metadata: run_metadata: 39 rows where experiment.library_strategy = "OTHER" and tissue

39 rows where experiment.library_strategy = "OTHER" 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.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	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
43842	43842	SRR6176750	SRX3287416	SRS2596889	SRP120009	PRJNA414416	Simultaneous single cell profiling of lineages and cell types in the vertebrate brain	GSE105010	Other	The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method GESTALT used CRISPR–Cas9 barcode editing for large scale lineage tracing but was restricted to early development and did not identify cell types. Here we present scGESTALT which combines the lineage recording capabilities of GESTALT with cell type identification by single cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points capturing lineage information from later stages of development. Sequencing of 60 000 transcriptomes from the juvenile zebrafish brain identified >100 cell types and marker genes. Using these data we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types brain regions and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease. Overall design: inDrops libraries of single cell transcriptomes and scGESTALT barcodes and genomic DNA GESTALT libraries	pubmed:29608178	ZF3 scGSTLT	GSM2813986	source name:zebrafish brain\|tissue:brain\|developmental stage:23 25dpf	ZF3 scGSTLT	Single cell RNA Sequencing data FASTQ files were processed using the inDrops.py bioinformatics pipeline available at https://github.com/indrops/indrops. Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. Bowtie version1.1.1 was used with parameter –e 200; UMI quantification was used with parameter –u 2 counts were ignored from UMIs split between more than 2 genes. genomic DNA GESTALT and scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 CSV files for transcriptome data were generated using the inDrops pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for genes. Txt files for genomic DNA GESTALT libraries allReadCounts contain lineage barcode sequences HMID column for each cell and their proportion in the sequenced libraries. scGESTALT data GestMaster.txt contains the inDrops cell identifiers CellBarcode and BarcodeKey that were used to match barcodes to transcriptomes. They also contain lineage barcode sequences HMID column for each cell with a corresponding inDrops single cell gene expression profile as well as the the t SNE cluster membership number ClusterIdent column Txt files ending in *stats.txt contain information about the each individually captured UMI or cell per sample. The barcode sequence aligned to a reference unedited sequence mergedRead column mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. inDropsExpMatrix noQ txt file is the gene expression matrix for the full dataset. Columns are individual cells from different batches of whole brains f1 f2 f3 f4 f5 f6 or brain regions fore mid hind . fall.inDrops.Robj is the processed Seurat R object which can be loaded into R and explored.	zebrafish brain		Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	tissue:brain\|developmental stage:23 25dpf	GSM2813986	GSM2813986: ZF3 scGSTLT; Danio rerio; OTHER	GSM2813986		1	Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	GEO Accession:GSM2813986	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq	SRP120009	loader:fastq load.py\|options: appendBCtoName	F6_UMI.merged.fq.gz	fastq	786192951.0	2901081.0	GSM2813986 r1	0:271	A:215364033;C:176865797;G:224444690;T:169518396;N:35	271				215364033	176865797	224444690	169518396	35	SRX3287416	SRS2596889	SRA619743	GEO	Harvard University	1	0.00904		0.0		0.99997		0.0		271		T		under 1.2% mapping rate	illumina	miseq	unknown	other	unknown	sc	single_cell_droplet	indrops	United States	2017-10-16	Larval	Larval	Brain	Nervous System
43843	43843	SRR6176749	SRX3287415	SRS2596888	SRP120009	PRJNA414416	Simultaneous single cell profiling of lineages and cell types in the vertebrate brain	GSE105010	Other	The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method GESTALT used CRISPR–Cas9 barcode editing for large scale lineage tracing but was restricted to early development and did not identify cell types. Here we present scGESTALT which combines the lineage recording capabilities of GESTALT with cell type identification by single cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points capturing lineage information from later stages of development. Sequencing of 60 000 transcriptomes from the juvenile zebrafish brain identified >100 cell types and marker genes. Using these data we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types brain regions and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease. Overall design: inDrops libraries of single cell transcriptomes and scGESTALT barcodes and genomic DNA GESTALT libraries	pubmed:29608178	ZF2 scGSTLT	GSM2813985	source name:zebrafish brain\|tissue:brain\|developmental stage:23 25dpf	ZF2 scGSTLT	Single cell RNA Sequencing data FASTQ files were processed using the inDrops.py bioinformatics pipeline available at https://github.com/indrops/indrops. Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. Bowtie version1.1.1 was used with parameter –e 200; UMI quantification was used with parameter –u 2 counts were ignored from UMIs split between more than 2 genes. genomic DNA GESTALT and scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 CSV files for transcriptome data were generated using the inDrops pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for genes. Txt files for genomic DNA GESTALT libraries allReadCounts contain lineage barcode sequences HMID column for each cell and their proportion in the sequenced libraries. scGESTALT data GestMaster.txt contains the inDrops cell identifiers CellBarcode and BarcodeKey that were used to match barcodes to transcriptomes. They also contain lineage barcode sequences HMID column for each cell with a corresponding inDrops single cell gene expression profile as well as the the t SNE cluster membership number ClusterIdent column Txt files ending in *stats.txt contain information about the each individually captured UMI or cell per sample. The barcode sequence aligned to a reference unedited sequence mergedRead column mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. inDropsExpMatrix noQ txt file is the gene expression matrix for the full dataset. Columns are individual cells from different batches of whole brains f1 f2 f3 f4 f5 f6 or brain regions fore mid hind . fall.inDrops.Robj is the processed Seurat R object which can be loaded into R and explored.	zebrafish brain		Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	tissue:brain\|developmental stage:23 25dpf	GSM2813985	GSM2813985: ZF2 scGSTLT; Danio rerio; OTHER	GSM2813985		1	Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	GEO Accession:GSM2813985	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq	SRP120009	loader:fastq load.py\|options: appendBCtoName	F5_UMI.merged.fq.gz	fastq	106145626.0	391949.0	GSM2813985 r1	0:270.81	A:29282656;C:22944139;G:29276360;T:24642464;N:7	270				29282656	22944139	29276360	24642464	7	SRX3287415	SRS2596888	SRA619743	GEO	Harvard University	1	2e-05		0.0		0.99995		0.0		270		T		under 1.2% mapping rate	illumina	miseq	unknown	other	unknown	sc	single_cell_droplet	indrops	United States	2017-10-16	Larval	Larval	Brain	Nervous System
43844	43844	SRR6176748	SRX3287414	SRS2596887	SRP120009	PRJNA414416	Simultaneous single cell profiling of lineages and cell types in the vertebrate brain	GSE105010	Other	The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method GESTALT used CRISPR–Cas9 barcode editing for large scale lineage tracing but was restricted to early development and did not identify cell types. Here we present scGESTALT which combines the lineage recording capabilities of GESTALT with cell type identification by single cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points capturing lineage information from later stages of development. Sequencing of 60 000 transcriptomes from the juvenile zebrafish brain identified >100 cell types and marker genes. Using these data we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types brain regions and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease. Overall design: inDrops libraries of single cell transcriptomes and scGESTALT barcodes and genomic DNA GESTALT libraries	pubmed:29608178	ZF1 scGSTLT	GSM2813984	source name:zebrafish brain\|tissue:brain\|developmental stage:23 25dpf	ZF1 scGSTLT	Single cell RNA Sequencing data FASTQ files were processed using the inDrops.py bioinformatics pipeline available at https://github.com/indrops/indrops. Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. Bowtie version1.1.1 was used with parameter –e 200; UMI quantification was used with parameter –u 2 counts were ignored from UMIs split between more than 2 genes. genomic DNA GESTALT and scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 CSV files for transcriptome data were generated using the inDrops pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for genes. Txt files for genomic DNA GESTALT libraries allReadCounts contain lineage barcode sequences HMID column for each cell and their proportion in the sequenced libraries. scGESTALT data GestMaster.txt contains the inDrops cell identifiers CellBarcode and BarcodeKey that were used to match barcodes to transcriptomes. They also contain lineage barcode sequences HMID column for each cell with a corresponding inDrops single cell gene expression profile as well as the the t SNE cluster membership number ClusterIdent column Txt files ending in *stats.txt contain information about the each individually captured UMI or cell per sample. The barcode sequence aligned to a reference unedited sequence mergedRead column mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. inDropsExpMatrix noQ txt file is the gene expression matrix for the full dataset. Columns are individual cells from different batches of whole brains f1 f2 f3 f4 f5 f6 or brain regions fore mid hind . fall.inDrops.Robj is the processed Seurat R object which can be loaded into R and explored.	zebrafish brain		Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	tissue:brain\|developmental stage:23 25dpf	GSM2813984	GSM2813984: ZF1 scGSTLT; Danio rerio; OTHER	GSM2813984		1	Single cell suspensions were processed through inDrops to generate single cell cDNA libraries. cDNAs were in vitro transcribed reverse transcribed and prepared for sequencing Gestalt barcode was PCR amplified by two step PCR. Sample indices and flow cell adaptors were then added by PCR.	GEO Accession:GSM2813984	OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina MiSeq	SRP120009	loader:fastq load.py\|options: appendBCtoName	F3_UMI.merged.fq.gz	fastq	817055786.0	3014966.0	GSM2813984 r1	0:271	A:235846657;C:170311176;G:222336783;T:188561170;N:0	271				235846657	170311176	222336783	188561170	0	SRX3287414	SRS2596887	SRA619743	GEO	Harvard University	1	4e-05		0.0		0.99995		0.4		271		T		under 1.2% mapping rate	illumina	miseq	unknown	other	unknown	sc	single_cell_droplet	indrops	United States	2017-10-16	Larval	Larval	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
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
68382	68382	SRR17720609	SRX13883476	SRS11752245	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m7G Normoxia IP	GSM5832287	source name:zebrafish brain tissue\|tissue:brain	m7G Normoxia IP	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832287	GSM5832287: m7G Normoxia IP; Danio rerio; OTHER	GSM5832287 r1	GSM5832287	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m7G_Normoxia_IP_R1.fastq.gz m7G_Normoxia_IP_R2.fastq.gz	fastq fastq	6634104000.0	22113680.0	GSM5832287 r1	0:150 1:150	A:1396464650;C:1688319426;G:2250091870;T:1299109891;N:118163	150	150			1396464650	1688319426	2250091870	1299109891	118163	SRX13883476	SRS11752245	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.9266	0.92801	0.07275	0.06866	0.89964	0.90601	0.65995	0.75535	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68383	68383	SRR17720610	SRX13883475	SRS11752244	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m7G Normoxia Input	GSM5832286	source name:zebrafish brain tissue\|tissue:brain	m7G Normoxia Input	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832286	GSM5832286: m7G Normoxia Input; Danio rerio; OTHER	GSM5832286 r1	GSM5832286	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m7G_Normoxia_Input_R1.fastq.gz m7G_Normoxia_Input_R2.fastq.gz	fastq fastq	6839977800.0	22799926.0	GSM5832286 r1	0:150 1:150	A:1986780958;C:1411210049;G:1509902094;T:1932043482;N:41217	150	150			1986780958	1411210049	1509902094	1932043482	41217	SRX13883475	SRS11752244	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.89709	0.89888	0.21747	0.21725	0.70021	0.69936	0.50469	0.51865	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68384	68384	SRR17720611	SRX13883474	SRS11752243	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m7G Hypoxia IP	GSM5832285	source name:zebrafish brain tissue\|tissue:brain	m7G Hypoxia IP	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832285	GSM5832285: m7G Hypoxia IP; Danio rerio; OTHER	GSM5832285 r1	GSM5832285	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m7G_Hypoxia_IP_R1.fastq.gz m7G_Hypoxia_IP_R2.fastq.gz	fastq fastq	7282575000.0	24275250.0	GSM5832285 r1	0:150 1:150	A:1512757767;C:1913587260;G:2472336371;T:1383764924;N:128678	150	150			1512757767	1913587260	2472336371	1383764924	128678	SRX13883474	SRS11752243	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.94526	0.9467	0.05248	0.05071	0.91946	0.91981	0.69303	0.78448	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68385	68385	SRR17720612	SRX13883473	SRS11752241	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m7G Hypoxia Input	GSM5832284	source name:zebrafish brain tissue\|tissue:brain	m7G Hypoxia Input	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832284	GSM5832284: m7G Hypoxia Input; Danio rerio; OTHER	GSM5832284 r1	GSM5832284	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m7G_Hypoxia_Input_R1.fastq.gz m7G_Hypoxia_Input_R2.fastq.gz	fastq fastq	7492311600.0	24974372.0	GSM5832284 r1	0:150 1:150	A:2208863421;C:1521950436;G:1608371217;T:2153082842;N:43684	150	150			2208863421	1521950436	1608371217	2153082842	43684	SRX13883473	SRS11752241	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.89264	0.89479	0.23239	0.23163	0.70496	0.70311	0.51741	0.52135	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68386	68386	SRR17720613	SRX13883472	SRS11752242	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m6A Normoxia IP	GSM5832283	source name:zebrafish brain tissue\|tissue:brain	m6A Normoxia IP	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832283	GSM5832283: m6A Normoxia IP; Danio rerio; OTHER	GSM5832283 r1	GSM5832283	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476		m6A_Normoxia_IP_R1.fastq.gz m6A_Normoxia_IP_R2.fastq.gz	fastq fastq	6583667700.0	21945559.0	GSM5832283 r1	0:150 1:150	A:1750230540;C:1500991424;G:1592129260;T:1740287575;N:28901	150	150			1750230540	1500991424	1592129260	1740287575	28901	SRX13883472	SRS11752242	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.87682	0.87986	0.18203	0.17239	0.74671	0.7472	0.55638	0.55861	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68387	68387	SRR17720614	SRX13883471	SRS11752240	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m6A Normoxia Input	GSM5832282	source name:zebrafish brain tissue\|tissue:brain	m6A Normoxia Input	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832282	GSM5832282: m6A Normoxia Input; Danio rerio; OTHER	GSM5832282 r1	GSM5832282	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m6A_Normoxia_Input_R1.fastq.gz m6A_Normoxia_Input_R2.fastq.gz	fastq fastq	6314076000.0	21046920.0	GSM5832282 r1	0:150 1:150	A:1815907910;C:1329572814;G:1378464668;T:1790102301;N:28307	150	150			1815907910	1329572814	1378464668	1790102301	28307	SRX13883471	SRS11752240	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.91754	0.91835	0.21273	0.20993	0.69702	0.69625	0.53456	0.53763	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68388	68388	SRR17720615	SRX13883470	SRS11752239	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m6A Hypoxia IP	GSM5832281	source name:zebrafish brain tissue\|tissue:brain	m6A Hypoxia IP	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832281	GSM5832281: m6A Hypoxia IP; Danio rerio; OTHER	GSM5832281 r1	GSM5832281	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476		m6A_Hypoxia_IP_R1.fastq.gz m6A_Hypoxia_IP_R2.fastq.gz	fastq fastq	6490349100.0	21634497.0	GSM5832281 r1	0:150 1:150	A:1714144102;C:1483635762;G:1606044832;T:1686496024;N:28380	150	150			1714144102	1483635762	1606044832	1686496024	28380	SRX13883470	SRS11752239	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.87598	0.88161	0.16783	0.16105	0.74588	0.74568	0.55361	0.55307	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68389	68389	SRR17720616	SRX13883469	SRS11752237	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m6A Hypoxia Input	GSM5832280	source name:zebrafish brain tissue\|tissue:brain	m6A Hypoxia Input	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832280	GSM5832280: m6A Hypoxia Input; Danio rerio; OTHER	GSM5832280 r1	GSM5832280	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m6A_Hypoxia_Input_R1.fastq.gz m6A_Hypoxia_Input_R2.fastq.gz	fastq fastq	7054483800.0	23514946.0	GSM5832280 r1	0:150 1:150	A:2000164754;C:1513377207;G:1570441784;T:1970468107;N:31948	150	150			2000164754	1513377207	1570441784	1970468107	31948	SRX13883469	SRS11752237	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.91916	0.91997	0.21403	0.21158	0.69716	0.69503	0.52616	0.51982	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68390	68390	SRR17720617	SRX13883468	SRS11752238	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m5C Normoxia IP	GSM5832279	source name:zebrafish brain tissue\|tissue:brain	m5C Normoxia IP	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832279	GSM5832279: m5C Normoxia IP; Danio rerio; OTHER	GSM5832279 r1	GSM5832279	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m5C_Normoxia_IP_R1.fastq.gz m5C_Normoxia_IP_R2.fastq.gz	fastq fastq	7385723100.0	24619077.0	GSM5832279 r1	0:150 1:150	A:1779838658;C:1853060139;G:2010257354;T:1742536078;N:30871	150	150			1779838658	1853060139	2010257354	1742536078	30871	SRX13883468	SRS11752238	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.88617	0.87633	0.42619	0.41974	0.71792	0.74016	0.69827	0.68649	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68391	68391	SRR17720618	SRX13883467	SRS11752236	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m5C Normoxia Input	GSM5832278	source name:zebrafish brain tissue\|tissue:brain	m5C Normoxia Input	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832278	GSM5832278: m5C Normoxia Input; Danio rerio; OTHER	GSM5832278 r1	GSM5832278	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m5C_Normoxia_Input_R1.fastq.gz m5C_Normoxia_Input_R2.fastq.gz	fastq fastq	6594811500.0	21982705.0	GSM5832278 r1	0:150 1:150	A:1941068575;C:1341378672;G:1414823713;T:1897501503;N:39037	150	150			1941068575	1341378672	1414823713	1897501503	39037	SRX13883467	SRS11752236	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.89423	0.89602	0.22595	0.2243	0.70212	0.70112	0.52954	0.52253	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68392	68392	SRR17720619	SRX13883466	SRS11752235	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m5C Hypoxia IP	GSM5832277	source name:zebrafish brain tissue\|tissue:brain	m5C Hypoxia IP	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832277	GSM5832277: m5C Hypoxia IP; Danio rerio; OTHER	GSM5832277 r1	GSM5832277	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m5C_Hypoxia_IP_R1.fastq.gz m5C_Hypoxia_IP_R2.fastq.gz	fastq fastq	7837067100.0	26123557.0	GSM5832277 r1	0:150 1:150	A:1881167242;C:1973697370;G:2143523979;T:1838645554;N:32955	150	150			1881167242	1973697370	2143523979	1838645554	32955	SRX13883466	SRS11752235	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.87593	0.87108	0.45438	0.45093	0.71664	0.7321	0.67861	0.69742	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68393	68393	SRR17720620	SRX13883465	SRS11752233	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m5C Hypoxia Input	GSM5832276	source name:zebrafish brain tissue\|tissue:brain	m5C Hypoxia Input	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832276	GSM5832276: m5C Hypoxia Input; Danio rerio; OTHER	GSM5832276 r1	GSM5832276	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m5C_Hypoxia_Input_R1.fastq.gz m5C_Hypoxia_Input_R2.fastq.gz	fastq fastq	8696183100.0	28987277.0	GSM5832276 r1	0:150 1:150	A:2564166903;C:1771446935;G:1858965930;T:2501551942;N:51390	150	150			2564166903	1771446935	1858965930	2501551942	51390	SRX13883465	SRS11752233	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.89379	0.89585	0.23898	0.23828	0.70272	0.70278	0.52965	0.50047	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68394	68394	SRR17720621	SRX13883464	SRS11752234	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m1A Normoxia IP	GSM5832275	source name:zebrafish brain tissue\|tissue:brain	m1A Normoxia IP	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832275	GSM5832275: m1A Normoxia IP; Danio rerio; OTHER	GSM5832275 r1	GSM5832275	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m1A_Normoxia_IP_R1.fastq.gz m1A_Normoxia_IP_R2.fastq.gz	fastq fastq	6882734400.0	22942448.0	GSM5832275 r1	0:150 1:150	A:1321946139;C:1977632664;G:2310916241;T:1272200359;N:38997	150	150			1321946139	1977632664	2310916241	1272200359	38997	SRX13883464	SRS11752234	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.88367	0.88951	0.09774	0.09525	0.86395	0.86401	0.70125	0.74894	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68395	68395	SRR17720622	SRX13883463	SRS11752232	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m1A Normoxia Input	GSM5832274	source name:zebrafish brain tissue\|tissue:brain	m1A Normoxia Input	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832274	GSM5832274: m1A Normoxia Input; Danio rerio; OTHER	GSM5832274 r1	GSM5832274	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m1A_Normoxia_Input_R1.fastq.gz m1A_Normoxia_Input_R2.fastq.gz	fastq fastq	7374452700.0	24581509.0	GSM5832274 r1	0:150 1:150	A:1511389847;C:2082118937;G:2325922232;T:1454979400;N:42284	150	150			1511389847	2082118937	2325922232	1454979400	42284	SRX13883463	SRS11752232	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.94589	0.94385	0.18226	0.18222	0.80878	0.8102	0.73686	0.71921	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68396	68396	SRR17720623	SRX13883462	SRS11752231	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m1A Hypoxia IP	GSM5832273	source name:zebrafish brain tissue\|tissue:brain	m1A Hypoxia IP	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832273	GSM5832273: m1A Hypoxia IP; Danio rerio; OTHER	GSM5832273 r1	GSM5832273	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m1A_Hypoxia_IP_R1.fastq.gz m1A_Hypoxia_IP_R2.fastq.gz	fastq fastq	4861573800.0	16205246.0	GSM5832273 r1	0:150 1:150	A:927063480;C:1355342107;G:1698345464;T:880801957;N:20792	150	150			927063480	1355342107	1698345464	880801957	20792	SRX13883462	SRS11752231	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.8575	0.86165	0.10013	0.09909	0.87249	0.87221	0.72225	0.66629	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
68397	68397	SRR17720624	SRX13883461	SRS11752229	SRP356476	PRJNA800053	Mapping the m1A m5C m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq	GSE194284	Other	The epigenetic modifications play important regulatory roles in tissue development maintenance of physiological functions and pathological process. RNA methylations including newly identified m1A m5C m6A and m7G are important epigenetic modifications. However how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A m5C m6A and m7G methylation of mRNA we found that within the whole brain transcriptome with the increase of the gene expression levels the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains the proportion of m1A is decreased affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A m5C m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A m5C m6A and m7G in the regulation of miRNA and repeat elements in vertebrates and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group 10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A m5C m6A m7G and RNA Seq the normoxia group and hypoxic group each consisted of 30 mixed …	pubmed:35135476	m1A Hypoxia Input	GSM5832272	source name:zebrafish brain tissue\|tissue:brain	m1A Hypoxia Input	Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3 command line software was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script findMotifGenome.pl from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites	zebrafish brain tissue	Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes when the fish became motionless the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq	tissue:brain	GSM5832272	GSM5832272: m1A Hypoxia Input; Danio rerio; OTHER	GSM5832272 r1	GSM5832272	1	Ribo Zero rRNA Removal Kits Illumina San Diego CA USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina San Diego CA USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc. China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs Inc. USA RNA seq and MeRIP seq		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP356476	loader:fastq load.py	m1A_Hypoxia_Input_R1.fastq.gz m1A_Hypoxia_Input_R2.fastq.gz	fastq fastq	7262130600.0	24207102.0	GSM5832272 r1	0:150 1:150	A:1553326396;C:2003023914;G:2214285414;T:1491453374;N:41502	150	150			1553326396	2003023914	2214285414	1491453374	41502	SRX13883461	SRS11752229	SRA1361294	Affiliated Hospital of Guangdong Medical University	Affiliated Hospital of Guangdong Medical University	2	0.94247	0.94013	0.20625	0.20507	0.80188	0.80137	0.70188	0.73891	150	150	B	B	biological fallback assumption	illumina	novaseq_era	full_length	rrna_depletion	nebnext	bulk	bulk	bulk	China	2022-01-24	Adult	Adult	Brain	Nervous System
74615	74615	SRR24037111	SRX19839674	SRS17198396	SRP427499	PRJNA945049	linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells	PRJNA945049	Other	Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep also called lnc rps25 and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein Hmgn1 and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions with implications for neurodevelopmental disorders and disease.		linc mipep scMultiome 6d brains Wild type linc mipep siblings scRNA seq [10x BAM]	linc mipep scMultiome 6d brains WT scRNA AGN002631 [10x BAM]	strain:TU/AB\|age:144\|dev stage:Day 6\|sex:pooled male and female\|tissue:brain\|genotype:+/+\|strain maternal:linc mipep WT\|strain paternal:linc mipep WT\|molecule:RNA\|sample ref:AGS002041\|replicate ref:AGN002631\|replicate order:1\|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains\|project label short:linc mipep scMultiome 6d brains\|sample label short:WT RNA\|replicate label short:WT scRNA\|filetype:bam\|BioSampleModel:Model organism or animal								linc mipep scMultiome 6d brains Wild type linc mipep siblings scRNA seq [10x BAM]	AGR003365 AGR003384	AGR003365 AGR003384	RNA			OTHER	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP427499	assembly:GRCz11	linc_mipep_scMultiome_6d_brains_WT_AGN002631_gex_possorted_bam.bam	10X Genomics bam file	17819875800.0	197998620.0	linc mipep scMultiome 6d brains WT AGN002631 gex possorted bam.bam	0:90	A:5656585750;C:3315807167;G:3546967171;T:5300024689;N:491023	90				5656585750	3315807167	3546967171	5300024689	491023	SRX19839674	SRS17198396	SRA1614141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.87958		0.45053		0.7709		0.50096		90		B		usable mapping rate	illumina	novaseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2023-03-31	Larval	Larval	Brain	Nervous System
74616	74616	SRR24037113	SRX19839672	SRS17198394	SRP427499	PRJNA945049	linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells	PRJNA945049	Other	Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep also called lnc rps25 and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein Hmgn1 and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions with implications for neurodevelopmental disorders and disease.		linc mipep scMultiome 6d brains linc mipep mutant scRNA seq [10x BAM]	linc mipep scMultiome 6d brains linc mipepMut scRNA AGN002629 [10x BAM]	strain:TU/AB\|age:144\|dev stage:Day 6\|sex:pooled male and female\|tissue:brain\|genotype: / \|strain maternal:linc mipep MUT\|strain paternal:linc mipep MUT\|molecule:RNA\|sample ref:AGS002016\|replicate ref:AGN002629\|replicate order:1\|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains\|project label short:linc mipep scMultiome 6d brains\|sample label short:Mut RNA\|replicate label short:linc mipepMut scRNA\|filetype:bam\|BioSampleModel:Model organism or animal								linc mipep scMultiome 6d brains linc mipep mutant scRNA seq [10x BAM]	AGR003363 AGR003382	AGR003363 AGR003382	RNA			OTHER	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP427499	assembly:GRCz11	linc_mipep_scMultiome_6d_brains_Mut_AGN002629_gex_possorted_bam.bam	10X Genomics bam file	18530138610.0	205890429.0	linc mipep scMultiome 6d brains Mut AGN002629 gex possorted bam.bam	0:90	A:5801406623;C:3514275581;G:3726649190;T:5487294607;N:512609	90				5801406623	3514275581	3726649190	5487294607	512609	SRX19839672	SRS17198394	SRA1614141	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.89012		0.4464		0.76867		0.52212		90		B		usable mapping rate	illumina	novaseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2023-03-31	Larval	Larval	Brain	Nervous System
74617	74617	SRR24010013	SRX19812857	SRS17053325	SRP427499	PRJNA945049	linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells	PRJNA945049	Other	Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep also called lnc rps25 and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein Hmgn1 and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions with implications for neurodevelopmental disorders and disease.		linc mipep scMultiome 6d brains Wild type linc mipep siblings scRNA seq	linc mipep scMultiome 6d brains WT scRNA AGN002631	strain:TU/AB\|age:144\|dev stage:Day 6\|sex:pooled male and female\|tissue:brain\|genotype:+/+\|strain maternal:linc mipep WT\|strain paternal:linc mipep WT\|molecule:RNA\|sample ref:AGS002041\|replicate ref:AGN002631\|replicate order:1\|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains\|project label short:linc mipep scMultiome 6d brains\|sample label short:WT RNA\|replicate label short:WT scRNA\|BioSampleModel:Model organism or animal								linc mipep scMultiome 6d brains Wild type linc mipep siblings scRNA seq	AGR003384	AGR003384	RNA			OTHER	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP427499		AGR003384_I1.fastq.gz AGR003384_R1.fastq.gz AGR003384_R2.fastq.gz AGR003384_R3.fastq.gz	fastq fastq fastq fastq	27323809560.0	197998620.0	AGR003384 I1.fastq.gz	0:10 1:28 2:10 3:90	A:5656585750;C:3315807167;G:3546967171;T:5300024689;N:491023	10	28	10	90	5656585750	3315807167	3546967171	5300024689	491023	SRX19812857	SRS17053325	SRA1612740	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.87892		0.45104		0.76976		0.49827		90		B		usable mapping rate	illumina	novaseq_era	unknown	unknown	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2023-03-29	Larval	Larval	Brain	Nervous System
74618	74618	SRR24010014	SRX19812856	SRS17053325	SRP427499	PRJNA945049	linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells	PRJNA945049	Other	Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep also called lnc rps25 and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein Hmgn1 and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions with implications for neurodevelopmental disorders and disease.		linc mipep scMultiome 6d brains Wild type linc mipep siblings scRNA seq	linc mipep scMultiome 6d brains WT scRNA AGN002631	strain:TU/AB\|age:144\|dev stage:Day 6\|sex:pooled male and female\|tissue:brain\|genotype:+/+\|strain maternal:linc mipep WT\|strain paternal:linc mipep WT\|molecule:RNA\|sample ref:AGS002041\|replicate ref:AGN002631\|replicate order:1\|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains\|project label short:linc mipep scMultiome 6d brains\|sample label short:WT RNA\|replicate label short:WT scRNA\|BioSampleModel:Model organism or animal								linc mipep scMultiome 6d brains Wild type linc mipep siblings scRNA seq	AGR003365	AGR003365	RNA			OTHER	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP427499		AGR003365_I1.fastq.gz AGR003365_R1.fastq.gz AGR003365_R2.fastq.gz AGR003365_R3.fastq.gz	fastq fastq fastq fastq	1086745584.0	7874968.0	AGR003365 I1.fastq.gz	0:10 1:28 2:10 3:90	A:224554980;C:132053090;G:141496532;T:210627089;N:15429	10	28	10	90	224554980	132053090	141496532	210627089	15429	SRX19812856	SRS17053325	SRA1612740	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.87972		0.45315		0.77011		0.49128		90		B		usable mapping rate	illumina	novaseq_era	unknown	unknown	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2023-03-29	Larval	Larval	Brain	Nervous System
74619	74619	SRR24010017	SRX19812853	SRS17053323	SRP427499	PRJNA945049	linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells	PRJNA945049	Other	Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep also called lnc rps25 and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein Hmgn1 and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions with implications for neurodevelopmental disorders and disease.		linc mipep scMultiome 6d brains linc mipep mutant scRNA seq	linc mipep scMultiome 6d brains linc mipepMut scRNA AGN002629	strain:TU/AB\|age:144\|dev stage:Day 6\|sex:pooled male and female\|tissue:brain\|genotype: / \|strain maternal:linc mipep MUT\|strain paternal:linc mipep MUT\|molecule:RNA\|sample ref:AGS002016\|replicate ref:AGN002629\|replicate order:1\|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains\|project label short:linc mipep scMultiome 6d brains\|sample label short:Mut RNA\|replicate label short:linc mipepMut scRNA\|BioSampleModel:Model organism or animal								linc mipep scMultiome 6d brains linc mipep mutant scRNA seq	AGR003382	AGR003382	RNA			OTHER	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP427499		AGR003382_I1.fastq.gz AGR003382_R1.fastq.gz AGR003382_R2.fastq.gz AGR003382_R3.fastq.gz	fastq fastq fastq fastq	28412879202.0	205890429.0	AGR003382 I1.fastq.gz	0:10 1:28 2:10 3:90	A:5801406623;C:3514275581;G:3726649190;T:5487294607;N:512609	10	28	10	90	5801406623	3514275581	3726649190	5487294607	512609	SRX19812853	SRS17053323	SRA1612740	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.89026		0.44521		0.76905		0.51993		90		B		usable mapping rate	illumina	novaseq_era	unknown	unknown	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2023-03-29	Larval	Larval	Brain	Nervous System
74620	74620	SRR24010018	SRX19812852	SRS17053323	SRP427499	PRJNA945049	linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells	PRJNA945049	Other	Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep also called lnc rps25 and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein Hmgn1 and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions with implications for neurodevelopmental disorders and disease.		linc mipep scMultiome 6d brains linc mipep mutant scRNA seq	linc mipep scMultiome 6d brains linc mipepMut scRNA AGN002629	strain:TU/AB\|age:144\|dev stage:Day 6\|sex:pooled male and female\|tissue:brain\|genotype: / \|strain maternal:linc mipep MUT\|strain paternal:linc mipep MUT\|molecule:RNA\|sample ref:AGS002016\|replicate ref:AGN002629\|replicate order:1\|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains\|project label short:linc mipep scMultiome 6d brains\|sample label short:Mut RNA\|replicate label short:linc mipepMut scRNA\|BioSampleModel:Model organism or animal								linc mipep scMultiome 6d brains linc mipep mutant scRNA seq	AGR003363	AGR003363	RNA			OTHER	TRANSCRIPTOMIC	unspecified	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP427499		AGR003363_I1.fastq.gz AGR003363_R1.fastq.gz AGR003363_R2.fastq.gz AGR003363_R3.fastq.gz	fastq fastq fastq fastq	1373742804.0	9954658.0	AGR003363 I1.fastq.gz	0:10 1:28 2:10 3:90	A:279788766;C:170196269;G:180765631;T:265150486;N:18068	10	28	10	90	279788766	170196269	180765631	265150486	18068	SRX19812852	SRS17053323	SRA1612740	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.88902		0.44548		0.76879		0.52005		90		B		usable mapping rate	illumina	novaseq_era	unknown	unknown	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2023-03-29	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");;