:1452205902;G:1601358930;T:1764533329;N:2572208	26	124	8		1913564054	1452205902	1601358930	1764533329	2572208	SRX8588728	SRS6880196	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.01026	0.95184	0.00128	0.07207	0.98244	0.835	0.40661	0.49631	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
60937	60937	SRR12661682	SRX9142646	SRS7383950	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf15	GSM4793263	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf15	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793263	GSM4793263: Gest zBr15dpf15; Danio rerio; RNA Seq	GSM4793263		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793263	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf15 I1 001.fastq.gz read2PairFiles=zBr15dpf15 R1 001.fastq.gz read3PairFiles=zBr15dpf15 R2 001.fastq.gz	zBr15dpf15_I1_001.fastq.gz zBr15dpf15_R1_001.fastq.gz zBr15dpf15_R2_001.fastq.gz	fastq fastq fastq	1075227972.0	3657238.0	GSM4793263 r1	0:8 1:26 2:260	A:264220338;C:327498888;G:273310788;T:210174269;N:23689	8	26	260		264220338	327498888	273310788	210174269	23689	SRX9142646	SRS7383950	SRA1127180	GEO	Harvard University	1	6e-05		0.0		0.99989		0.5		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60938	60938	SRR12661683	SRX9142646	SRS7383950	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf15	GSM4793263	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf15	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793263	GSM4793263: Gest zBr15dpf15; Danio rerio; RNA Seq	GSM4793263		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793263	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf15 I1b 001.fastq.gz read2PairFiles=zBr15dpf15 R1b 001.fastq.gz read3PairFiles=zBr15dpf15 R2b 001.fastq.gz	zBr15dpf15_I1b_001.fastq.gz zBr15dpf15_R1b_001.fastq.gz zBr15dpf15_R2b_001.fastq.gz	fastq fastq fastq	891761388.0	3033202.0	GSM4793263 r2	0:8 1:26 2:260	A:218560342;C:271225746;G:227471470;T:174453887;N:49943	8	26	260		218560342	271225746	227471470	174453887	49943	SRX9142646	SRS7383950	SRA1127180	GEO	Harvard University	1	4e-05		0.0		0.99989		0.8		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60939	60939	SRR12661680	SRX9142645	SRS7383949	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf14	GSM4793262	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf14	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793262	GSM4793262: Gest zBr15dpf14; Danio rerio; RNA Seq	GSM4793262		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793262	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf14 I1 001.fastq.gz read2PairFiles=zBr15dpf14 R1 001.fastq.gz read3PairFiles=zBr15dpf14 R2 001.fastq.gz	zBr15dpf14_I1_001.fastq.gz zBr15dpf14_R1_001.fastq.gz zBr15dpf14_R2_001.fastq.gz	fastq fastq fastq	983963610.0	3346815.0	GSM4793262 r1	0:8 1:26 2:260	A:235372337;C:303668583;G:253370222;T:191530163;N:22305	8	26	260		235372337	303668583	253370222	191530163	22305	SRX9142645	SRS7383949	SRA1127180	GEO	Harvard University	1	6e-05		0.0		0.99989		0.6		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60940	60940	SRR12661681	SRX9142645	SRS7383949	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf14	GSM4793262	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf14	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793262	GSM4793262: Gest zBr15dpf14; Danio rerio; RNA Seq	GSM4793262		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793262	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf14 I1b 001.fastq.gz read2PairFiles=zBr15dpf14 R1b 001.fastq.gz read3PairFiles=zBr15dpf14 R2b 001.fastq.gz	zBr15dpf14_I1b_001.fastq.gz zBr15dpf14_R1b_001.fastq.gz zBr15dpf14_R2b_001.fastq.gz	fastq fastq fastq	860359248.0	2926392.0	GSM4793262 r2	0:8 1:26 2:260	A:204445657;C:265202143;G:222616322;T:168046600;N:48526	8	26	260		204445657	265202143	222616322	168046600	48526	SRX9142645	SRS7383949	SRA1127180	GEO	Harvard University	1	4e-05		0.0		0.99993		0.33333		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60941	60941	SRR12661678	SRX9142644	SRS7383948	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf13	GSM4793261	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf13	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793261	GSM4793261: Gest zBr15dpf13; Danio rerio; RNA Seq	GSM4793261		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793261	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf13 I1 001.fastq.gz read2PairFiles=zBr15dpf13 R1 001.fastq.gz read3PairFiles=zBr15dpf13 R2 001.fastq.gz	zBr15dpf13_I1_001.fastq.gz zBr15dpf13_R1_001.fastq.gz zBr15dpf13_R2_001.fastq.gz	fastq fastq fastq	1044599934.0	3553061.0	GSM4793261 r1	0:8 1:26 2:260	A:273346341;C:308296690;G:259881225;T:203052969;N:22709	8	26	260		273346341	308296690	259881225	203052969	22709	SRX9142644	SRS7383948	SRA1127180	GEO	Harvard University	1	0.00013		0.0		0.99993		0.66666		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60942	60942	SRR12661679	SRX9142644	SRS7383948	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf13	GSM4793261	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf13	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793261	GSM4793261: Gest zBr15dpf13; Danio rerio; RNA Seq	GSM4793261		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793261	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf13 I1b 001.fastq.gz read2PairFiles=zBr15dpf13 R1b 001.fastq.gz read3PairFiles=zBr15dpf13 R2b 001.fastq.gz	zBr15dpf13_I1b_001.fastq.gz zBr15dpf13_R1b_001.fastq.gz zBr15dpf13_R2b_001.fastq.gz	fastq fastq fastq	792769530.0	2696495.0	GSM4793261 r2	0:8 1:26 2:260	A:199210347;C:234589882;G:203291722;T:155635777;N:41802	8	26	260		199210347	234589882	203291722	155635777	41802	SRX9142644	SRS7383948	SRA1127180	GEO	Harvard University	1	3e-05		0.0		0.99997		0.0		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60943	60943	SRR12661676	SRX9142643	SRS7383947	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf12	GSM4793260	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf12	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793260	GSM4793260: Gest zBr15dpf12; Danio rerio; RNA Seq	GSM4793260		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793260	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf12 I1 001.fastq.gz read2PairFiles=zBr15dpf12 R1 001.fastq.gz read3PairFiles=zBr15dpf12 R2 001.fastq.gz	zBr15dpf12_I1_001.fastq.gz zBr15dpf12_R1_001.fastq.gz zBr15dpf12_R2_001.fastq.gz	fastq fastq fastq	1077176310.0	3663865.0	GSM4793260 r1	0:8 1:26 2:260	A:267515738;C:322832426;G:276056686;T:210748138;N:23322	8	26	260		267515738	322832426	276056686	210748138	23322	SRX9142643	SRS7383947	SRA1127180	GEO	Harvard University	1	2e-05		0.0		0.99995		0.5		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60944	60944	SRR12661677	SRX9142643	SRS7383947	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf12	GSM4793260	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf12	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793260	GSM4793260: Gest zBr15dpf12; Danio rerio; RNA Seq	GSM4793260		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793260	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf12 I1b 001.fastq.gz read2PairFiles=zBr15dpf12 R1b 001.fastq.gz read3PairFiles=zBr15dpf12 R2b 001.fastq.gz	zBr15dpf12_I1b_001.fastq.gz zBr15dpf12_R1b_001.fastq.gz zBr15dpf12_R2b_001.fastq.gz	fastq fastq fastq	831284118.0	2827497.0	GSM4793260 r2	0:8 1:26 2:260	A:205460386;C:248836207;G:214412777;T:162526707;N:48041	8	26	260		205460386	248836207	214412777	162526707	48041	SRX9142643	SRS7383947	SRA1127180	GEO	Harvard University	1	5e-05		0.0		0.99989		0.33333		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60945	60945	SRR12661674	SRX9142642	SRS7383946	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf11	GSM4793259	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf11	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793259	GSM4793259: Gest zBr15dpf11; Danio rerio; RNA Seq	GSM4793259		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793259	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf11 I1 001.fastq.gz read2PairFiles=zBr15dpf11 R1 001.fastq.gz read3PairFiles=zBr15dpf11 R2 001.fastq.gz	zBr15dpf11_I1_001.fastq.gz zBr15dpf11_R1_001.fastq.gz zBr15dpf11_R2_001.fastq.gz	fastq fastq fastq	1071244272.0	3643688.0	GSM4793259 r1	0:8 1:26 2:260	A:281707370;C:294636132;G:257074087;T:237826590;N:93	8	26	260		281707370	294636132	257074087	237826590	93	SRX9142642	SRS7383946	SRA1127180	GEO	Harvard University	1	0.0001		1e-05		0.99983		0.625		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60946	60946	SRR12661675	SRX9142642	SRS7383946	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf11	GSM4793259	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf11	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793259	GSM4793259: Gest zBr15dpf11; Danio rerio; RNA Seq	GSM4793259		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793259	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf11 I1b 001.fastq.gz read2PairFiles=zBr15dpf11 R1b 001.fastq.gz read3PairFiles=zBr15dpf11 R2b 001.fastq.gz	zBr15dpf11_I1b_001.fastq.gz zBr15dpf11_R1b_001.fastq.gz zBr15dpf11_R2b_001.fastq.gz	fastq fastq fastq	879366348.0	2991042.0	GSM4793259 r2	0:8 1:26 2:260	A:229947121;C:242181902;G:208941594;T:195292436;N:3003295	8	26	260		229947121	242181902	208941594	195292436	3003295	SRX9142642	SRS7383946	SRA1127180	GEO	Harvard University	1	8e-05		2e-05		0.99987		0.5		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60947	60947	SRR12661672	SRX9142641	SRS7383944	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf10	GSM4793258	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf10	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793258	GSM4793258: Gest zBr15dpf10; Danio rerio; RNA Seq	GSM4793258		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793258	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf10 I1 001.fastq.gz read2PairFiles=zBr15dpf10 R1 001.fastq.gz read3PairFiles=zBr15dpf10 R2 001.fastq.gz	zBr15dpf10_I1_001.fastq.gz zBr15dpf10_R1_001.fastq.gz zBr15dpf10_R2_001.fastq.gz	fastq fastq fastq	1100096844.0	3741826.0	GSM4793258 r1	0:8 1:26 2:260	A:278799797;C:311806242;G:266621265;T:242869469;N:71	8	26	260		278799797	311806242	266621265	242869469	71	SRX9142641	SRS7383944	SRA1127180	GEO	Harvard University	1	0.00016		2e-05		0.99987		0.4		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60948	60948	SRR12661673	SRX9142641	SRS7383944	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf10	GSM4793258	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf10	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793258	GSM4793258: Gest zBr15dpf10; Danio rerio; RNA Seq	GSM4793258		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793258	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf10 I1b 001.fastq.gz read2PairFiles=zBr15dpf10 R1b 001.fastq.gz read3PairFiles=zBr15dpf10 R2b 001.fastq.gz	zBr15dpf10_I1b_001.fastq.gz zBr15dpf10_R1b_001.fastq.gz zBr15dpf10_R2b_001.fastq.gz	fastq fastq fastq	894468540.0	3042410.0	GSM4793258 r2	0:8 1:26 2:260	A:225022139;C:252241661;G:216581348;T:197575358;N:3048034	8	26	260		225022139	252241661	216581348	197575358	3048034	SRX9142641	SRS7383944	SRA1127180	GEO	Harvard University	1	9e-05		1e-05		0.99989		0.42857		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60949	60949	SRR12661670	SRX9142640	SRS7383945	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf9	GSM4793257	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf9	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793257	GSM4793257: Gest zBr15dpf9; Danio rerio; RNA Seq	GSM4793257		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793257	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf9 I1 001.fastq.gz read2PairFiles=zBr15dpf9 R1 001.fastq.gz read3PairFiles=zBr15dpf9 R2 001.fastq.gz	zBr15dpf9_I1_001.fastq.gz zBr15dpf9_R1_001.fastq.gz zBr15dpf9_R2_001.fastq.gz	fastq fastq fastq	1163191008.0	3956432.0	GSM4793257 r1	0:8 1:26 2:260	A:308171463;C:340381340;G:278095474;T:236542634;N:97	8	26	260		308171463	340381340	278095474	236542634	97	SRX9142640	SRS7383945	SRA1127180	GEO	Harvard University	1	8e-05		3e-05		0.99997		1.0		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60950	60950	SRR12661671	SRX9142640	SRS7383945	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf9	GSM4793257	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf9	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793257	GSM4793257: Gest zBr15dpf9; Danio rerio; RNA Seq	GSM4793257		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793257	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf9 I1b 001.fastq.gz read2PairFiles=zBr15dpf9 R1b 001.fastq.gz read3PairFiles=zBr15dpf9 R2b 001.fastq.gz	zBr15dpf9_I1b_001.fastq.gz zBr15dpf9_R1b_001.fastq.gz zBr15dpf9_R2b_001.fastq.gz	fastq fastq fastq	595217406.0	2024549.0	GSM4793257 r2	0:8 1:26 2:260	A:154618288;C:174303551;G:145199497;T:119074527;N:2021543	8	26	260		154618288	174303551	145199497	119074527	2021543	SRX9142640	SRS7383945	SRA1127180	GEO	Harvard University	1	7e-05		1e-05		0.99995		0.66666		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60951	60951	SRR12661668	SRX9142639	SRS7383943	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf8	GSM4793256	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf8	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793256	GSM4793256: Gest zBr15dpf8; Danio rerio; RNA Seq	GSM4793256		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793256	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf8 I1 001.fastq.gz read2PairFiles=zBr15dpf8 R1 001.fastq.gz read3PairFiles=zBr15dpf8 R2 001.fastq.gz	zBr15dpf8_I1_001.fastq.gz zBr15dpf8_R1_001.fastq.gz zBr15dpf8_R2_001.fastq.gz	fastq fastq fastq	1359124662.0	4622873.0	GSM4793256 r1	0:8 1:26 2:260	A:354477725;C:396204041;G:333049617;T:275393147;N:132	8	26	260		354477725	396204041	333049617	275393147	132	SRX9142639	SRS7383943	SRA1127180	GEO	Harvard University	1	5e-05		1e-05		0.99993		0.66666		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60952	60952	SRR12661669	SRX9142639	SRS7383943	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	Gest zBr15dpf8	GSM4793256	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	Gest zBr15dpf8	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793256	GSM4793256: Gest zBr15dpf8; Danio rerio; RNA Seq	GSM4793256		1	Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR. Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793256	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf8 I1b 001.fastq.gz read2PairFiles=zBr15dpf8 R1b 001.fastq.gz read3PairFiles=zBr15dpf8 R2b 001.fastq.gz	zBr15dpf8_I1b_001.fastq.gz zBr15dpf8_R1b_001.fastq.gz zBr15dpf8_R2b_001.fastq.gz	fastq fastq fastq	702794946.0	2390459.0	GSM4793256 r2	0:8 1:26 2:260	A:181118310;C:205297819;G:171997224;T:141993611;N:2387982	8	26	260		181118310	205297819	171997224	141993611	2387982	SRX9142639	SRS7383943	SRA1127180	GEO	Harvard University	1	3e-05		1e-05		0.99997		1.0		260		T		under 1.2% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60953	60953	SRR12661660	SRX9142638	SRS7383942	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf21 S1	GSM4793255	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf21 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793255	GSM4793255: zBr15dpf21 S1; Danio rerio; RNA Seq	GSM4793255		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793255	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf21 S1 L001 I1 001.fastq.gz read2PairFiles=zBr15dpf21 S1 L001 R1 001.fastq.gz read3PairFiles=zBr15dpf21 S1 L001 R2 001.fastq.gz	zBr15dpf21_S1_L001_I1_001.fastq.gz zBr15dpf21_S1_L001_R1_001.fastq.gz zBr15dpf21_S1_L001_R2_001.fastq.gz	fastq fastq fastq	1486804548.0	16160919.0	GSM4793255 r1	0:8 1:26 2:58	A:401433704;C:326345906;G:355088454;T:401807963;N:2128521	8	26	58		401433704	326345906	355088454	401807963	2128521	SRX9142638	SRS7383942	SRA1127180	GEO	Harvard University	1	0.93087		0.11105		0.78352		0.52041		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60954	60954	SRR12661661	SRX9142638	SRS7383942	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf21 S1	GSM4793255	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf21 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793255	GSM4793255: zBr15dpf21 S1; Danio rerio; RNA Seq	GSM4793255		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793255	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf21 S1 L002 I1 001.fastq.gz read2PairFiles=zBr15dpf21 S1 L002 R1 001.fastq.gz read3PairFiles=zBr15dpf21 S1 L002 R2 001.fastq.gz	zBr15dpf21_S1_L002_R2_001.fastq.gz zBr15dpf21_S1_L002_R1_001.fastq.gz zBr15dpf21_S1_L002_I1_001.fastq.gz	fastq fastq fastq	1490623652.0	16202431.0	GSM4793255 r2	0:8 1:26 2:58	A:401860587;C:327076265;G:356810703;T:402705404;N:2170693	8	26	58		401860587	327076265	356810703	402705404	2170693	SRX9142638	SRS7383942	SRA1127180	GEO	Harvard University	1	0.93139		0.11221		0.78407		0.51897		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60955	60955	SRR12661662	SRX9142638	SRS7383942	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf21 S1	GSM4793255	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf21 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793255	GSM4793255: zBr15dpf21 S1; Danio rerio; RNA Seq	GSM4793255		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793255	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf21 S1 L003 I1 001.fastq.gz read2PairFiles=zBr15dpf21 S1 L003 R1 001.fastq.gz read3PairFiles=zBr15dpf21 S1 L003 R2 001.fastq.gz	zBr15dpf21_S1_L003_I1_001.fastq.gz zBr15dpf21_S1_L003_R1_001.fastq.gz zBr15dpf21_S1_L003_R2_001.fastq.gz	fastq fastq fastq	1499062168.0	16294154.0	GSM4793255 r3	0:8 1:26 2:58	A:403518767;C:328474398;G:360346226;T:405001475;N:1721302	8	26	58		403518767	328474398	360346226	405001475	1721302	SRX9142638	SRS7383942	SRA1127180	GEO	Harvard University	1	0.92969		0.11213		0.78423		0.51472		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60956	60956	SRR12661663	SRX9142638	SRS7383942	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf21 S1	GSM4793255	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf21 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793255	GSM4793255: zBr15dpf21 S1; Danio rerio; RNA Seq	GSM4793255		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793255	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf21 S1 L004 I1 001.fastq.gz read2PairFiles=zBr15dpf21 S1 L004 R1 001.fastq.gz read3PairFiles=zBr15dpf21 S1 L004 R2 001.fastq.gz	zBr15dpf21_S1_L004_I1_001.fastq.gz zBr15dpf21_S1_L004_R1_001.fastq.gz zBr15dpf21_S1_L004_R2_001.fastq.gz	fastq fastq fastq	1497041020.0	16272185.0	GSM4793255 r4	0:8 1:26 2:58	A:404012068;C:328407627;G:358074645;T:404774954;N:1771726	8	26	58		404012068	328407627	358074645	404774954	1771726	SRX9142638	SRS7383942	SRA1127180	GEO	Harvard University	1	0.93029		0.11263		0.78457		0.51497		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60957	60957	SRR12661664	SRX9142638	SRS7383942	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf21 S1	GSM4793255	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf21 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793255	GSM4793255: zBr15dpf21 S1; Danio rerio; RNA Seq	GSM4793255		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793255	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf21b S1 L001 I1 001.fastq.gz read2PairFiles=zBr15dpf21b S1 L001 R1 001.fastq.gz read3PairFiles=zBr15dpf21b S1 L001 R2 001.fastq.gz	zBr15dpf21b_S1_L001_I1_001.fastq.gz zBr15dpf21b_S1_L001_R1_001.fastq.gz zBr15dpf21b_S1_L001_R2_001.fastq.gz	fastq fastq fastq	1536131544.0	16697082.0	GSM4793255 r5	0:8 1:26 2:58	A:415450203;C:336714702;G:368612306;T:414940778;N:413555	8	26	58		415450203	336714702	368612306	414940778	413555	SRX9142638	SRS7383942	SRA1127180	GEO	Harvard University	1	0.93028		0.11192		0.78709		0.51854		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60958	60958	SRR12661665	SRX9142638	SRS7383942	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf21 S1	GSM4793255	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf21 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793255	GSM4793255: zBr15dpf21 S1; Danio rerio; RNA Seq	GSM4793255		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793255	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf21b S1 L002 I1 001.fastq.gz read2PairFiles=zBr15dpf21b S1 L002 R1 001.fastq.gz read3PairFiles=zBr15dpf21b S1 L002 R2 001.fastq.gz	zBr15dpf21b_S1_L002_R2_001.fastq.gz zBr15dpf21b_S1_L002_R1_001.fastq.gz zBr15dpf21b_S1_L002_I1_001.fastq.gz	fastq fastq fastq	1523835468.0	16563429.0	GSM4793255 r6	0:8 1:26 2:58	A:412473305;C:334268948;G:365305032;T:411407695;N:380488	8	26	58		412473305	334268948	365305032	411407695	380488	SRX9142638	SRS7383942	SRA1127180	GEO	Harvard University	1	0.93026		0.11046		0.7867		0.50918		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60959	60959	SRR12661666	SRX9142638	SRS7383942	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf21 S1	GSM4793255	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf21 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793255	GSM4793255: zBr15dpf21 S1; Danio rerio; RNA Seq	GSM4793255		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793255	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf21b S1 L003 I1 001.fastq.gz read2PairFiles=zBr15dpf21b S1 L003 R1 001.fastq.gz read3PairFiles=zBr15dpf21b S1 L003 R2 001.fastq.gz	zBr15dpf21b_S1_L003_I1_001.fastq.gz zBr15dpf21b_S1_L003_R1_001.fastq.gz zBr15dpf21b_S1_L003_R2_001.fastq.gz	fastq fastq fastq	1521229752.0	16535106.0	GSM4793255 r7	0:8 1:26 2:58	A:411212325;C:333161605;G:365517056;T:411135305;N:203461	8	26	58		411212325	333161605	365517056	411135305	203461	SRX9142638	SRS7383942	SRA1127180	GEO	Harvard University	1	0.93147		0.11167		0.78524		0.52126		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60960	60960	SRR12661667	SRX9142638	SRS7383942	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf21 S1	GSM4793255	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf21 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793255	GSM4793255: zBr15dpf21 S1; Danio rerio; RNA Seq	GSM4793255		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793255	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf21b S1 L004 I1 001.fastq.gz read2PairFiles=zBr15dpf21b S1 L004 R1 001.fastq.gz read3PairFiles=zBr15dpf21b S1 L004 R2 001.fastq.gz	zBr15dpf21b_S1_L004_I1_001.fastq.gz zBr15dpf21b_S1_L004_R1_001.fastq.gz zBr15dpf21b_S1_L004_R2_001.fastq.gz	fastq fastq fastq	1396668192.0	15181176.0	GSM4793255 r8	0:8 1:26 2:58	A:379911658;C:306043898;G:332409162;T:378136642;N:166832	8	26	58		379911658	306043898	332409162	378136642	166832	SRX9142638	SRS7383942	SRA1127180	GEO	Harvard University	1	0.92992		0.11451		0.78946		0.51534		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60961	60961	SRR12661652	SRX9142637	SRS7383941	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf20 S2	GSM4793254	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf20 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793254	GSM4793254: zBr15dpf20 S2; Danio rerio; RNA Seq	GSM4793254		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793254	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf20 S2 L001 I1 001.fastq.gz read2PairFiles=zBr15dpf20 S2 L001 R1 001.fastq.gz read3PairFiles=zBr15dpf20 S2 L001 R2 001.fastq.gz	zBr15dpf20_S2_L001_I1_001.fastq.gz zBr15dpf20_S2_L001_R1_001.fastq.gz zBr15dpf20_S2_L001_R2_001.fastq.gz	fastq fastq fastq	1527601120.0	16604360.0	GSM4793254 r1	0:8 1:26 2:58	A:416374112;C:333656130;G:359389378;T:415960912;N:2220588	8	26	58		416374112	333656130	359389378	415960912	2220588	SRX9142637	SRS7383941	SRA1127180	GEO	Harvard University	1	0.92937		0.11243		0.78427		0.5229		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60962	60962	SRR12661653	SRX9142637	SRS7383941	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf20 S2	GSM4793254	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf20 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793254	GSM4793254: zBr15dpf20 S2; Danio rerio; RNA Seq	GSM4793254		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793254	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf20 S2 L002 I1 001.fastq.gz read2PairFiles=zBr15dpf20 S2 L002 R1 001.fastq.gz read3PairFiles=zBr15dpf20 S2 L002 R2 001.fastq.gz	zBr15dpf20_S2_L002_I1_001.fastq.gz zBr15dpf20_S2_L002_R1_001.fastq.gz zBr15dpf20_S2_L002_R2_001.fastq.gz	fastq fastq fastq	1529724296.0	16627438.0	GSM4793254 r2	0:8 1:26 2:58	A:416236276;C:334007621;G:360770766;T:416466211;N:2243422	8	26	58		416236276	334007621	360770766	416466211	2243422	SRX9142637	SRS7383941	SRA1127180	GEO	Harvard University	1	0.92969		0.11201		0.78482		0.51636		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60963	60963	SRR12661654	SRX9142637	SRS7383941	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf20 S2	GSM4793254	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf20 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793254	GSM4793254: zBr15dpf20 S2; Danio rerio; RNA Seq	GSM4793254		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793254	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf20 S2 L003 I1 001.fastq.gz read2PairFiles=zBr15dpf20 S2 L003 R1 001.fastq.gz read3PairFiles=zBr15dpf20 S2 L003 R2 001.fastq.gz	zBr15dpf20_S2_L003_I1_001.fastq.gz zBr15dpf20_S2_L003_R1_001.fastq.gz zBr15dpf20_S2_L003_R2_001.fastq.gz	fastq fastq fastq	1540206684.0	16741377.0	GSM4793254 r3	0:8 1:26 2:58	A:418349132;C:335859276;G:364921952;T:419288596;N:1787728	8	26	58		418349132	335859276	364921952	419288596	1787728	SRX9142637	SRS7383941	SRA1127180	GEO	Harvard University	1	0.92848		0.11312		0.78673		0.52035		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60964	60964	SRR12661655	SRX9142637	SRS7383941	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf20 S2	GSM4793254	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf20 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793254	GSM4793254: zBr15dpf20 S2; Danio rerio; RNA Seq	GSM4793254		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793254	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf20 S2 L004 I1 001.fastq.gz read2PairFiles=zBr15dpf20 S2 L004 R1 001.fastq.gz read3PairFiles=zBr15dpf20 S2 L004 R2 001.fastq.gz	zBr15dpf20_S2_L004_I1_001.fastq.gz zBr15dpf20_S2_L004_R1_001.fastq.gz zBr15dpf20_S2_L004_R2_001.fastq.gz	fastq fastq fastq	1536082784.0	16696552.0	GSM4793254 r4	0:8 1:26 2:58	A:418347213;C:335471900;G:362035689;T:418395473;N:1832509	8	26	58		418347213	335471900	362035689	418395473	1832509	SRX9142637	SRS7383941	SRA1127180	GEO	Harvard University	1	0.93054		0.11371		0.78504		0.52091		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60965	60965	SRR12661656	SRX9142637	SRS7383941	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf20 S2	GSM4793254	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf20 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793254	GSM4793254: zBr15dpf20 S2; Danio rerio; RNA Seq	GSM4793254		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793254	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf20b S2 L001 I1 001.fastq.gz read2PairFiles=zBr15dpf20b S2 L001 R1 001.fastq.gz read3PairFiles=zBr15dpf20b S2 L001 R2 001.fastq.gz	zBr15dpf20b_S2_L001_I1_001.fastq.gz zBr15dpf20b_S2_L001_R1_001.fastq.gz zBr15dpf20b_S2_L001_R2_001.fastq.gz	fastq fastq fastq	1585533888.0	17234064.0	GSM4793254 r5	0:8 1:26 2:58	A:432862266;C:345872566;G:374996323;T:431371348;N:431385	8	26	58		432862266	345872566	374996323	431371348	431385	SRX9142637	SRS7383941	SRA1127180	GEO	Harvard University	1	0.9303		0.11275		0.78595		0.52238		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60966	60966	SRR12661657	SRX9142637	SRS7383941	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf20 S2	GSM4793254	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf20 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793254	GSM4793254: zBr15dpf20 S2; Danio rerio; RNA Seq	GSM4793254		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793254	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf20b S2 L002 I1 001.fastq.gz read2PairFiles=zBr15dpf20b S2 L002 R1 001.fastq.gz read3PairFiles=zBr15dpf20b S2 L002 R2 001.fastq.gz	zBr15dpf20b_S2_L002_I1_001.fastq.gz zBr15dpf20b_S2_L002_R1_001.fastq.gz zBr15dpf20b_S2_L002_R2_001.fastq.gz	fastq fastq fastq	1569149516.0	17055973.0	GSM4793254 r6	0:8 1:26 2:58	A:428743999;C:342544974;G:370667308;T:426800062;N:393173	8	26	58		428743999	342544974	370667308	426800062	393173	SRX9142637	SRS7383941	SRA1127180	GEO	Harvard University	1	0.92989		0.11414		0.78386		0.51724		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60967	60967	SRR12661658	SRX9142637	SRS7383941	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf20 S2	GSM4793254	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf20 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793254	GSM4793254: zBr15dpf20 S2; Danio rerio; RNA Seq	GSM4793254		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793254	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf20b S2 L003 I1 001.fastq.gz read2PairFiles=zBr15dpf20b S2 L003 R1 001.fastq.gz read3PairFiles=zBr15dpf20b S2 L003 R2 001.fastq.gz	zBr15dpf20b_S2_L003_I1_001.fastq.gz zBr15dpf20b_S2_L003_R1_001.fastq.gz zBr15dpf20b_S2_L003_R2_001.fastq.gz	fastq fastq fastq	1570317272.0	17068666.0	GSM4793254 r7	0:8 1:26 2:58	A:428417868;C:342328811;G:371881955;T:427483424;N:205214	8	26	58		428417868	342328811	371881955	427483424	205214	SRX9142637	SRS7383941	SRA1127180	GEO	Harvard University	1	0.92934		0.11257		0.7848		0.51304		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60968	60968	SRR12661659	SRX9142637	SRS7383941	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf20 S2	GSM4793254	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf20 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793254	GSM4793254: zBr15dpf20 S2; Danio rerio; RNA Seq	GSM4793254		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793254	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf20b S2 L004 I1 001.fastq.gz read2PairFiles=zBr15dpf20b S2 L004 R1 001.fastq.gz read3PairFiles=zBr15dpf20b S2 L004 R2 001.fastq.gz	zBr15dpf20b_S2_L004_I1_001.fastq.gz zBr15dpf20b_S2_L004_R1_001.fastq.gz zBr15dpf20b_S2_L004_R2_001.fastq.gz	fastq fastq fastq	1444856412.0	15704961.0	GSM4793254 r8	0:8 1:26 2:58	A:396739567;C:315165387;G:338739579;T:394032675;N:179204	8	26	58		396739567	315165387	338739579	394032675	179204	SRX9142637	SRS7383941	SRA1127180	GEO	Harvard University	1	0.92959		0.11443		0.78977		0.52607		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60969	60969	SRR12661644	SRX9142636	SRS7383940	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf19 S3	GSM4793253	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf19 S3	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793253	GSM4793253: zBr15dpf19 S3; Danio rerio; RNA Seq	GSM4793253		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793253	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf19 S3 L001 I1 001.fastq.gz read2PairFiles=zBr15dpf19 S3 L001 R1 001.fastq.gz read3PairFiles=zBr15dpf19 S3 L001 R2 001.fastq.gz	zBr15dpf19_S3_L001_I1_001.fastq.gz zBr15dpf19_S3_L001_R1_001.fastq.gz zBr15dpf19_S3_L001_R2_001.fastq.gz	fastq fastq fastq	1489920772.0	16194791.0	GSM4793253 r1	0:8 1:26 2:58	A:407062014;C:321593172;G:351649525;T:407464400;N:2151661	8	26	58		407062014	321593172	351649525	407464400	2151661	SRX9142636	SRS7383940	SRA1127180	GEO	Harvard University	1	0.9331		0.14403		0.77989		0.50985		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60970	60970	SRR12661645	SRX9142636	SRS7383940	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf19 S3	GSM4793253	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf19 S3	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793253	GSM4793253: zBr15dpf19 S3; Danio rerio; RNA Seq	GSM4793253		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793253	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf19 S3 L002 I1 001.fastq.gz read2PairFiles=zBr15dpf19 S3 L002 R1 001.fastq.gz read3PairFiles=zBr15dpf19 S3 L002 R2 001.fastq.gz	zBr15dpf19_S3_L002_I1_001.fastq.gz zBr15dpf19_S3_L002_R1_001.fastq.gz zBr15dpf19_S3_L002_R2_001.fastq.gz	fastq fastq fastq	1495992956.0	16260793.0	GSM4793253 r2	0:8 1:26 2:58	A:408054829;C:322778394;G:353999305;T:408963378;N:2197050	8	26	58		408054829	322778394	353999305	408963378	2197050	SRX9142636	SRS7383940	SRA1127180	GEO	Harvard University	1	0.93042		0.14077		0.77938		0.51934		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous System
60971	60971	SRR12661646	SRX9142636	SRS7383940	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532	zBr15dpf19 S3	GSM4793253	source name:zebrafish brain\|tissue:brain\|developmental stage:15dpf	zBr15dpf19 S3	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:15dpf	GSM4793253	GSM4793253: zBr15dpf19 S3; Danio rerio; RNA Seq	GSM4793253		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793253	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr15dpf19 S3 L003 I1 001.fastq.gz read2PairFiles=zBr15dpf19 S3 L003 R1 001.fastq.gz read3PairFiles=zBr15dpf19 S3 L003 R2 001.fastq.gz	zBr15dpf19_S3_L003_I1_001.fastq.gz zBr15dpf19_S3_L003_R1_001.fastq.gz zBr15dpf19_S3_L003_R2_001.fastq.gz	fastq fastq fastq	1501252504.0	16317962.0	GSM4793253 r3	0:8 1:26 2:58	A:408798507;C:323500512;G:356835387;T:410394320;N:1723778	8	26	58		408798507	323500512	356835387	410394320	1723778	SRX9142636	SRS7383940	SRA1127180	GEO	Harvard University	1	0.93178		0.13909		0.7805		0.51876		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Larval	Larval	Brain	Nervous 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");;