metadata: run_metadata: 74 rows where devstage_curation_coarse = "Adult" and experiment.library

74 rows where devstage_curation_coarse = "Adult" and experiment.library_strategy = "OTHER"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.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
29746	29746	SRR27467679	SRX23139227	SRS20090270	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary BS R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: ovary BS rep2	EV02003	EV02003	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	NextSeq 500	SRP482074		EV02003.R1.fastq.gz EV02003.R2.fastq.gz	fastq fastq	1031891720.0	3416860.0	EV02003.R1.fastq.gz	0:151 1:151	A:264464363;C:153440613;G:408557241;T:205367487;N:62016	151	151		264464363	153440613	408557241	205367487	62016	SRX23139227	SRS20090270	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	2	0.0	0.00019	0.0	0.00015	1.0	0.99993		1.0	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Adult	Adult	Gonad	Reproductive System
29755	29755	SRR27467688	SRX23139218	SRS20090261	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary DM R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: ovary DM rep2	EV02002	EV02002	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	NextSeq 500	SRP482074		EV02002.R1.fastq.gz EV02002.R2.fastq.gz	fastq fastq	861320308.0	2852054.0	EV02002.R1.fastq.gz	0:151 1:151	A:205625519;C:162178974;G:334206312;T:159256900;N:52603	151	151		205625519	162178974	334206312	159256900	52603	SRX23139218	SRS20090261	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	2	2e-05	0.00049	0.0	0.00027	1.0	0.99947		0.44444	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Adult	Adult	Gonad	Reproductive System
29756	29756	SRR27467689	SRX23139217	SRS20090260	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary mock R2	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: ovary mock rep2	EV02001	EV02001	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	PAIRED	ILLUMINA	NextSeq 500	SRP482074		EV02001.R1.fastq.gz EV02001.R2.fastq.gz	fastq fastq	520371066.0	1723083.0	EV02001.R1.fastq.gz	0:151 1:151	A:116107273;C:90896560;G:218652568;T:94682244;N:32421	151	151		116107273	90896560	218652568	94682244	32421	SRX23139217	SRS20090260	SRA1781872	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	2	2e-05	0.00086	0.0	0.00078	0.99995	0.99981	0.0	0.61538	151	151	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-09	Adult	Adult	Gonad	Reproductive System
29765	29765	SRR27437485	SRX23109812	SRS20064566	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary BS R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: ovary BS rep3	EV04017	EV04017	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074		EV04017.R1.fastq.gz	fastq	576584540.0	4118461.0	EV04017.R1.fastq.gz	0:140	A:149516980;C:91163801;G:169046762;T:166831111;N:25886	140			149516980	91163801	169046762	166831111	25886	SRX23109812	SRS20064566	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.0		0.0		1.0				140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Adult	Adult	Gonad	Reproductive System
29776	29776	SRR27437496	SRX23109801	SRS20064555	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary DM R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: ovary DM rep3	EV04016	EV04016	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074		EV04016.R1.fastq.gz	fastq	635752880.0	4541092.0	EV04016.R1.fastq.gz	0:140	A:160072248;C:143996869;G:189137330;T:142516059;N:30374	140			160072248	143996869	189137330	142516059	30374	SRX23109801	SRS20064555	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	1e-05		0.0		0.99997		1.0		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Adult	Adult	Gonad	Reproductive System
29777	29777	SRR27437497	SRX23109800	SRS20064554	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary mock R3	strain:TLAB fish\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: ovary mock rep3	EV04015	EV04015	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074		EV04015.R1.fastq.gz	fastq	489700680.0	3497862.0	EV04015.R1.fastq.gz	0:140	A:126641754;C:126582886;G:130564204;T:105889815;N:22021	140			126641754	126582886	130564204	105889815	22021	SRX23109800	SRS20064554	SRA1780298	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	6e-05		0.0		0.99983		0.55555		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-06	Adult	Adult	Gonad	Reproductive System
29786	29786	SRR27435871	SRX23108225	SRS20063062	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary BS R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:BS\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: ovary BS rep4	EV08003	EV08003	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074		EV08003.R1.fastq.gz	fastq	571689580.0	4083497.0	EV08003.R1.fastq.gz	0:140	A:141414131;C:88722455;G:138790445;T:202723075;N:39474	140			141414131	88722455	138790445	202723075	39474	SRX23108225	SRS20063062	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	3e-05		0.0		0.99991		0.75		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Adult	Adult	Gonad	Reproductive System
29797	29797	SRR27435882	SRX23108214	SRS20063050	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary DM R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:DM\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: ovary DM rep4	EV08002	EV08002	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074		EV08002.R1.fastq.gz	fastq	668593800.0	4775670.0	EV08002.R1.fastq.gz	0:140	A:164584224;C:175789134;G:175538168;T:152637106;N:45168	140			164584224	175789134	175538168	152637106	45168	SRX23108214	SRS20063050	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00525		2e-05		0.99192		0.63501		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Adult	Adult	Gonad	Reproductive System
29798	29798	SRR27435883	SRX23108213	SRS20063051	SRP482074	PRJNA1061456	tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development	PRJNA1061456	Other					ovary mock R4	strain:TLAB fish\|isolate:NA\|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin\|cultivar:NA\|ecotype:NA\|dev stage:adult\|collection date:2022\|geo loc name:Austria\|sex:female\|tissue:ovary\|treatment:mock\|BioSampleModel:Model organism or animal									tRAM seq of zebrafish: ovary mock rep4	EV08001	EV08001	RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.			OTHER	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP482074		EV08001.R1.fastq.gz	fastq	753247460.0	5380339.0	EV08001.R1.fastq.gz	0:140	A:183862675;C:196453674;G:197604061;T:175275086;N:51964	140			183862675	196453674	197604061	175275086	51964	SRX23108213	SRS20063051	SRA1780265	Medical University of Vienna\|Cell and Developmental Biology	Medical University of Vienna	1	0.00754		4e-05		0.98957		0.51048		140		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Austria	2024-01-05	Adult	Adult	Gonad	Reproductive System
32508	32508	SRR29290248	SRX24807391	SRS21522263	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		15 days experimental group parallel 1	liver transcriptome	L4 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 09\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 14\|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L4 1	L4 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TMFA6-7L.R1.fq.gz TMFA6-7L.R2.fq.gz	fastq fastq	5892231600.0	19640772.0	TMFA6 7L.R1.fq.gz	0:150 1:150	A:1471743634;C:1450664701;G:1502453832;T:1466956960;N:412473	150	150		1471743634	1450664701	1502453832	1466956960	412473	SRX24807391	SRS21522263	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32509	32509	SRR29290249	SRX24807390	SRS21522262	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		30 days experimental group parallel 3	liver transcriptome	L3 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 23\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 13\|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L3 3	L3 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TLSC-5L.R1.fq.gz TLSC-5L.R2.fq.gz	fastq fastq	6269295000.0	20897650.0	TLSC 5L.R1.fq.gz	0:150 1:150	A:1541736942;C:1578334203;G:1620160556;T:1528907120;N:156179	150	150		1541736942	1578334203	1620160556	1528907120	156179	SRX24807390	SRS21522262	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32510	32510	SRR29290250	SRX24807389	SRS21522261	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		30 days experimental group parallel 2	liver transcriptome	L3 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 23\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 12\|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L3 2	L3 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TLSB-3L.R1.fq.gz TLSB-3L.R2.fq.gz	fastq fastq	6206673000.0	20688910.0	TLSB 3L.R1.fq.gz	0:150 1:150	A:1592564670;C:1487253074;G:1531600191;T:1595004475;N:250590	150	150		1592564670	1487253074	1531600191	1595004475	250590	SRX24807389	SRS21522261	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32511	32511	SRR29290251	SRX24807388	SRS21522260	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		30 days experimental group parallel 1	liver transcriptome	L3 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 23\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 11\|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L3 1	L3 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TLSA-1L.R1.fq.gz TLSA-1L.R2.fq.gz	fastq fastq	6188928300.0	20629761.0	TLSA 1L.R1.fq.gz	0:150 1:150	A:1584479312;C:1464260894;G:1549296685;T:1590644766;N:246643	150	150		1584479312	1464260894	1549296685	1590644766	246643	SRX24807388	SRS21522260	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32512	32512	SRR29290252	SRX24807387	SRS21522259	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		15 days experimental group parallel 3	liver transcriptome	L2 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 08\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 16\|experiment description:Exposed to 120 or above tire wear particles for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L2 3	L2 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TLFC1-3L.R1.fq.gz TLFC1-3L.R2.fq.gz	fastq fastq	6367070400.0	21223568.0	TLFC1 3L.R1.fq.gz	0:150 1:150	A:1579430230;C:1587605262;G:1613210542;T:1586578782;N:245584	150	150		1579430230	1587605262	1613210542	1586578782	245584	SRX24807387	SRS21522259	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32513	32513	SRR29290253	SRX24807386	SRS21522258	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		15 days experimental group parallel 2	liver transcriptome	L2 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 08\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 15\|experiment description:Exposed to 120 or above tire wear particles for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L2 2	L2 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TLFB1-3L.R1.fq.gz TLFB1-3L.R2.fq.gz	fastq fastq	6996653100.0	23322177.0	TLFB1 3L.R1.fq.gz	0:150 1:150	A:1803878205;C:1678057588;G:1715367000;T:1799170285;N:180022	150	150		1803878205	1678057588	1715367000	1799170285	180022	SRX24807386	SRS21522258	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32514	32514	SRR29290254	SRX24807385	SRS21522257	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		15 days experimental group parallel 1	liver transcriptome	L2 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 08\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 14\|experiment description:Exposed to 120 or above tire wear particles for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L2 1	L2 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TLFA6-7L.R1.fq.gz TLFA6-7L.R2.fq.gz	fastq fastq	6109509300.0	20365031.0	TLFA6 7L.R1.fq.gz	0:150 1:150	A:1525902154;C:1507317327;G:1549698641;T:1526193716;N:397462	150	150		1525902154	1507317327	1549698641	1526193716	397462	SRX24807385	SRS21522257	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32515	32515	SRR29290255	SRX24807384	SRS21522256	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		30 days experimental group parallel 3	liver transcriptome	L7 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 25\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 13\|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L7 3	L7 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TSSC-5L.R1.fq.gz TSSC-5L.R2.fq.gz	fastq fastq	6846271200.0	22820904.0	TSSC 5L.R1.fq.gz	0:150 1:150	A:1704275603;C:1639794530;G:1792628691;T:1709317043;N:255333	150	150		1704275603	1639794530	1792628691	1709317043	255333	SRX24807384	SRS21522256	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32516	32516	SRR29290256	SRX24807383	SRS21522255	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		Control parallel 3	liver transcriptome	L1 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 11\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 13\|experiment description:Sample from control group\|BioSampleModel:Model organism or animal									Zebrafish liver	L1 3	L1 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		FCFC1-3L.R1.fq.gz FCFC1-3L.R2.fq.gz	fastq fastq	6360438000.0	21201460.0	FCFC1 3L.R1.fq.gz	0:150 1:150	A:1591177652;C:1544470038;G:1615057708;T:1609485267;N:247335	150	150		1591177652	1544470038	1615057708	1609485267	247335	SRX24807383	SRS21522255	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32517	32517	SRR29290257	SRX24807382	SRS21522254	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		30 days experimental group parallel 2	liver transcriptome	L7 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 25\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 12\|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L7 2	L7 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TSSB-3L.R1.fq.gz TSSB-3L.R2.fq.gz	fastq fastq	6285285600.0	20950952.0	TSSB 3L.R1.fq.gz	0:150 1:150	A:1584093051;C:1516123512;G:1599998121;T:1584824364;N:246552	150	150		1584093051	1516123512	1599998121	1584824364	246552	SRX24807382	SRS21522254	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32518	32518	SRR29290258	SRX24807381	SRS21522253	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		30 days experimental group parallel 1	liver transcriptome	L7 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 25\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 11\|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L7 1	L7 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TSSA-1L.R1.fq.gz TSSA-1L.R2.fq.gz	fastq fastq	6078740100.0	20262467.0	TSSA 1L.R1.fq.gz	0:150 1:150	A:1530149533;C:1486474895;G:1528868563;T:1533006599;N:240510	150	150		1530149533	1486474895	1528868563	1533006599	240510	SRX24807381	SRS21522253	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32519	32519	SRR29290259	SRX24807380	SRS21522252	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		15 days experimental group parallel 3	liver transcriptome	L6 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 10\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 16\|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L6 3	L6 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TSFC1-3L.R1.fq.gz TSFC1-3L.R2.fq.gz	fastq fastq	6857466600.0	22858222.0	TSFC1 3L.R1.fq.gz	0:150 1:150	A:1755136176;C:1642995302;G:1688825155;T:1770233592;N:276375	150	150		1755136176	1642995302	1688825155	1770233592	276375	SRX24807380	SRS21522252	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32520	32520	SRR29290260	SRX24807379	SRS21522251	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		15 days experimental group parallel 2	liver transcriptome	L6 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 10\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 15\|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L6 2	L6 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TSFB1-3L.R1.fq.gz TSFB1-3L.R2.fq.gz	fastq fastq	7250329800.0	24167766.0	TSFB1 3L.R1.fq.gz	0:150 1:150	A:1825803037;C:1766132142;G:1813762639;T:1844348502;N:283480	150	150		1825803037	1766132142	1813762639	1844348502	283480	SRX24807379	SRS21522251	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32521	32521	SRR29290261	SRX24807378	SRS21522250	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		15 days experimental group parallel 1	liver transcriptome	L6 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 10\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 14\|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L6 1	L6 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TSFA1-3L.R1.fq.gz TSFA1-3L.R2.fq.gz	fastq fastq	6257752800.0	20859176.0	TSFA1 3L.R1.fq.gz	0:150 1:150	A:1588621972;C:1490176001;G:1573465475;T:1605244426;N:244926	150	150		1588621972	1490176001	1573465475	1605244426	244926	SRX24807378	SRS21522250	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32522	32522	SRR29290262	SRX24807377	SRS21522249	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		30 days experimental group parallel 3	liver transcriptome	L5 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 24\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 13\|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L5 3	L5 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TMSC-5L.R1.fq.gz TMSC-5L.R2.fq.gz	fastq fastq	6227549100.0	20758497.0	TMSC 5L.R1.fq.gz	0:150 1:150	A:1601663321;C:1467885504;G:1549957271;T:1607796578;N:246426	150	150		1601663321	1467885504	1549957271	1607796578	246426	SRX24807377	SRS21522249	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32523	32523	SRR29290263	SRX24807376	SRS21522248	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		30 days experimental group parallel 2	liver transcriptome	L5 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 24\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 12\|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L5 2	L5 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TMSB-3L.R1.fq.gz TMSB-3L.R2.fq.gz	fastq fastq	5889087600.0	19630292.0	TMSB 3L.R1.fq.gz	0:150 1:150	A:1507527640;C:1395223794;G:1475557797;T:1510549619;N:228750	150	150		1507527640	1395223794	1475557797	1510549619	228750	SRX24807376	SRS21522248	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32524	32524	SRR29290264	SRX24807375	SRS21522247	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		30 days experimental group parallel 1	liver transcriptome	L5 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 24\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 11\|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L5 1	L5 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TMSA-1L.R1.fq.gz TMSA-1L.R2.fq.gz	fastq fastq	6438780300.0	21462601.0	TMSA 1L.R1.fq.gz	0:150 1:150	A:1651115385;C:1542448300;G:1589631411;T:1655336061;N:249143	150	150		1651115385	1542448300	1589631411	1655336061	249143	SRX24807375	SRS21522247	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32525	32525	SRR29290265	SRX24807374	SRS21522246	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		15 days experimental group parallel 3	liver transcriptome	L4 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 09\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 16\|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L4 3	L4 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TMFC1-3L.R1.fq.gz TMFC1-3L.R2.fq.gz	fastq fastq	6083883300.0	20279611.0	TMFC1 3L.R1.fq.gz	0:150 1:150	A:1510698562;C:1511134044;G:1540128451;T:1521679717;N:242526	150	150		1510698562	1511134044	1540128451	1521679717	242526	SRX24807374	SRS21522246	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32526	32526	SRR29290266	SRX24807373	SRS21522245	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		15 days experimental group parallel 2	liver transcriptome	L4 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 09\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 15\|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal									Zebrafish liver	L4 2	L4 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		TMFB1-3L.R1.fq.gz TMFB1-3L.R2.fq.gz	fastq fastq	5908013700.0	19693379.0	TMFB1 3L.R1.fq.gz	0:150 1:150	A:1507137134;C:1415511620;G:1463261753;T:1521838130;N:265063	150	150		1507137134	1415511620	1463261753	1521838130	265063	SRX24807373	SRS21522245	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32527	32527	SRR29290267	SRX24807372	SRS21522244	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		Control parallel 2	liver transcriptome	L1 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 11\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 12\|experiment description:Sample from control group\|BioSampleModel:Model organism or animal									Zebrafish liver	L1 2	L1 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		FCFB1-3L.R1.fq.gz FCFB1-3L.R2.fq.gz	fastq fastq	6637856700.0	22126189.0	FCFB1 3L.R1.fq.gz	0:150 1:150	A:1714779556;C:1575842801;G:1628771136;T:1718209685;N:253522	150	150		1714779556	1575842801	1628771136	1718209685	253522	SRX24807372	SRS21522244	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32528	32528	SRR29290268	SRX24807371	SRS21522243	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles		Control parallel 1	liver transcriptome	L1 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 11\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 11\|experiment description:Sample from control group\|BioSampleModel:Model organism or animal									Zebrafish liver	L1 1	L1 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP511901		FCFA1-3L.R1.fq.gz FCFA1-3L.R2.fq.gz	fastq fastq	7360809900.0	24536033.0	FCFA1 3L.R1.fq.gz	0:150 1:150	A:1885247052;C:1777296186;G:1818891778;T:1879185198;N:189686	150	150		1885247052	1777296186	1818891778	1879185198	189686	SRX24807371	SRS21522243	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32858	32858	SRR29482326	SRX24993370	SRS21694834	SRP515140	PRJNA1126247	Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq]	GSE270356	Other	Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly melanoma only develops from melanocytes lining internal organs analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations. Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.			Internal melanocytes	GSM8340241	source name:Internal melanocytes\|tissue:Internal melanocytes\|cell type:melanocytes\|genotype:mitfa / ; roy / fish injected with mitfa:GFP\|geo loc name:missing\|collection date:missing	Internal melanocytes	BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq	Internal melanocytes		Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.	mitfa / ; roy / zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues	tissue:Internal melanocytes\|cell type:melanocytes\|genotype:mitfa / ; roy / fish injected with mitfa:GFP	GSM8340241	GSM8340241: Internal melanocytes; Danio rerio; OTHER	GSM8340241 r1	GSM8340241	1	Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP515140		HAR-MI-002_H5GCWBGXF_R2.fastq.gz HAR-MI-002_H5GCWBGXF_R1.fastq.gz	fastq fastq	2957975418.0	34395063.0	GSM8340241 r1	0:26 1:60	A:738954503;C:560052455;G:520746060;T:1137116132;N:1106268	26	60		738954503	560052455	520746060	1137116132	1106268	SRX24993370	SRS21694834	SRA1904773	Insco Lab, Medical Oncology, Dana Farber Cancer Institute	Insco Lab, Medical Oncology, Dana Farber Cancer Institute	2	0.11637	0.84116	0.10894	0.31188	0.98851	0.71526	0.6688	0.60221	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	small_rna	trueseq	sc	single_cell_plate	celseq	United States	2024-06-20	Undetermined	Adult	Skin	Surface Structure
32859	32859	SRR29482327	SRX24993369	SRS21694833	SRP515140	PRJNA1126247	Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq]	GSE270356	Other	Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly melanoma only develops from melanocytes lining internal organs analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations. Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.			Cutaneous melanocytes	GSM8340240	source name:Cutaneous melanocytes\|tissue:Cutaneous melanocytes\|cell type:melanocytes\|genotype:mitfa / ; roy / fish injected with mitfa:GFP\|geo loc name:missing\|collection date:missing	Cutaneous melanocytes	BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq	Cutaneous melanocytes		Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.	mitfa / ; roy / zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues	tissue:Cutaneous melanocytes\|cell type:melanocytes\|genotype:mitfa / ; roy / fish injected with mitfa:GFP	GSM8340240	GSM8340240: Cutaneous melanocytes; Danio rerio; OTHER	GSM8340240 r1	GSM8340240	1	Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP515140		HAR-MI-001_H5GCWBGXF_R2.fastq.gz HAR-MI-001_H5GCWBGXF_R1.fastq.gz	fastq fastq	2680460212.0	31168142.0	GSM8340240 r1	0:26 1:60	A:704357434;C:519158361;G:467098420;T:988838604;N:1007393	26	60		704357434	519158361	467098420	988838604	1007393	SRX24993369	SRS21694833	SRA1904773	Insco Lab, Medical Oncology, Dana Farber Cancer Institute	Insco Lab, Medical Oncology, Dana Farber Cancer Institute	2	0.11679	0.81545	0.10693	0.5033	0.9808	0.76404	0.44749	0.57623	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	small_rna	trueseq	sc	single_cell_plate	celseq	United States	2024-06-20	Undetermined	Adult	Skin	Surface Structure
43987	43987	SRR6811828	SRX3768868	SRS3023414	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		Pancreas 3 exo scar	GSM3032171	source name:Pancreas except primary islet liver\|strain/background:Zebrabow M\|tissue:Pancreas except primary islet liver\|developmental stage:Adult	Pancreas 3 exo 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…	Pancreas except primary islet liver		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Pancreas except primary islet liver\|developmental stage:Adult	GSM3032171	GSM3032171: Pancreas 3 exo scar; Danio rerio; OTHER	GSM3032171		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM3032171	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343		P7exo_scar_R1.fastq.gz P7exo_scar_R2.fastq.gz	fastq fastq	4291410352.0	34608148.0	GSM3032171 r1	0:26 1:98	A:1266869162;C:1345773385;G:950601988;T:726078376;N:2087441	26	98		1266869162	1345773385	950601988	726078376	2087441	SRX3768868	SRS3023414	SRA623333	GEO	Max Delbrück Center	2	0.00014	0.00241	0.00012	0.00024	0.99995	0.99691	0.0	0.65306	26	98	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2018-03-06	Adult	Adult	Multi-tissue	Multi-system
43988	43988	SRR6811827	SRX3768867	SRS3023384	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		Pancreas 3 endo scar	GSM3032170	source name:Primary pancreatic islet\|strain/background:Zebrabow M\|tissue:Primary pancreatic islet\|developmental stage:Adult	Pancreas 3 endo 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…	Primary pancreatic islet		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Primary pancreatic islet\|developmental stage:Adult	GSM3032170	GSM3032170: Pancreas 3 endo scar; Danio rerio; OTHER	GSM3032170		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM3032170	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343		P7endo_scar_R1.fastq.gz P7endo_scar_R2.fastq.gz	fastq fastq	2537781396.0	20465979.0	GSM3032170 r1	0:26 1:98	A:741745261;C:801599713;G:561531527;T:431666561;N:1238334	26	98		741745261	801599713	561531527	431666561	1238334	SRX3768867	SRS3023384	SRA623333	GEO	Max Delbrück Center	2	0.00014	0.00289	0.00012	0.00028	0.99995	0.99602	1.0	0.68478	26	98	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2018-03-06	Adult	Adult	Pancreas	Endocrine System
43989	43989	SRR6811826	SRX3768866	SRS3023382	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		Heart 3 scar	GSM3032169	source name:Heart and blood\|strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	Heart 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…	Heart and blood		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	GSM3032169	GSM3032169: Heart 3 scar; Danio rerio; OTHER	GSM3032169		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM3032169	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343		H7_scar_R1.fastq.gz H7_scar_R2.fastq.gz	fastq fastq	3999397296.0	32253204.0	GSM3032169 r1	0:26 1:98	A:1170970784;C:1255843391;G:881154893;T:689473188;N:1955040	26	98		1170970784	1255843391	881154893	689473188	1955040	SRX3768866	SRS3023382	SRA623333	GEO	Max Delbrück Center	2	0.00018	0.00228	0.00015	0.00019	0.99991	0.99659	0.8	0.67235	26	98	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2018-03-06	Adult	Adult	Multi-tissue	Multi-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
44008	44008	SRR6211484	SRX3320759	SRS2626332	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		Heart 2 scar	GSM2830055	source name:Heart and blood\|strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	Heart 2 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…	Heart and blood		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	GSM2830055	GSM2830055: Heart 2 scar; Danio rerio; OTHER	GSM2830055		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830055	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343		H6_scar_R1.fastq.gz H6_scar_R2.fastq.gz	fastq fastq	2079107172.0	15065994.0	GSM2830055 r1	0:28 1:110	A:580640871;C:641740953;G:501505035;T:355092832;N:127481	28	110		580640871	641740953	501505035	355092832	127481	SRX3320759	SRS2626332	SRA623333	GEO	Max Delbrück Center	2	5e-05	0.00253	4e-05	0.00023	1.0	0.99778		0.58419	28	110	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-system
44009	44009	SRR6211483	SRX3320758	SRS2626348	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		Pancreas 2 scar	GSM2830054	source name:Pancreas and liver\|strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	Pancreas 2 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…	Pancreas and liver		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	GSM2830054	GSM2830054: Pancreas 2 scar; Danio rerio; OTHER	GSM2830054		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830054	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343		P6_scar_R1.fastq.gz P6_scar_R2.fastq.gz	fastq fastq	1026715860.0	7439970.0	GSM2830054 r1	0:28 1:110	A:287816843;C:320879355;G:243598630;T:174359452;N:61580	28	110		287816843	320879355	243598630	174359452	61580	SRX3320758	SRS2626348	SRA623333	GEO	Max Delbrück Center	2	0.00029	0.00123	0.00028	6e-05	1.0	0.99914		0.25714	28	110	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-system
44010	44010	SRR6211482	SRX3320757	SRS2626331	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		Heart 1 scar	GSM2830053	source name:Heart and blood\|strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	Heart 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…	Heart and blood		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	GSM2830053	GSM2830053: Heart 1 scar; Danio rerio; OTHER	GSM2830053		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830053	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343		H5_scar_R1.fastq.gz H5_scar_R2.fastq.gz	fastq fastq	1287546624.0	10218624.0	GSM2830053 r1	0:26 1:100	A:365272675;C:413037677;G:296495693;T:212570153;N:170426	26	100		365272675	413037677	296495693	212570153	170426	SRX3320757	SRS2626331	SRA623333	GEO	Max Delbrück Center	2	0.00023	0.00044	0.00022	3e-05	1.0	0.99955		0.32653	26	100	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-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
44012	44012	SRR6211480	SRX3320755	SRS2626329	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		Pancreas 1 scar	GSM2830051	source name:Pancreas and liver\|strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	Pancreas 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…	Pancreas and liver		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	GSM2830051	GSM2830051: Pancreas 1 scar; Danio rerio; OTHER	GSM2830051		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830051	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343		P5_scar_R1.fastq.gz P5_scar_R2.fastq.gz	fastq fastq	1192602600.0	9465100.0	GSM2830051 r1	0:26 1:100	A:346841760;C:383266222;G:268916933;T:193424756;N:152929	26	100		346841760	383266222	268916933	193424756	152929	SRX3320755	SRS2626329	SRA623333	GEO	Max Delbrück Center	2	0.00021	0.00091	0.00014	2e-05	0.99997	0.99892	0.0	0.23931	26	100	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-system
59501	59501	SRR11924323	SRX8469995	SRS6770646	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.	pubmed:32912962		Adult tail 2	GSM4591062	source name:adult tail trunk\|tissue:adult tail trunk\|rna fraction:size fractionated 20 40 nt whole cell RNA	Adult tail 2	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	adult tail trunk		Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description		tissue:adult tail trunk\|rna fraction:size fractionated 20 40 nt whole cell RNA	GSM4591062	GSM4591062: Adult tail 2; Danio rerio; OTHER	GSM4591062		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	GEO Accession:GSM4591062	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP265951	intentional duplicate	Adult_tail_2.bam GSE151797_Reference_sequence.fa	bam bam	156647953.0	5517527.0	GSM4591062 r1	0:28.39	A:32903673;C:49609293;G:39096775;T:35038212;N:0	28			32903673	49609293	39096775	35038212	0	SRX8469995	SRS6770646	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.80662		0.20653		0.88722		0.58074		37		B		usable mapping rate	ion_torrent	ion_torrent	5prime	small_rna	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Adult	Adult	Multi-tissue	Multi-system
59502	59502	SRR11924321	SRX8469994	SRS6770645	SRP265951	PRJNA637293	The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites	GSE151797	Other	A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.	pubmed:32912962		Adult tail 1	GSM4591061	source name:adult tail trunk\|tissue:adult tail trunk\|rna fraction:size fractionated 20 40 nt whole cell RNA	Adult tail 1	Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.	adult tail trunk		Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description		tissue:adult tail trunk\|rna fraction:size fractionated 20 40 nt whole cell RNA	GSM4591061	GSM4591061: Adult tail 1; Danio rerio; OTHER	GSM4591061		1	Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description	GEO Accession:GSM4591061	OTHER	TRANSCRIPTOMIC	other	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP265951	intentional duplicate	Adult_tail_1.bam GSE151797_Reference_sequence.fa	bam bam	50029636.0	1968329.0	GSM4591061 r1	0:25.42	A:9571393;C:14825016;G:13276309;T:12356918;N:0	25			9571393	14825016	13276309	12356918	0	SRX8469994	SRS6770645	SRA1083099	GEO	RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen	1	0.46312		0.12127		0.91806		0.67424		44		B		usable mapping rate	ion_torrent	ion_torrent	5prime	small_rna	unknown	bulk	unknown	unknown	Denmark	2020-06-04	Adult	Adult	Multi-tissue	Multi-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
72561	72561	SRR22722190	SRX18683720	SRS16126888	SRP412911	PRJNA911847	Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia	PRJNA911847	Other	Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity full blown leukemia ensued with multi lineage dysplasia increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion the zebrafish models of IDH2 mutated AML recapitulated the morphologic clinical functional and transcriptomic characteristics of human diseases and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening				Transgenic FLT3 ITD IDH2 R140Q	strain:TU\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:8 month\|dev stage:8 month\|sex:pooled male and female\|tissue:kidney marrow\|genotype:Transgenic Runx1:FLT3ITDIDH2R140Q\|BioSampleModel:Model organism or animal									Single cell RNA seq of Danio rerio: Transgenic FLT3 ITD IDH2 R140Q	ITD140Q	ITD140Q	Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics Pleasanton CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI HK China.			OTHER	TRANSCRIPTOMIC	other	PAIRED	DNBSEQ	DNBSEQ-G400	SRP412911	loader:fastq load.py	ITD172KA_S1_L001_I1_001.fastq.gz ITD172KA_S1_L001_R1_001.fastq.gz ITD172KA_S1_L001_R2_001.fastq.gz	fastq fastq fastq	52149830422.0	410628586.0	ITD172KA S1 L001 I1 001.fastq.gz	0:8 1:28 2:91	A:10282953217;C:8459559201;G:8851285287;T:9772343870;N:1059751	8	28	91	10282953217	8459559201	8851285287	9772343870	1059751	SRX18683720	SRS16126888	SRA1558824	The University of Hong Kong\|Department of Medicine	The University of Hong Kong	1	0.88465		0.13112		0.81789		0.55842		91		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2022-12-14	Adult	Adult	Kidney	Renal System
72562	72562	SRR22722191	SRX18683719	SRS16126887	SRP412911	PRJNA911847	Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia	PRJNA911847	Other	Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity full blown leukemia ensued with multi lineage dysplasia increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion the zebrafish models of IDH2 mutated AML recapitulated the morphologic clinical functional and transcriptomic characteristics of human diseases and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening				Transgenic FLT3 ITD IDH2 R172K	strain:TU\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:8 month\|dev stage:8 month\|sex:pooled male and female\|tissue:kidney marrow\|genotype:Transgenic Runx1:FLT3ITDIDH2R172K\|BioSampleModel:Model organism or animal									Single cell RNA seq of Danio rerio: Transgenic FLT3 ITD IDH2 R172K	ITD172K	ITD172K	Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics Pleasanton CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI HK China.			OTHER	TRANSCRIPTOMIC	other	PAIRED	DNBSEQ	DNBSEQ-G400	SRP412911	loader:fastq load.py	ITD140QA_S1_L004_I1_001.fastq.gz ITD140QA_S1_L004_R1_001.fastq.gz ITD140QA_S1_L004_R2_001.fastq.gz	fastq fastq fastq	28595025233.0	225157679.0	ITD140QA S1 L004 I1 001.fastq.gz	0:8 1:28 2:91	A:5628987577;C:4565848641;G:4959209904;T:5302394659;N:32908008	8	28	91	5628987577	4565848641	4959209904	5302394659	32908008	SRX18683719	SRS16126887	SRA1558824	The University of Hong Kong\|Department of Medicine	The University of Hong Kong	1	0.81404		0.11315		0.83327		0.56222		91		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2022-12-13	Adult	Adult	Kidney	Renal System
72563	72563	SRR22722192	SRX18683718	SRS16126886	SRP412911	PRJNA911847	Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukaemia	PRJNA911847	Other	Isocitrate dehydrogenase 2 IDH2 mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia CN AML but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to maturity full blown leukemia ensued with multi lineage dysplasia increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in T cell development at embryonic and adult stage. Single cell transcriptomic analysis revealed increased myeloid skewing differentiation blockade and enrichment of leukemia associated gene signatures in both zebrafish models. TgRunx1:FLT3ITDIDH2R172K but not TgRunx1:FLT3ITDIDH2R140Q zebrafish showed increase in interferon signals at adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion the zebrafish models of IDH2 mutated AML recapitulated the morphologic clinical functional and transcriptomic characteristics of human diseases and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening				Wild type	strain:TU\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:8 month\|dev stage:8 month\|sex:pooled male and female\|tissue:kidney marrow\|genotype:Wild type\|BioSampleModel:Model organism or animal									Single cell RNA seq of Danio rerio: Wild type	Control	Control	Single cell RNA seq library.Single viable KM cells were collected from the transgenic double mutant n=3; pooled and WT n=3; pooled fish at 7 mpf into 0.9X PBS with 5% FBS. Their viability was examined by 0.4% Trypan blue staining under microscopy. The single cell library was constructed using the ChromiumTM Controller and ChromiumTM Next GEM Single Cell 3 Kit v3.1 10x Genomics Pleasanton CA. Complementary DNA cDNA was synthesized from the fragmentated RNAs using N6 random primers followed by end repair and ligation to BGISEQ sequencer compatible adapters. Quality control of the final library was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantification was performed by real time quantitative PCR using TaqMan probes. The final products were sequenced using the DNBSEQTM platform BGI HK China.			OTHER	TRANSCRIPTOMIC	other	PAIRED	DNBSEQ	DNBSEQ-G400	SRP412911	loader:fastq load.py	ControlA_S1_L003_R2_001.fastq.gz ControlA_S1_L003_R1_001.fastq.gz ControlA_S1_L003_I1_001.fastq.gz	fastq fastq fastq	37892727491.0	298367933.0	ControlA S1 L003 I1 001.fastq.gz	0:8 1:28 2:91	A:7386602298;C:6174680460;G:6579652828;T:6955791213;N:54755104	8	28	91	7386602298	6174680460	6579652828	6955791213	54755104	SRX18683718	SRS16126886	SRA1558824	The University of Hong Kong\|Department of Medicine	The University of Hong Kong	1	0.81686		0.11049		0.84139		0.46084		91		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	sc	single_cell_droplet	10x	China	2022-12-14	Adult	Adult	Kidney	Renal 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");;