metadata: run_metadata: 170 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation

170 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation_coarse = "Multi-system"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
29808	29808	SRR27450807	SRX23122487	SRS20076037	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673	Zebrafish EC 24hpf Aktmutant	GSM8004755	source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf Aktmutant	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant	GSM8004755	GSM8004755: Zebrafish EC 24hpf Aktmutant; Danio rerio; RNA Seq	GSM8004755 r1	GSM8004755	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328	loader:fastq load.py	mu1-23-19_DRT_S2_L001_I1_001.fastq.gz mu1-23-19_DRT_S2_L001_R1_001.fastq.gz mu1-23-19_DRT_S2_L001_R2_001.fastq.gz	fastq fastq fastq	23281472741.0	183318683.0	GSM8004755 r1	0:8 1:28 2:91	A:4703583066;C:3702175361;G:3998796644;T:4271932211;N:5512871	8	28	91		4703583066	3702175361	3998796644	4271932211	5512871	SRX23122487	SRS20076037	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
29809	29809	SRR27450808	SRX23122487	SRS20076037	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673	Zebrafish EC 24hpf Aktmutant	GSM8004755	source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf Aktmutant	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:Aktmutant	GSM8004755	GSM8004755: Zebrafish EC 24hpf Aktmutant; Danio rerio; RNA Seq	GSM8004755 r1	GSM8004755	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328	loader:fastq load.py	mu1-23-19_DRT_S2_L002_I1_001.fastq.gz mu1-23-19_DRT_S2_L002_R1_001.fastq.gz mu1-23-19_DRT_S2_L002_R2_001.fastq.gz	fastq fastq fastq	21009317138.0	165427694.0	GSM8004755 r2	0:8 1:28 2:91	A:4231955850;C:3363548064;G:3603913589;T:3849411287;N:5091364	8	28	91		4231955850	3363548064	3603913589	3849411287	5091364	SRX23122487	SRS20076037	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
29810	29810	SRR27450809	SRX23122486	SRS20076036	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673	Zebrafish EC 24hpf WT	GSM8004754	source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf WT	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT	GSM8004754	GSM8004754: Zebrafish EC 24hpf WT; Danio rerio; RNA Seq	GSM8004754 r1	GSM8004754	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328	loader:fastq load.py	wt1-23-19_DRT_S1_L001_I1_001.fastq.gz wt1-23-19_DRT_S1_L001_R1_001.fastq.gz wt1-23-19_DRT_S1_L001_R2_001.fastq.gz	fastq fastq fastq	22261273232.0	175285616.0	GSM8004754 r1	0:8 1:28 2:91	A:4475749188;C:3578353646;G:3836029871;T:4055646794;N:5211557	8	28	91		4475749188	3578353646	3836029871	4055646794	5211557	SRX23122486	SRS20076036	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
29811	29811	SRR27450810	SRX23122486	SRS20076036	SRP482328	PRJNA1061565	Akt is the main kinase mediating the embryonic specification of artery cells	GSE252648	Transcriptome Analysis	This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.		pubmed:39101673	Zebrafish EC 24hpf WT	GSM8004754	source name:FAC sorted cells\|tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT\|geo loc name:missing\|collection date:missing	Zebrafish EC 24hpf WT	The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix	FAC sorted cells	No treatments	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics	Normal zebrafish growth condition	tissue:FAC sorted cells\|cell line:kdrl:mCherry+\|cell type:Endothelial Cells\|genotype:WT	GSM8004754	GSM8004754: Zebrafish EC 24hpf WT; Danio rerio; RNA Seq	GSM8004754 r1	GSM8004754	1	Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP482328	loader:fastq load.py	wt1-23-19_DRT_S1_L002_I1_001.fastq.gz wt1-23-19_DRT_S1_L002_R1_001.fastq.gz wt1-23-19_DRT_S1_L002_R2_001.fastq.gz	fastq fastq fastq	20084395188.0	158144844.0	GSM8004754 r2	0:8 1:28 2:91	A:4028678970;C:3250176957;G:3455600305;T:3651884457;N:4840115	8	28	91		4028678970	3250176957	3455600305	3651884457	4840115	SRX23122486	SRS20076036	SRA1780571	Nicoli lab, School of Medicine, Yale University	Nicoli lab, School of Medicine, Yale University												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-05	Pharyngula	Embryo	Multi-tissue	Multi-system
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
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
43993	43993	SRR6811822	SRX3768862	SRS3023379	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 mRNA	GSM3032165	source name:Pancreas except primary islet liver\|strain/background:Zebrabow M\|tissue:Pancreas except primary islet liver\|developmental stage:Adult	Pancreas 3 exo mRNA	Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.	Pancreas except primary islet liver		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Pancreas except primary islet liver\|developmental stage:Adult	GSM3032165	GSM3032165: Pancreas 3 exo mRNA; Danio rerio; RNA Seq	GSM3032165		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM3032165	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP121343		P7exo_wt_R1.fastq.gz P7exo_wt_R2.fastq.gz	fastq fastq	38574026764.0	311080861.0	GSM3032165 r1	0:26 1:98	A:10751580091;C:8744299142;G:9264760851;T:9795905887;N:17480793	26	98			10751580091	8744299142	9264760851	9795905887	17480793	SRX3768862	SRS3023379	SRA623333	GEO	Max Delbrück Center	2	0.00463	0.93239	0.00336	0.04555	0.99671	0.87207	0.46341	0.57662	26	98	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2018-03-06	Adult	Adult	Multi-tissue	Multi-system
43995	43995	SRR6811820	SRX3768860	SRS3023377	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 mRNA	GSM3032163	source name:Heart and blood\|strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	Heart 3 mRNA	Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.	Heart and blood		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	GSM3032163	GSM3032163: Heart 3 mRNA; Danio rerio; RNA Seq	GSM3032163		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM3032163	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP121343		H7_wt_R2.fastq.gz H7_wt_R1.fastq.gz	fastq fastq	45826897248.0	369571752.0	GSM3032163 r1	0:26 1:98	A:12856871948;C:10721924215;G:10335821801;T:11891517482;N:20761802	26	98			12856871948	10721924215	10335821801	11891517482	20761802	SRX3768860	SRS3023377	SRA623333	GEO	Max Delbrück Center	2	0.00303	0.90293	0.00206	0.05991	0.99746	0.86918	0.3421	0.66847	26	98	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2018-03-06	Adult	Adult	Multi-tissue	Multi-system
44000	44000	SRR6211492	SRX3320767	SRS2626340	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 mRNA	GSM2830062	source name:Heart and blood\|strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	Heart 2 mRNA	Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.	Heart and blood		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	GSM2830062	GSM2830062: Heart 2 mRNA; Danio rerio; RNA Seq	GSM2830062		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830062	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP121343		H6_wt_R2.fastq.gz H6_wt_R1.fastq.gz	fastq fastq	19466673438.0	141062851.0	GSM2830062 r1	0:28 1:110	A:5788453893;C:4266605110;G:4479895656;T:4930437501;N:1281278	28	110			5788453893	4266605110	4479895656	4930437501	1281278	SRX3320767	SRS2626340	SRA623333	GEO	Max Delbrück Center	2	0.00114	0.94531	0.00026	0.06835	0.99819	0.88308	0.68098	0.70993	28	110	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-system
44001	44001	SRR6211491	SRX3320766	SRS2626339	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 mRNA	GSM2830061	source name:Pancreas and liver\|strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	Pancreas 2 mRNA	Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.	Pancreas and liver		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	GSM2830061	GSM2830061: Pancreas 2 mRNA; Danio rerio; RNA Seq	GSM2830061		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP121343		P6_wt_R1.fastq.gz P6_wt_R2.fastq.gz	fastq fastq	17563278078.0	127270131.0	GSM2830061 r1	0:28 1:110	A:5146142876;C:3830859355;G:4368254000;T:4216873712;N:1148135	28	110			5146142876	3830859355	4368254000	4216873712	1148135	SRX3320766	SRS2626339	SRA623333	GEO	Max Delbrück Center	2	0.0023	0.93516	0.00062	0.07613	0.99667	0.8798	0.62666	0.6399	28	110	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-system
44002	44002	SRR6211490	SRX3320765	SRS2626338	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 mRNA	GSM2830060	source name:Heart and blood\|strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	Heart 1 mRNA	Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.	Heart and blood		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Heart and blood\|developmental stage:Adult	GSM2830060	GSM2830060: Heart 1 mRNA; Danio rerio; RNA Seq	GSM2830060		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830060	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP121343		H5_wt_R1.fastq.gz H5_wt_R2.fastq.gz	fastq fastq	11175332616.0	88693116.0	GSM2830060 r1	0:26 1:100	A:3373517159;C:2470603501;G:2531314673;T:2798372007;N:1525276	26	100			3373517159	2470603501	2531314673	2798372007	1525276	SRX3320765	SRS2626338	SRA623333	GEO	Max Delbrück Center	2	0.00264	0.95153	0.00046	0.05429	0.99669	0.88958	0.57635	0.67876	26	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-system
44004	44004	SRR6211488	SRX3320763	SRS2626336	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 mRNA	GSM2830058	source name:Pancreas and liver\|strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	Pancreas 1 mRNA	Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode a UMI and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode we counted the number of molecules mapped to each gene using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = K ln1 – k o/K with t the final number of transcripts k o the observed UMIs and K the total number of UMIs possible. As protection against barcode sequencing errors we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10 release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.	Pancreas and liver		Single cell dissociation. 10X Genomics Chromium		strain/background:Zebrabow M\|tissue:Pancreas and liver\|developmental stage:Adult	GSM2830058	GSM2830058: Pancreas 1 mRNA; Danio rerio; RNA Seq	GSM2830058		1	Single cell dissociation. 10X Genomics Chromium	GEO Accession:GSM2830058	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP121343		P5_wt_R1.fastq.gz P5_wt_R2.fastq.gz	fastq fastq	18116725914.0	143783539.0	GSM2830058 r1	0:26 1:100	A:5348935548;C:3950936592;G:4404689151;T:4409667387;N:2497236	26	100			5348935548	3950936592	4404689151	4409667387	2497236	SRX3320763	SRS2626336	SRA623333	GEO	Max Delbrück Center	2	0.00319	0.93498	0.00092	0.08656	0.9947	0.86097	0.45652	0.53817	26	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2017-10-24	Adult	Adult	Multi-tissue	Multi-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
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
52243	52243	SRR9050632	SRX5827023	SRS4754837	SRP198298	PRJNA542704	Thyroid hormone regulates distinct paths to maturation in pigment cell lineages	GSE131136	Transcriptome Analysis	Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.		pubmed:31140974;pubmed:33933422	Neural crest derived cells from 5 dpf euthyroid zebrafish tails	GSM3764579	tissue:sox10:Cre+ cells from 5 dpf zebrafish tail tissue\|cell type:2154 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from tails of 5 dpf zebrafish.\|treatment:Untreated	Neural crest derived cells from 5 dpf euthyroid zebrafish tails	Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.	sox10:Cre+ cells from 5 dpf zebrafish tail tissue	Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.	10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.	Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms.	cell type:2154 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from tails of 5 dpf zebrafish.\|treatment:Untreated	GSM3764579	GSM3764579: Neural crest derived cells from 5 dpf euthyroid zebrafish tails; Danio rerio; RNA Seq	GSM3764579		1	10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP198298	dangling references:treat as unmapped	5dpf_possorted_genome_bam.bam	10X Genomics bam file	6566978892.0	115210156.0	GSM3764579 r1	0:57	A:1984051591;C:1302406550;G:1514564296;T:1762601545;N:3354910	57				1984051591	1302406550	1514564296	1762601545	3354910	SRX5827023	SRS4754837	SRA886020	GEO	Biology, University of Virginia	1	0.9291		0.194		0.81466		0.53116		57		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-05-13	Larval	Larval	Tail	Multi-system
53493	53493	SRR9881612	SRX6634133	SRS5205093	SRP217216	PRJNA558070	N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells	GSE135246	Transcriptome Analysis	Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT but these mechanisms do not explain its tight spatiotemporal regulation during development. Here we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans a common co translational modification9 12 that influences several pathophysiological processes but has not yet been implicated in EHT. Using an N glycosensor we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds		pubmed:33273096	223mut 27hpf EC1	GSM3996907	source name:endothelial cell\|tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303\|genotype:223mut	223mut 27hpf EC1	The reads were demultiplexed using bcl2fastq provided by the 10X genomics. The demultiplexed reads were aligned to the reference genome Grz11 modified to add mCherry GAL4 and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared. All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform and then clustered. The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster per condition. This is a tab separated values file where each row represents a gene and each column represents the cluster and the condition and each cell represents normalized expression values across all the cells in that cluster for that condition.	endothelial cell		Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1	Zebrafish were raised and maintained at 28.5˚C using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473.	tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya363; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896; miR 223ya303\|genotype:223mut	GSM3996907	GSM3996907: 223mut 27hpf EC1; Danio rerio; RNA Seq	GSM3996907		1	Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1	GEO Accession:GSM3996907	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP217216		Mut_pssorted_genome_bam.bam	10X Genomics bam file	31174899854.0	318111223.0	GSM3996907 r1	0:98	A:8464403532;C:7291172763;G:7282393533;T:8131647604;N:5282422	98				8464403532	7291172763	7282393533	8131647604	5282422	SRX6634133	SRS5205093	SRA930499	GEO	Internal Medicine, Yale University	1	0.92745		0.05306		0.84502		0.46383		98		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	sc	single_cell_droplet	10x	United States	2019-08-01	Pharyngula	Embryo	Multi-tissue	Multi-system
53494	53494	SRR9881611	SRX6634132	SRS5205092	SRP217216	PRJNA558070	N Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells	GSE135246	Transcriptome Analysis	Hematopoietic stem and progenitor cells HSPCs are required to establish and maintain the adult blood system in vertebrates. During development HPSCs are generated from hemogenic endothelial cells that undergo an endothelial to hematopoietic transition EHT. Growth factors and epigenetic changes can promote EHT but these mechanisms do not explain its tight spatiotemporal regulation during development. Here we show that microRNA miR miR 223 mediated regulation of N glycan biosynthesis intrinsically restrains EHT representing a new pathway that prevents excessive HSPC production. We find that miR 223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR 223 promotes the expansion of these cells in the zebrafish and mouse aorta gonad mesonephros AGM where EHT occurs. miR 223 targets alg2 alpha 1 3/ 1 6 mannosyltransferase in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N glycans a common co translational modification9 12 that influences several pathophysiological processes but has not yet been implicated in EHT. Using an N glycosensor we demonstrate that abundant protein N glycan attachment occurs in vascular cells during EHT and this process is required for HSPC production. High throughput glycome analysis upon loss of miR 223 revealed that terminal alpha 1 3/6 mannose modifications are increased at the expense of alpha 2 3/6 sialic acid sugars. Importantly pharmacological manipulation targeting these N glycan types in wild type embryos phenocopies the loss of miR 223 and enhances EHT as well as HSPC production. Thus the N glycome plays a previously unappreciated role as an intrinsic regulator of EHT with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate. Overall design: Single cell RNA sequencing for zebrafish Tgkdrl:hras mCherrys896 endothelial cells at 27 hpf for wildtype and miR 223ya303 backgrounds		pubmed:33273096	wildtype 27hpf EC1	GSM3996906	source name:endothelial cell\|tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896\|genotype:wildtype	wildtype 27hpf EC1	The reads were demultiplexed using bcl2fastq provided by the 10X genomics. The demultiplexed reads were aligned to the reference genome Grz11 modified to add mCherry GAL4 and eGFP to obtain digital gene expression matrix data using cellranger program The output of the cellranger was then processed using Seurat in R. All the cells with less than 200 unique transcripts were eliminared. All genes which are expressed in less than 3 cells were also eliminated. The data was normalized using sctransform and then clustered. The clusters were projected for viualization in R using the PHATE algorithm. Genome build: GRCz11 Supplementary files format and content: Average Gene expression matrix for average gene expression per cluster per condition. This is a tab separated values file where each row represents a gene and each column represents the cluster and the condition and each cell represents normalized expression values across all the cells in that cluster for that condition.	endothelial cell		Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1	Zebrafish were raised and maintained at 28.5˚C using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2017 11473.	tissue:trunk endothelium\|cell type:endothelial cell\|developmental stage:27 hpf 223:KalTA4ya362; Tg5xUAS:eGFPnkuasgfp1a; Tgkdrl:hras mCherrys896\|genotype:wildtype	GSM3996906	GSM3996906: wildtype 27hpf EC1; Danio rerio; RNA Seq	GSM3996906		1	Trunk tissue was dissected from 27 hpf zebrafish embryos under 0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tgkdrl:hras mCherrys896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform. 10 X genomics Chromium Next GEM Single Cell three prime Library Construction Kit v2.1	GEO Accession:GSM3996906	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP217216		WT_pssorted_genome_bam.bam	10X Genomics bam file	26866951370.0	274152565.0	GSM3996906 r1	0:98	A:7373453026;C:6169004304;G:6196779570;T:7121490110;N:6224360	98				7373453026	6169004304	6196779570	7121490110	6224360	SRX6634132	SRS5205092	SRA930499	GEO	Internal Medicine, Yale University	1	0.93015		0.0602		0.83853		0.4683		98		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	sc	single_cell_droplet	10x	United States	2019-08-01	Pharyngula	Embryo	Multi-tissue	Multi-system
56706	56706	SRR11040640	SRX7692417	SRS6118510	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	2 fgfr3lof/lof	GSM4301251	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	2 fgfr3lof/lof	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	GSM4301251	GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq	GSM4301251		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301251	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		2-fgfr3lof-R3-ZF-0519_S3_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S3_L001_R2_001.fastq.gz	fastq fastq	2956636039.0	24845681.0	GSM4301251 r1	0:28 1:91	A:805752236;C:683372886;G:699894274;T:767405768;N:210875	28	91			805752236	683372886	699894274	767405768	210875	SRX7692417	SRS6118510	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00944	0.95293	0.0032	0.11845	0.98863	0.79573	0.31275	0.48226	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56707	56707	SRR11040641	SRX7692417	SRS6118510	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	2 fgfr3lof/lof	GSM4301251	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	2 fgfr3lof/lof	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	GSM4301251	GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq	GSM4301251		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301251	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		2-fgfr3lof-R3-ZF-0519_S4_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S4_L001_R2_001.fastq.gz	fastq fastq	2943149888.0	24732352.0	GSM4301251 r2	0:28 1:91	A:801299410;C:680335967;G:696876648;T:764428085;N:209778	28	91			801299410	680335967	696876648	764428085	209778	SRX7692417	SRS6118510	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00982	0.95341	0.00295	0.11853	0.98798	0.79429	0.32383	0.48491	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56708	56708	SRR11040642	SRX7692417	SRS6118510	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	2 fgfr3lof/lof	GSM4301251	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	2 fgfr3lof/lof	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	GSM4301251	GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq	GSM4301251		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301251	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		2-fgfr3lof-R3-ZF-0519_S8_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S8_L001_R2_001.fastq.gz	fastq fastq	2930322283.0	24624557.0	GSM4301251 r3	0:28 1:91	A:800017449;C:676370110;G:692286275;T:761438555;N:209894	28	91			800017449	676370110	692286275	761438555	209894	SRX7692417	SRS6118510	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.0091	0.95344	0.00277	0.11835	0.98863	0.79523	0.30888	0.47399	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56709	56709	SRR11040643	SRX7692417	SRS6118510	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	2 fgfr3lof/lof	GSM4301251	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	2 fgfr3lof/lof	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	GSM4301251	GSM4301251: 2 fgfr3lof/lof; Danio rerio; RNA Seq	GSM4301251		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301251	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		2-fgfr3lof-R3-ZF-0519_S10_L001_R1_001.fastq.gz 2-fgfr3lof-R3-ZF-0519_S10_L001_R2_001.fastq.gz	fastq fastq	3086393758.0	25936082.0	GSM4301251 r4	0:28 1:91	A:842498816;C:712567363;G:729291108;T:801817022;N:219449	28	91			842498816	712567363	729291108	801817022	219449	SRX7692417	SRS6118510	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00907	0.95227	0.00303	0.11898	0.98906	0.79555	0.32194	0.48998	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56710	56710	SRR11040636	SRX7692416	SRS6118508	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	1 fgfr3lof/lof	GSM4301250	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	1 fgfr3lof/lof	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	GSM4301250	GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq	GSM4301250		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301250	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		1-fgfr3lof-R3-ZF-0519_S2_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S2_L001_R2_001.fastq.gz	fastq fastq	3809919113.0	32016127.0	GSM4301250 r1	0:28 1:91	A:1051323356;C:870053361;G:886403932;T:1001865374;N:273090	28	91			1051323356	870053361	886403932	1001865374	273090	SRX7692416	SRS6118508	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.0073	0.95159	0.00239	0.13839	0.98979	0.78293	0.32315	0.49047	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56711	56711	SRR11040637	SRX7692416	SRS6118508	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	1 fgfr3lof/lof	GSM4301250	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	1 fgfr3lof/lof	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	GSM4301250	GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq	GSM4301250		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301250	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		1-fgfr3lof-R3-ZF-0519_S5_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S5_L001_R2_001.fastq.gz	fastq fastq	5231239643.0	43959997.0	GSM4301250 r2	0:28 1:91	A:1444902743;C:1193884261;G:1216010955;T:1376068197;N:373487	28	91			1444902743	1193884261	1216010955	1376068197	373487	SRX7692416	SRS6118508	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00703	0.95125	0.00257	0.13933	0.99062	0.78417	0.33564	0.4777	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56712	56712	SRR11040638	SRX7692416	SRS6118508	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	1 fgfr3lof/lof	GSM4301250	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	1 fgfr3lof/lof	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	GSM4301250	GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq	GSM4301250		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301250	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		1-fgfr3lof-R3-ZF-0519_S14_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S14_L001_R2_001.fastq.gz	fastq fastq	6034697060.0	50711740.0	GSM4301250 r3	0:28 1:91	A:1667295741;C:1376061258;G:1401956669;T:1588951873;N:431519	28	91			1667295741	1376061258	1401956669	1588951873	431519	SRX7692416	SRS6118508	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00707	0.94822	0.00239	0.13943	0.99038	0.78311	0.36655	0.47115	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56713	56713	SRR11040639	SRX7692416	SRS6118508	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	1 fgfr3lof/lof	GSM4301250	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	1 fgfr3lof/lof	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3lof1/lof1\|length:9 mm	GSM4301250	GSM4301250: 1 fgfr3lof/lof; Danio rerio; RNA Seq	GSM4301250		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301250	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		1-fgfr3lof-R3-ZF-0519_S15_L001_R1_001.fastq.gz 1-fgfr3lof-R3-ZF-0519_S15_L001_R2_001.fastq.gz	fastq fastq	5425038164.0	45588556.0	GSM4301250 r4	0:28 1:91	A:1498130539;C:1238395410;G:1261876829;T:1426249730;N:385656	28	91			1498130539	1238395410	1261876829	1426249730	385656	SRX7692416	SRS6118508	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00733	0.94973	0.0026	0.13793	0.99068	0.78423	0.3337	0.48233	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56714	56714	SRR11040632	SRX7692415	SRS6118509	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	2 fgfr3+/+	GSM4301249	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	2 fgfr3+/+	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	GSM4301249	GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq	GSM4301249		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301249	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		2-fgfr3plus-R3-ZF-0519_S6_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S6_L001_R2_001.fastq.gz	fastq fastq	4962416501.0	41700979.0	GSM4301249 r1	0:28 1:91	A:1356709063;C:1139750321;G:1170875983;T:1294727572;N:353562	28	91			1356709063	1139750321	1170875983	1294727572	353562	SRX7692415	SRS6118509	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00727	0.95235	0.00248	0.13046	0.98981	0.78054	0.33659	0.48621	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56715	56715	SRR11040633	SRX7692415	SRS6118509	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	2 fgfr3+/+	GSM4301249	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	2 fgfr3+/+	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	GSM4301249	GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq	GSM4301249		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301249	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		2-fgfr3plus-R3-ZF-0519_S12_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S12_L001_R2_001.fastq.gz	fastq fastq	6695697316.0	56266364.0	GSM4301249 r2	0:28 1:91	A:1829441811;C:1538021924;G:1580312219;T:1747444971;N:476391	28	91			1829441811	1538021924	1580312219	1747444971	476391	SRX7692415	SRS6118509	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00744	0.95393	0.0026	0.13086	0.98969	0.78139	0.34081	0.50162	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56716	56716	SRR11040634	SRX7692415	SRS6118509	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	2 fgfr3+/+	GSM4301249	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	2 fgfr3+/+	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	GSM4301249	GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq	GSM4301249		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301249	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		2-fgfr3plus-R3-ZF-0519_S13_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S13_L001_R2_001.fastq.gz	fastq fastq	4853594809.0	40786511.0	GSM4301249 r3	0:28 1:91	A:1328029955;C:1113808349;G:1144735618;T:1266673333;N:347554	28	91			1328029955	1113808349	1144735618	1266673333	347554	SRX7692415	SRS6118509	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00737	0.95245	0.00274	0.12891	0.99038	0.78228	0.3487	0.4977	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56717	56717	SRR11040635	SRX7692415	SRS6118509	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	2 fgfr3+/+	GSM4301249	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	2 fgfr3+/+	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	GSM4301249	GSM4301249: 2 fgfr3+/+; Danio rerio; RNA Seq	GSM4301249		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301249	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		2-fgfr3plus-R3-ZF-0519_S16_L001_R1_001.fastq.gz 2-fgfr3plus-R3-ZF-0519_S16_L001_R2_001.fastq.gz	fastq fastq	6323597406.0	53139474.0	GSM4301249 r4	0:28 1:91	A:1727515649;C:1453521438;G:1493844843;T:1648265752;N:449724	28	91			1727515649	1453521438	1493844843	1648265752	449724	SRX7692415	SRS6118509	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00737	0.95341	0.00266	0.12818	0.98934	0.78151	0.32417	0.4918	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56718	56718	SRR11040628	SRX7692414	SRS6118507	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	1 fgfr3+/+	GSM4301248	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	1 fgfr3+/+	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	GSM4301248	GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq	GSM4301248		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301248	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		1-fgfr3plus-R3-ZF-0519_S1_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S1_L001_R2_001.fastq.gz	fastq fastq	6286029939.0	52823781.0	GSM4301248 r1	0:28 1:91	A:1726222024;C:1448493933;G:1483478967;T:1627385939;N:449076	28	91			1726222024	1448493933	1483478967	1627385939	449076	SRX7692414	SRS6118507	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00651	0.95215	0.0021	0.11197	0.99099	0.79914	0.32593	0.49237	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56719	56719	SRR11040629	SRX7692414	SRS6118507	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	1 fgfr3+/+	GSM4301248	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	1 fgfr3+/+	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	GSM4301248	GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq	GSM4301248		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301248	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		1-fgfr3plus-R3-ZF-0519_S7_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S7_L001_R2_001.fastq.gz	fastq fastq	5384386336.0	45246944.0	GSM4301248 r2	0:28 1:91	A:1482057664;C:1241359922;G:1266945881;T:1393638700;N:384169	28	91			1482057664	1241359922	1266945881	1393638700	384169	SRX7692414	SRS6118507	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00644	0.9527	0.00205	0.11156	0.99111	0.80217	0.3568	0.48853	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56720	56720	SRR11040630	SRX7692414	SRS6118507	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	1 fgfr3+/+	GSM4301248	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	1 fgfr3+/+	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	GSM4301248	GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq	GSM4301248		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301248	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		1-fgfr3plus-R3-ZF-0519_S9_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S9_L001_R2_001.fastq.gz	fastq fastq	5916050133.0	49714707.0	GSM4301248 r3	0:28 1:91	A:1628484212;C:1362413135;G:1391038139;T:1533691145;N:423502	28	91			1628484212	1362413135	1391038139	1533691145	423502	SRX7692414	SRS6118507	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.0066	0.95312	0.00209	0.11367	0.99109	0.79857	0.336	0.47399	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56721	56721	SRR11040631	SRX7692414	SRS6118507	SRP247644	PRJNA605419	FGFR3 is a positive regulator of osteoblast expansion and differentiation during zebrafish skull vault development	GSE144944	Transcriptome Analysis	In order to study FGFRthree primes role in cranial vault development we generated the first fgfr3 loss of function zebrafish fgfr3lof1/lof1. The mutant fish exhibited major changes in the craniofacial skeleton with a lack of sutures abnormal frontal and parietal bones and the presence of ectopic bones. In order to define cellular and molecular processes responsible for this phenotype we performed single cell RNA sequencing of cranial vault cells from fgfr3lof1/lof1 and fgfr3+/+ zebrafish. Our data allow us to define transcriptomic profile of each osteogenic subpopulation involved in cranial vault formation and we revealed a defect in osteoblast differentiation associated with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis and we conclude that changes in the extracellular matrix within growing bone impair cell cell communication mineralization and new osteoblast recruitment. Overall design: Using cells isolated from cranial vaults from two fgfr3lof1/lof1 fish and two fgfr3+/+ zebrafish fgfr3lof/lof: zebrafish line was obtained using CrisPR/Cas9 technology with a stop codon at position 377 we profiled the transcriptome of nearly 28000 single cells using the Chromium system 10x Genomics. Cells suspensions were obtained using both collagenase digestion and cell sorting to eliminate death cells. Cells of the cranial vault is a mix of several cell types osteogenic cells chondrogenic cells immune cells epidermal cells endothelial cells. The scRNA seq libraries were generated with a Chromium Single Cell three prime Library & Gel Bead Kit v.3 10x Genomics. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		pubmed:32379366	1 fgfr3+/+	GSM4301248	source name:Cranial vault\|tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	1 fgfr3+/+	Fastq files from the scRNA 10X libraries were processed using the Cell Ranger Count pipeline with its default parameters. Reads were aligned against the GRCz11 3.0.0 reference transcriptome. The RNA data quality control and downstream analysis were performed using the Seurat R package version 3.0.2 and the standard Seurat v3 integration workflow. We filtered cells that had i unique feature counts over 2000 or below 500 or ii more than 20% of mitochondrial counts. post data filtering we obtained an expression matrix with 21176 genes and 19245 cells. The matrix’s dimensions were reduced by running the 20 significant principal components against scaled data. Corresponding to an object of class Seurat SC fgfr3 Cranial Vault ZF combined samples. We used the FindMarkers function to define marker of each cluster Findmarkers by cluster.xlsx file. We used the FindMarkers function to compute differentially expressed genes DEGs for each of the identity classes in the dataset DEGS.xlsx file. We subset cluster 4 from SC fgfr3 Cranial Vault ZF combined samples matrix and performed new clustering resolution 0.2 and we obtained SC fgfr3 Cranial Vault ZF Subset Cluster4. Genome build: GRCz11 3.0.0 Supplementary files format and content: * raw feature bc matrix.h5 Supplementary files format and content: Findmarkers by cluster.xlsx Supplementary files format and content: DEGS.xlsx	Cranial vault		The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer’s instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.		tissue:Cranial vault\|genotype/variation:fgfr3+/+\|length:9 mm	GSM4301248	GSM4301248: 1 fgfr3+/+; Danio rerio; RNA Seq	GSM4301248		1	The cranial vault was isolated from the head of 9SL zebrafish and dissected in PBS. The olfactory bulbs the anterior parts of the frontal bones and the suboccipital bones were removed. The soft tissue was partially degraded by incubation with 0.2% collagenase and 4 mM EDTA in PBS for 10 min at 28°C. post a wash in PBS cells were dissociated for 40 min at 28°C in 0.2% collagenase in PBS. The solution was strained using a 40 μm cell strainer and the cells were washed in a MEM supplement with 10% FBS. Prior to flow cytometry the cells were suspended in FacsMax and stained with SytoxTM green nucleic acid stain and Hoechst. To sort the cells beads were used to select events larger than 3 µm. Hoechst positive cells cells with a nucleus and Syber green negative cells live cells were sorted. The scRNA seq libraries were generated with a Chromium Single Cell 3′ Library & Gel Bead Kit v.3 10x Genomics according to the manufacturer's instructions. Briefly cells were counted diluted at 1000 cells/µL in PBS+0.04% BSA and 6500 cells were loaded in the 10x Chromium Controller to generate single cell gel beads in an emulsion. post reverse transcription the gel beads in the emulsion were disrupted. Barcoded complementary DNA was isolated and amplified in PCRs. Following fragmentation end repair and A tailing sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq 6000 Illumina on paired end strands read 1: 28bp; read 2: 91bp with a mean read depth of 25000 reads per cell.	GEO Accession:GSM4301248	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP247644		1-fgfr3plus-R3-ZF-0519_S11_L001_R1_001.fastq.gz 1-fgfr3plus-R3-ZF-0519_S11_L001_R2_001.fastq.gz	fastq fastq	5591429319.0	46986801.0	GSM4301248 r4	0:28 1:91	A:1539075154;C:1286758672;G:1316467634;T:1448729317;N:398542	28	91			1539075154	1286758672	1316467634	1448729317	398542	SRX7692414	SRS6118507	SRA1039424	GEO	Molecular and physiopathological bases of osteochondrodysplasia, U1163, Institut Imagine	2	0.00664	0.95136	0.00216	0.11396	0.99131	0.8003	0.32678	0.49629	28	91	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	sc	single_cell_droplet	10x	France	2020-02-07	Undetermined	Undetermined	Multi-tissue	Multi-system
56820	56820	SRR15414667	SRX11716797	SRS9747215	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.		pubmed:34518542	UI 2DG	GSM5513441	tissue:Developing embryonic zebrafish tail\|strain:TAB 5\|embryo age:3 dpf mM 2 deoxyglucose	UI 2DG	Binary Base Call BCL files generated from an Illumina 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics Genome build: Danio Rerio 11 Supplementary files format and content: clouple files are provided which can be visiualized with the Loupe Cell Browser 10x Genomics	Developing embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics		strain:TAB 5\|embryo age:3 dpf mM 2 deoxyglucose	GSM5513441	GSM5513441: UI 2DG; Danio rerio; RNA Seq	GSM5513441		1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics	GEO Accession:GSM5513441	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	assembly:Danio Rerio 11\|intentional duplicate	UI_2DG.bam	10X Genomics bam file	7617244817.0	83705987.0	GSM5513441 r1	0:91	A:2234691645;C:1513876602;G:1889440050;T:1970597369;N:8639151	91				2234691645	1513876602	1889440050	1970597369	8639151	SRX11716797	SRS9747215	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.93814		0.15677		0.8254		0.52455		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-11	Larval	Larval	Tail	Multi-system
56821	56821	SRR15414666	SRX11716796	SRS9747214	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.		pubmed:34518542	UI ctrl	GSM5513440	tissue:Regenerating embryonic zebrafish tail\|strain:TAB 5\|embryo age:3 dpf	UI ctrl	Binary Base Call BCL files generated from an Illumina 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics Genome build: Danio Rerio 11 Supplementary files format and content: clouple files are provided which can be visiualized with the Loupe Cell Browser 10x Genomics	Regenerating embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics		strain:TAB 5\|embryo age:3 dpf	GSM5513440	GSM5513440: UI ctrl; Danio rerio; RNA Seq	GSM5513440		1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics	GEO Accession:GSM5513440	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	assembly:Danio Rerio 11\|intentional duplicate	UI_ctrl.bam	10X Genomics bam file	8002896265.0	87943915.0	GSM5513440 r1	0:91	A:2325005630;C:1613869115;G:2033844364;T:2021144325;N:9032831	91				2325005630	1613869115	2033844364	2021144325	9032831	SRX11716796	SRS9747214	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.93599		0.15189		0.83603		0.50802		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-11	Larval	Larval	Tail	Multi-system
56822	56822	SRR11107235	SRX7744906	SRS6164695	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.		pubmed:34518542	48hpa 2DG	GSM4319213	source name:Regenerating embryonic zebrafish tail\|strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:5 dpf mM 2 deoxyglucose\|time point:48hpa	48hpa 2DG	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files.	Regenerating embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.		strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:5 dpf mM 2 deoxyglucose\|time point:48hpa	GSM4319213	GSM4319213: 48hpa 2DG; Danio rerio; RNA Seq	GSM4319213		1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.	GEO Accession:GSM4319213	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	intentional duplicate	48hpa_2DG.bam	10X Genomics bam file	6786532025.0	74577275.0	GSM4319213 r1	0:91	A:1972992538;C:1368168542;G:1707658855;T:1729990330;N:7721760	91				1972992538	1368168542	1707658855	1729990330	7721760	SRX7744906	SRS6164695	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.9456		0.16065		0.80852		0.56712		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-02-18	Larval	Larval	Tail	Multi-system
56823	56823	SRR11107234	SRX7744905	SRS6165316	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.		pubmed:34518542	48hpa ctrl	GSM4319212	source name:Regenerating embryonic zebrafish tail\|strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:5 dpf point:48hpa	48hpa ctrl	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files.	Regenerating embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.		strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:5 dpf point:48hpa	GSM4319212	GSM4319212: 48hpa ctrl; Danio rerio; RNA Seq	GSM4319212		1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.	GEO Accession:GSM4319212	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	intentional duplicate	48hpa_ctrl.bam	10X Genomics bam file	6315141924.0	69397164.0	GSM4319212 r1	0:91	A:1820671652;C:1274680094;G:1600555332;T:1612090454;N:7144392	91				1820671652	1274680094	1600555332	1612090454	7144392	SRX7744905	SRS6165316	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.94831		0.155		0.80866		0.5428		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-02-18	Larval	Larval	Tail	Multi-system
56824	56824	SRR11107233	SRX7744904	SRS6165317	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.		pubmed:34518542	24hpa 2DG	GSM4319211	source name:Regenerating embryonic zebrafish tail\|strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:4 dpf mM 2 deoxyglucose\|time point:24hpa	24hpa 2DG	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files.	Regenerating embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.		strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:4 dpf mM 2 deoxyglucose\|time point:24hpa	GSM4319211	GSM4319211: 24hpa 2DG; Danio rerio; RNA Seq	GSM4319211		1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.	GEO Accession:GSM4319211	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	intentional duplicate	24hpa_2DG.bam	10X Genomics bam file	4751770569.0	52217259.0	GSM4319211 r1	0:91	A:1367937805;C:991264209;G:1237114736;T:1153230321;N:2223498	91				1367937805	991264209	1237114736	1153230321	2223498	SRX7744904	SRS6165317	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.8338		0.14372		0.82108		0.57161		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-02-18	Larval	Larval	Tail	Multi-system
56825	56825	SRR11107232	SRX7744903	SRS6164694	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.		pubmed:34518542	24hpa ctrl	GSM4319210	source name:Regenerating embryonic zebrafish tail\|strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:4 dpf point:24hpa	24hpa ctrl	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files.	Regenerating embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.		strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:4 dpf point:24hpa	GSM4319210	GSM4319210: 24hpa ctrl; Danio rerio; RNA Seq	GSM4319210		1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.	GEO Accession:GSM4319210	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	intentional duplicate	24hpa_ctrl.bam	10X Genomics bam file	5461996085.0	60021935.0	GSM4319210 r1	0:91	A:1578516213;C:1146696708;G:1390321964;T:1344258467;N:2202733	91				1578516213	1146696708	1390321964	1344258467	2202733	SRX7744903	SRS6164694	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.83781		0.14102		0.81264		0.58676		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-02-18	Larval	Larval	Tail	Multi-system
59196	59196	SRR11777188	SRX8330063	SRS6649550	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	dominant 3	GSM4547702	tissue:dominant\|cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	dominant 3	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	dominant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	GSM4547702	GSM4547702: dominant 3; Danio rerio; RNA Seq	GSM4547702		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547702	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample8 I1.fastq.gz read2PairFiles=Next sample8 R1.fastq.gz read3PairFiles=Next sample8 R2.fastq.gz	Next_sample8_I1.fastq.gz Next_sample8_R1.fastq.gz Next_sample8_R2.fastq.gz	fastq fastq fastq	6949629860.0	75539455.0	GSM4547702 r1	0:8 1:26 2:58	A:1844979631;C:1603125876;G:1713257721;T:1782703901;N:5562731	8	26	58		1844979631	1603125876	1713257721	1782703901	5562731	SRX8330063	SRS6649550	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95614		0.07196		0.85527		0.53876		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59197	59197	SRR11777189	SRX8330063	SRS6649550	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	dominant 3	GSM4547702	tissue:dominant\|cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	dominant 3	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	dominant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	GSM4547702	GSM4547702: dominant 3; Danio rerio; RNA Seq	GSM4547702		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547702	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample8 S8 L001 I1 001.fastq.gz read2PairFiles=sample8 S8 L001 R1 001.fastq.gz read3PairFiles=sample8 S8 L001 R2 001.fastq.gz	sample8_S8_L001_R2_001.fastq.gz sample8_S8_L001_R1_001.fastq.gz sample8_S8_L001_I1_001.fastq.gz	fastq fastq fastq	37968081102.0	301333977.0	GSM4547702 r2	0:8 1:26 2:92	A:10580168599;C:8638562811;G:9024245345;T:9723132070;N:1972277	8	26	92		10580168599	8638562811	9024245345	9723132070	1972277	SRX8330063	SRS6649550	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95282		0.06548		0.8546		0.52648		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59198	59198	SRR11777190	SRX8330063	SRS6649550	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	dominant 3	GSM4547702	tissue:dominant\|cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	dominant 3	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	dominant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	GSM4547702	GSM4547702: dominant 3; Danio rerio; RNA Seq	GSM4547702		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547702	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample8 S8 L002 I1 001.fastq.gz read2PairFiles=sample8 S8 L002 R1 001.fastq.gz read3PairFiles=sample8 S8 L002 R2 001.fastq.gz	sample8_S8_L002_R2_001.fastq.gz sample8_S8_L002_R1_001.fastq.gz sample8_S8_L002_I1_001.fastq.gz	fastq fastq fastq	37640109906.0	298731031.0	GSM4547702 r3	0:8 1:26 2:92	A:10490817242;C:8564221041;G:8946179351;T:9637119181;N:1773091	8	26	92		10490817242	8564221041	8946179351	9637119181	1773091	SRX8330063	SRS6649550	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95231		0.06664		0.85326		0.52977		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59199	59199	SRR11777185	SRX8330062	SRS6649549	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	dominant 2	GSM4547701	tissue:dominant\|cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	dominant 2	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	dominant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	GSM4547701	GSM4547701: dominant 2; Danio rerio; RNA Seq	GSM4547701		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547701	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample7 I1.fastq.gz read2PairFiles=Next sample7 R1.fastq.gz read3PairFiles=Next sample7 R2.fastq.gz	Next_sample7_R2.fastq.gz Next_sample7_R1.fastq.gz Next_sample7_I1.fastq.gz	fastq fastq fastq	8529279244.0	92709557.0	GSM4547701 r1	0:8 1:26 2:58	A:2302811456;C:1921371420;G:2078302909;T:2219976032;N:6817427	8	26	58		2302811456	1921371420	2078302909	2219976032	6817427	SRX8330062	SRS6649549	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.94004		0.09046		0.85555		0.50147		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59200	59200	SRR11777186	SRX8330062	SRS6649549	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	dominant 2	GSM4547701	tissue:dominant\|cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	dominant 2	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	dominant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	GSM4547701	GSM4547701: dominant 2; Danio rerio; RNA Seq	GSM4547701		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547701	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample7 S7 L001 I1 001.fastq.gz read2PairFiles=sample7 S7 L001 R1 001.fastq.gz read3PairFiles=sample7 S7 L001 R2 001.fastq.gz	sample7_S7_L001_R2_001.fastq.gz sample7_S7_L001_R1_001.fastq.gz sample7_S7_L001_I1_001.fastq.gz	fastq fastq fastq	34725493026.0	275599151.0	GSM4547701 r2	0:8 1:26 2:92	A:9769026986;C:7706289537;G:8194381066;T:9053981896;N:1813541	8	26	92		9769026986	7706289537	8194381066	9053981896	1813541	SRX8330062	SRS6649549	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.9448		0.0817		0.85336		0.52553		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59201	59201	SRR11777187	SRX8330062	SRS6649549	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	dominant 2	GSM4547701	tissue:dominant\|cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	dominant 2	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	dominant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	GSM4547701	GSM4547701: dominant 2; Danio rerio; RNA Seq	GSM4547701		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547701	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample7 S7 L002 I1 001.fastq.gz read2PairFiles=sample7 S7 L002 R1 001.fastq.gz read3PairFiles=sample7 S7 L002 R2 001.fastq.gz	sample7_S7_L002_R2_001.fastq.gz sample7_S7_L002_R1_001.fastq.gz sample7_S7_L002_I1_001.fastq.gz	fastq fastq fastq	34468767648.0	273561648.0	GSM4547701 r3	0:8 1:26 2:92	A:9700179724;C:7649330815;G:8132966012;T:8984661489;N:1629608	8	26	92		9700179724	7649330815	8132966012	8984661489	1629608	SRX8330062	SRS6649549	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.94359		0.08201		0.85206		0.52394		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59202	59202	SRR11777182	SRX8330061	SRS6649548	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	dominant 1	GSM4547700	tissue:dominant\|cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	dominant 1	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	dominant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	GSM4547700	GSM4547700: dominant 1; Danio rerio; RNA Seq	GSM4547700		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547700	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample6 I1.fastq.gz read2PairFiles=Next sample6 R1.fastq.gz read3PairFiles=Next sample6 R2.fastq.gz	Next_sample6_R2.fastq.gz Next_sample6_R1.fastq.gz Next_sample6_I1.fastq.gz	fastq fastq fastq	7186504192.0	78114176.0	GSM4547700 r1	0:8 1:26 2:58	A:1890231359;C:1687648873;G:1767027837;T:1835889658;N:5706465	8	26	58		1890231359	1687648873	1767027837	1835889658	5706465	SRX8330061	SRS6649548	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95103		0.08633		0.84997		0.5111		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59203	59203	SRR11777183	SRX8330061	SRS6649548	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	dominant 1	GSM4547700	tissue:dominant\|cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	dominant 1	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	dominant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	GSM4547700	GSM4547700: dominant 1; Danio rerio; RNA Seq	GSM4547700		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547700	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample6 S6 L001 I1 001.fastq.gz read2PairFiles=sample6 S6 L001 R1 001.fastq.gz read3PairFiles=sample6 S6 L001 R2 001.fastq.gz	sample6_S6_L001_R2_001.fastq.gz sample6_S6_L001_R1_001.fastq.gz sample6_S6_L001_I1_001.fastq.gz	fastq fastq fastq	35787988152.0	284031652.0	GSM4547700 r2	0:8 1:26 2:92	A:9781991861;C:8320736351;G:8552750572;T:9130655372;N:1853996	8	26	92		9781991861	8320736351	8552750572	9130655372	1853996	SRX8330061	SRS6649548	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95998		0.0809		0.84891		0.53314		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59204	59204	SRR11777184	SRX8330061	SRS6649548	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	dominant 1	GSM4547700	tissue:dominant\|cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	dominant 1	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	dominant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:sorted single color kidney marrow cells\|sorting:sorted\|age:8 mpf\|genotype/variation:dominant Zebrabow color	GSM4547700	GSM4547700: dominant 1; Danio rerio; RNA Seq	GSM4547700		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547700	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample6 S6 L002 I1 001.fastq.gz read2PairFiles=sample6 S6 L002 R1 001.fastq.gz read3PairFiles=sample6 S6 L002 R2 001.fastq.gz	sample6_S6_L002_R2_001.fastq.gz sample6_S6_L002_R1_001.fastq.gz sample6_S6_L002_I1_001.fastq.gz	fastq fastq fastq	35545836942.0	282109817.0	GSM4547700 r3	0:8 1:26 2:92	A:9719207479;C:8264195207;G:8494199037;T:9066565654;N:1669565	8	26	92		9719207479	8264195207	8494199037	9066565654	1669565	SRX8330061	SRS6649548	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95974		0.0796		0.85036		0.54185		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59205	59205	SRR11777179	SRX8330060	SRS6649547	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	mutant 3	GSM4547699	tissue:mutant\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	mutant 3	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	mutant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	GSM4547699	GSM4547699: mutant 3; Danio rerio; RNA Seq	GSM4547699		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547699	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample5 I1.fastq.gz read2PairFiles=Next sample5 R1.fastq.gz read3PairFiles=Next sample5 R2.fastq.gz	Next_sample5_R2.fastq.gz Next_sample5_R1.fastq.gz Next_sample5_I1.fastq.gz	fastq fastq fastq	7160703436.0	77833733.0	GSM4547699 r1	0:8 1:26 2:58	A:1816363574;C:1765855914;G:1734024608;T:1838721304;N:5738036	8	26	58		1816363574	1765855914	1734024608	1838721304	5738036	SRX8330060	SRS6649547	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95273		0.06131		0.85693		0.50453		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59206	59206	SRR11777180	SRX8330060	SRS6649547	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	mutant 3	GSM4547699	tissue:mutant\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	mutant 3	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	mutant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	GSM4547699	GSM4547699: mutant 3; Danio rerio; RNA Seq	GSM4547699		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547699	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample5 S5 L001 I1 001.fastq.gz read2PairFiles=sample5 S5 L001 R1 001.fastq.gz read3PairFiles=sample5 S5 L001 R2 001.fastq.gz	sample5_S5_L001_R2_001.fastq.gz sample5_S5_L001_R1_001.fastq.gz sample5_S5_L001_I1_001.fastq.gz	fastq fastq fastq	39409717914.0	312775539.0	GSM4547699 r2	0:8 1:26 2:92	A:10331447053;C:9658224477;G:9315034438;T:10102971653;N:2040293	8	26	92		10331447053	9658224477	9315034438	10102971653	2040293	SRX8330060	SRS6649547	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.96833		0.05626		0.85336		0.50422		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59207	59207	SRR11777181	SRX8330060	SRS6649547	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	mutant 3	GSM4547699	tissue:mutant\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	mutant 3	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	mutant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	GSM4547699	GSM4547699: mutant 3; Danio rerio; RNA Seq	GSM4547699		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547699	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample5 S5 L002 I1 001.fastq.gz read2PairFiles=sample5 S5 L002 R1 001.fastq.gz read3PairFiles=sample5 S5 L002 R2 001.fastq.gz	sample5_S5_L002_R2_001.fastq.gz sample5_S5_L002_R1_001.fastq.gz sample5_S5_L002_I1_001.fastq.gz	fastq fastq fastq	39156927138.0	310769263.0	GSM4547699 r3	0:8 1:26 2:92	A:10269040558;C:9596019625;G:9255122700;T:10034901230;N:1843025	8	26	92		10269040558	9596019625	9255122700	10034901230	1843025	SRX8330060	SRS6649547	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.96923		0.05633		0.85356		0.5018		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59208	59208	SRR11777176	SRX8330059	SRS6649546	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	mutant 2	GSM4547698	tissue:mutant\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	mutant 2	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	mutant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	GSM4547698	GSM4547698: mutant 2; Danio rerio; RNA Seq	GSM4547698		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547698	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample4 I1.fastq.gz read2PairFiles=Next sample4 R1.fastq.gz read3PairFiles=Next sample4 R2.fastq.gz	Next_sample4_R2.fastq.gz Next_sample4_R1.fastq.gz Next_sample4_I1.fastq.gz	fastq fastq fastq	6117699620.0	66496735.0	GSM4547698 r1	0:8 1:26 2:58	A:1585513100;C:1461263890;G:1493383278;T:1572628286;N:4911066	8	26	58		1585513100	1461263890	1493383278	1572628286	4911066	SRX8330059	SRS6649546	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95122		0.07021		0.85638		0.50527		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59209	59209	SRR11777177	SRX8330059	SRS6649546	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	mutant 2	GSM4547698	tissue:mutant\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	mutant 2	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	mutant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	GSM4547698	GSM4547698: mutant 2; Danio rerio; RNA Seq	GSM4547698		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547698	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample4 S4 L001 I1 001.fastq.gz read2PairFiles=sample4 S4 L001 R1 001.fastq.gz read3PairFiles=sample4 S4 L001 R2 001.fastq.gz	sample4_S4_L001_R2_001.fastq.gz sample4_S4_L001_R1_001.fastq.gz sample4_S4_L001_I1_001.fastq.gz	fastq fastq fastq	34901689032.0	276997532.0	GSM4547698 r2	0:8 1:26 2:92	A:9403468365;C:8264174645;G:8233892651;T:8998340867;N:1812504	8	26	92		9403468365	8264174645	8233892651	8998340867	1812504	SRX8330059	SRS6649546	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.9607		0.06192		0.85251		0.5091		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59210	59210	SRR11777178	SRX8330059	SRS6649546	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	mutant 2	GSM4547698	tissue:mutant\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	mutant 2	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	mutant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	GSM4547698	GSM4547698: mutant 2; Danio rerio; RNA Seq	GSM4547698		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547698	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample4 S4 L002 I1 001.fastq.gz read2PairFiles=sample4 S4 L002 R1 001.fastq.gz read3PairFiles=sample4 S4 L002 R2 001.fastq.gz	sample4_S4_L002_I1_001.fastq.gz sample4_S4_L002_R1_001.fastq.gz sample4_S4_L002_R2_001.fastq.gz	fastq fastq fastq	34667396694.0	275138069.0	GSM4547698 r3	0:8 1:26 2:92	A:9343712751;C:8208672454;G:8177795137;T:8935581933;N:1634419	8	26	92		9343712751	8208672454	8177795137	8935581933	1634419	SRX8330059	SRS6649546	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95991		0.06275		0.85269		0.51362		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59211	59211	SRR11777173	SRX8330058	SRS6649545	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	mutant 1	GSM4547697	tissue:mutant\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	mutant 1	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	mutant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	GSM4547697	GSM4547697: mutant 1; Danio rerio; RNA Seq	GSM4547697		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547697	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample3 I1.fastq.gz read2PairFiles=Next sample3 R1.fastq.gz read3PairFiles=Next sample3 R2.fastq.gz	Next_sample3_R2.fastq.gz Next_sample3_R1.fastq.gz Next_sample3_I1.fastq.gz	fastq fastq fastq	6871405756.0	74689193.0	GSM4547697 r1	0:8 1:26 2:58	A:1758336575;C:1648937548;G:1652034299;T:1806605610;N:5491724	8	26	58		1758336575	1648937548	1652034299	1806605610	5491724	SRX8330058	SRS6649545	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95127		0.08969		0.8478		0.50938		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59212	59212	SRR11777174	SRX8330058	SRS6649545	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	mutant 1	GSM4547697	tissue:mutant\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	mutant 1	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	mutant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	GSM4547697	GSM4547697: mutant 1; Danio rerio; RNA Seq	GSM4547697		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547697	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample3 S3 L001 I1 001.fastq.gz read2PairFiles=sample3 S3 L001 R1 001.fastq.gz read3PairFiles=sample3 S3 L001 R2 001.fastq.gz	sample3_S3_L001_R2_001.fastq.gz sample3_S3_L001_R1_001.fastq.gz sample3_S3_L001_I1_001.fastq.gz	fastq fastq fastq	37240131222.0	295556597.0	GSM4547697 r2	0:8 1:26 2:92	A:9746145692;C:8895600775;G:8808801890;T:9787657360;N:1925505	8	26	92		9746145692	8895600775	8808801890	9787657360	1925505	SRX8330058	SRS6649545	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.96592		0.08198		0.84642		0.50173		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59213	59213	SRR11777175	SRX8330058	SRS6649545	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	mutant 1	GSM4547697	tissue:mutant\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	mutant 1	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	mutant	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:guide RNAs targeting 20 different genes and cas9 mRNA	GSM4547697	GSM4547697: mutant 1; Danio rerio; RNA Seq	GSM4547697		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547697	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample3 S3 L002 I1 001.fastq.gz read2PairFiles=sample3 S3 L002 R1 001.fastq.gz read3PairFiles=sample3 S3 L002 R2 001.fastq.gz	sample3_S3_L002_R2_001.fastq.gz sample3_S3_L002_R1_001.fastq.gz sample3_S3_L002_I1_001.fastq.gz	fastq fastq fastq	36987042078.0	293547953.0	GSM4547697 r3	0:8 1:26 2:92	A:9682800852;C:8835028777;G:8748767711;T:9718714620;N:1730118	8	26	92		9682800852	8835028777	8748767711	9718714620	1730118	SRX8330058	SRS6649545	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.96466		0.08156		0.84605		0.5026		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59214	59214	SRR11777170	SRX8330057	SRS6649544	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	control 2	GSM4547696	tissue:control\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	control 2	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	control	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	GSM4547696	GSM4547696: control 2; Danio rerio; RNA Seq	GSM4547696		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547696	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample2 I1.fastq.gz read2PairFiles=Next sample2 R1.fastq.gz read3PairFiles=Next sample2 R2.fastq.gz	Next_sample2_R2.fastq.gz Next_sample2_R1.fastq.gz Next_sample2_I1.fastq.gz	fastq fastq fastq	6538688308.0	71072699.0	GSM4547696 r1	0:8 1:26 2:58	A:1703837705;C:1534065984;G:1616771717;T:1678792786;N:5220116	8	26	58		1703837705	1534065984	1616771717	1678792786	5220116	SRX8330057	SRS6649544	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95552		0.0991		0.85178		0.51494		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59215	59215	SRR11777171	SRX8330057	SRS6649544	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	control 2	GSM4547696	tissue:control\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	control 2	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	control	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	GSM4547696	GSM4547696: control 2; Danio rerio; RNA Seq	GSM4547696		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547696	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample2 S2 L001 I1 001.fastq.gz read2PairFiles=sample2 S2 L001 R1 001.fastq.gz read3PairFiles=sample2 S2 L001 R2 001.fastq.gz	sample2_S2_L001_R2_001.fastq.gz sample2_S2_L001_R1_001.fastq.gz sample2_S2_L001_I1_001.fastq.gz	fastq fastq fastq	40686172002.0	322906127.0	GSM4547696 r2	0:8 1:26 2:92	A:11105689093;C:9483757136;G:9622172382;T:10472439389;N:2114002	8	26	92		11105689093	9483757136	9622172382	10472439389	2114002	SRX8330057	SRS6649544	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.96005		0.09149		0.8479		0.52442		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59216	59216	SRR11777172	SRX8330057	SRS6649544	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	control 2	GSM4547696	tissue:control\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	control 2	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	control	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	GSM4547696	GSM4547696: control 2; Danio rerio; RNA Seq	GSM4547696		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547696	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample2 S2 L002 I1 001.fastq.gz read2PairFiles=sample2 S2 L002 R1 001.fastq.gz read3PairFiles=sample2 S2 L002 R2 001.fastq.gz	sample2_S2_L002_I1_001.fastq.gz sample2_S2_L002_R1_001.fastq.gz sample2_S2_L002_R2_001.fastq.gz	fastq fastq fastq	40394060784.0	320587784.0	GSM4547696 r3	0:8 1:26 2:92	A:11030989263;C:9415697570;G:9551942377;T:10393536337;N:1895237	8	26	92		11030989263	9415697570	9551942377	10393536337	1895237	SRX8330057	SRS6649544	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.96032		0.09188		0.84571		0.51147		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59217	59217	SRR11777167	SRX8330056	SRS6649543	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	control 1	GSM4547695	tissue:control\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	control 1	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	control	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	GSM4547695	GSM4547695: control 1; Danio rerio; RNA Seq	GSM4547695		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547695	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Next sample1 I1.fastq.gz read2PairFiles=Next sample1 R1.fastq.gz read3PairFiles=Next sample1 R2.fastq.gz	Next_sample1_I1.fastq.gz Next_sample1_R1.fastq.gz Next_sample1_R2.fastq.gz	fastq fastq fastq	6194482636.0	67331333.0	GSM4547695 r1	0:8 1:26 2:58	A:1570433644;C:1511080065;G:1496787496;T:1611232189;N:4949242	8	26	58		1570433644	1511080065	1496787496	1611232189	4949242	SRX8330056	SRS6649543	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.95006		0.07448		0.85563		0.43909		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59218	59218	SRR11777168	SRX8330056	SRS6649543	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	control 1	GSM4547695	tissue:control\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	control 1	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	control	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	GSM4547695	GSM4547695: control 1; Danio rerio; RNA Seq	GSM4547695		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547695	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample1 S1 L001 I1 001.fastq.gz read2PairFiles=sample1 S1 L001 R1 001.fastq.gz read3PairFiles=sample1 S1 L001 R2 001.fastq.gz	sample1_S1_L001_I1_001.fastq.gz sample1_S1_L001_R1_001.fastq.gz sample1_S1_L001_R2_001.fastq.gz	fastq fastq fastq	42139701324.0	334442074.0	GSM4547695 r2	0:8 1:26 2:92	A:10979793082;C:10192056919;G:10036291604;T:10929392375;N:2167344	8	26	92		10979793082	10192056919	10036291604	10929392375	2167344	SRX8330056	SRS6649543	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.96205		0.06669		0.85234		0.51114		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59219	59219	SRR11777169	SRX8330056	SRS6649543	SRP261272	PRJNA631927	Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis [I]	GSE150373	Transcriptome Analysis	Clonal hematopoiesis CH results from enhanced fitness of a mutant hematopoietic stem and progenitor cell HSPC but how such clones expand is unclear. Here we developed a technique that combines mosaic mutagenesis with color labeling of HSPCs to study how acquired mutations affect clonal fitness in a native environment. Mutations in CH associated genes like asxl1 promoted clonal dominance. Single cell transcriptional analysis revealed that mutations stimulated expression of proinflammatory genes in mature myeloid cells and anti inflammatory genes in progenitor cells of the mutant clone. Biallelic loss of one such immunomodulator nr4a1 abrogated the ability of asxl1 mutant clones to establish clonal dominance. These results support a model where clonal fitness of mutant clones is driven by enhanced resistance to inflammatory signals from their mutant mature cell progeny. Overall design: To analyze the effect of multiplex CRISPR mutagenesis on zebrafish marrow cells we injected Zebrabow zebrafish embryos with guide RNAs targeting 20 different genes and cas9 mRNA. Control clutchmates were injected with 2 control guide RNAs and cas9 mRNA. These fish were grown to maturity. Whole kidney marrow cells from 2 control and 3 mutant zebrafish were collected for preparation for 10x single cell RNA sequencing. A third set of samples were sorted kidney marrow cells of the dominant Zebrabow color from the same three mutant zebrafish.	parent bioproject:PRJNA734615	pubmed:34735227	control 1	GSM4547695	tissue:control\|cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	control 1	The libraries were sequenced on NextSeq and NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Gene level counts were imported into R using the Seurat suite version 3.0 Count matrices from the NextSeq and NovaSeq platforms were merged together prior to quality control and filtering. For each cell that was present in both datasets gene level count values were summed to retain a final count matrix of 35 227 features across 39 424 cells. Low quality cells were filtered out by keeping cellular barcodes with the following metrics: 1 >= 500 UMIs per cell; 2 >= 200 genes per cell; 3 >= 0.7 novelty score calculated as log10genes detected / log10UMI counts per cell; and 4 <= 10 percentage of reads mapping to mitochondrial genes. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: FASTQ files and merged count matrices from the NextSeq and NovaSeq platforms	control	No additional treatment for unsorted cells; dominant cell samples were sorted into PBS over 30 minutes per sample	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	Freshly isolated kidney marrow cells from euthanized adult zebrafish at 8 month	cell type:unsorted whole kidney marrow cells\|sorting:unsorted\|age:8 mpf\|genotype/variation:2 control guide RNAs and cas9 mRNA	GSM4547695	GSM4547695: control 1; Danio rerio; RNA Seq	GSM4547695		1	post euthanasia the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40 μm nylon mesh. Part of the mutant marrow cell preparation was used for sorting the dominant color marrow cells on BD Aria 2 into 500ul 1x PBS. All 8 samples were washed by spinning down at 350 x g for 5 min at 4C. The cell pellelts were collected in 300ul of 1x DPBS with 0.04% BSA Gemini Bio Products then washed again post spinning down at 350 x g for 5 minutes at 4°C and counted post resuspension in DPBS/BSA to target 10 000 cells per reaction. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell RNA sequencing V2 library preparation single cell RNA sequencing 10x genomics	GEO Accession:GSM4547695	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP261272	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=sample1 S1 L002 I1 001.fastq.gz read2PairFiles=sample1 S1 L002 R1 001.fastq.gz read3PairFiles=sample1 S1 L002 R2 001.fastq.gz	sample1_S1_L002_R2_001.fastq.gz sample1_S1_L002_R1_001.fastq.gz sample1_S1_L002_I1_001.fastq.gz	fastq fastq fastq	41867006580.0	332277830.0	GSM4547695 r3	0:8 1:26 2:92	A:10912078962;C:10125686513;G:9971217295;T:10856057042;N:1966768	8	26	92		10912078962	10125686513	9971217295	10856057042	1966768	SRX8330056	SRS6649543	SRA1074695	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.96295		0.06599		0.85299		0.51294		92		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-05-12	Adult	Adult	Multi-tissue	Multi-system
59870	59870	SRR12055985	SRX8584378	SRS6875885	SRP268040	PRJNA640655	Emx2 defines bidirectional polarity of neuromasts by changing hair bundle orientation and not hair cell positions	GSE152859	Other	The bidirectional sensitivity of neuromasts to water flow in the zebrafish lateral line system is attributed to the opposite orientation of the hair bundles on top of sensory hair cells HC within a neuromast. post each HC precursor divides to form two nascent HCs HCs of the same bundle orientation are positioned on one side of the neuromast across from HCs with opposite bundle orientation. The transcription factor emx2 is expressed in only one of the sibling HCs. Loss or gain of function of emx2 in HCs causes unidirectional hair bundle orientation in neuromasts. It is not clear whether Emx2 is required specifically in establishing hair bundle orientation post HC formation or Emx2 has an earlier role in HC fate and/or positioning which indirectly changes hair bundle orientation. A phenomenon in which nascent sibling HCs exchange positions with each other has been postulated to be the mechanism for HCs to acquire their designated positions within the neuromast. We asked whether Emx2 is involved in positional acquisition of HCs within the neuromast. Using live imaging and our emx2 reporter we find that the HC rearrangement redefined as two processes named Rock & Roll are required for HCs to acquire their positions. Although Emx2 regulates the duration of the Rock and the frequency of Roll of nascent HCs it is not required for their positional acquisition. Instead Emx2 regulates the morphology of nascent HCs which facilitates the rearrangement process. Overall design: Single cell RNA sequencing on FACS sorted Hair Cells from zebrafish neuromast in 4dpf wild type larvae.		pubmed:33377867	scRNA seq zebrafish 4dpf neuromast hair cells	GSM4628143	tissue:P4 zebrafish hair cell\|genotype/variation:Tgmyo6b:RiboTag\|developmental stage:4 dpf\|cell type:Neuromast hair cells	scRNA seq zebrafish 4dpf neuromast hair cells	Basecalls performed using Illumina’s RTA 2.0.12. Sample demultiplexing alignment and gene counts were performed using the 10X Genomics CellRanger v3.0.1 pipeline using default settings. Secondary analysis was performed using SCANPY version 1.4.4. Genome build: not provided Supplementary files format and content: barcodes.tsv.gz: cell barcodes Supplementary files format and content: features.tsv.gz: gene names Supplementary files format and content: matrix.mtx.gz: expression matrix Supplementary files format and content: filtered feature bc matrix.h5: expression matrix in HDF5 format	P4 zebrafish hair cell	n/a	Zebrafish larvae Tgmyo6b: RiboTag at 4 dpf were dissected to remove the head which included the ear. Approximately 400 dissected bodies in batches of 50 were dissociated by adding 0.5 ml of 0.5% trypsin Gibco cat# 15400054 and triturated with 1 ml pipette tip for 30 seconds at 30°C. The dissociated cells were filtered with 40 μm strainer Pluriselect cat# 43 50040 50 and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C. Cells were resuspended and kept in DMEM before processing for FACS. scRNA seq was carried out with 10X Genomics single cell platform 10X Genomics Pleasanton CA. USA. Approximately 5000 live cells post FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller 10x Genomics. Chromium Single Cell three prime Library and Gel Bead Kit v2 10X Genomics was used for libraries preparation according to manufacturer’s instructions. Quality of the libraries was evaluated on a Fragment Analyzer instrument Agilent and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1 8 bp I7 Index and 98 bp Read 2.	n/a	genotype/variation:Tgmyo6b:RiboTag\|developmental stage:4 dpf\|cell type:Neuromast hair cells	GSM4628143	GSM4628143: scRNA seq zebrafish 4dpf neuromast hair cells; Danio rerio; RNA Seq	GSM4628143		1	Zebrafish larvae Tgmyo6b: RiboTag at 4 dpf were dissected to remove the head which included the ear. Approximately 400 dissected bodies in batches of 50 were dissociated by adding 0.5 ml of 0.5% trypsin Gibco cat# 15400054 and triturated with 1 ml pipette tip for 30 seconds at 30°C. The dissociated cells were filtered with 40 μm strainer Pluriselect cat# 43 50040 50 and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C. Cells were resuspended and kept in DMEM before processing for FACS. scRNA seq was carried out with 10X Genomics single cell platform 10X Genomics Pleasanton CA. USA. Approximately 5000 live cells post FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller 10x Genomics. Chromium Single Cell three prime Library and Gel Bead Kit v2 10X Genomics was used for libraries preparation according to manufacturer's instructions. Quality of the libraries was evaluated on a Fragment Analyzer instrument Agilent and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1 8 bp I7 Index and 98 bp Read 2.	GEO Accession:GSM4628143	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268040	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ZM4 S1 L001 I1 001.fastq.gz read2PairFiles=ZM4 S1 L001 R1 001.fastq.gz read3PairFiles=ZM4 S1 L001 R2 001.fastq.gz	ZM4_S1_L001_I1_001.fastq.gz ZM4_S1_L001_R1_001.fastq.gz ZM4_S1_L001_R2_001.fastq.gz	fastq fastq fastq	5422224324.0	41077457.0	GSM4628143 r1	0:8 1:26 2:98	A:1539837924;C:1167111399;G:1177239259;T:1536971308;N:1064434	8	26	98		1539837924	1167111399	1177239259	1536971308	1064434	SRX8584378	SRS6875885	SRA1089164	GEO	Molecular Biology, NIDCD	1	0.93866		0.12434		0.8229		0.42198		98		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Larval	Larval	Multi-tissue	Multi-system
59871	59871	SRR12055986	SRX8584378	SRS6875885	SRP268040	PRJNA640655	Emx2 defines bidirectional polarity of neuromasts by changing hair bundle orientation and not hair cell positions	GSE152859	Other	The bidirectional sensitivity of neuromasts to water flow in the zebrafish lateral line system is attributed to the opposite orientation of the hair bundles on top of sensory hair cells HC within a neuromast. post each HC precursor divides to form two nascent HCs HCs of the same bundle orientation are positioned on one side of the neuromast across from HCs with opposite bundle orientation. The transcription factor emx2 is expressed in only one of the sibling HCs. Loss or gain of function of emx2 in HCs causes unidirectional hair bundle orientation in neuromasts. It is not clear whether Emx2 is required specifically in establishing hair bundle orientation post HC formation or Emx2 has an earlier role in HC fate and/or positioning which indirectly changes hair bundle orientation. A phenomenon in which nascent sibling HCs exchange positions with each other has been postulated to be the mechanism for HCs to acquire their designated positions within the neuromast. We asked whether Emx2 is involved in positional acquisition of HCs within the neuromast. Using live imaging and our emx2 reporter we find that the HC rearrangement redefined as two processes named Rock & Roll are required for HCs to acquire their positions. Although Emx2 regulates the duration of the Rock and the frequency of Roll of nascent HCs it is not required for their positional acquisition. Instead Emx2 regulates the morphology of nascent HCs which facilitates the rearrangement process. Overall design: Single cell RNA sequencing on FACS sorted Hair Cells from zebrafish neuromast in 4dpf wild type larvae.		pubmed:33377867	scRNA seq zebrafish 4dpf neuromast hair cells	GSM4628143	tissue:P4 zebrafish hair cell\|genotype/variation:Tgmyo6b:RiboTag\|developmental stage:4 dpf\|cell type:Neuromast hair cells	scRNA seq zebrafish 4dpf neuromast hair cells	Basecalls performed using Illumina’s RTA 2.0.12. Sample demultiplexing alignment and gene counts were performed using the 10X Genomics CellRanger v3.0.1 pipeline using default settings. Secondary analysis was performed using SCANPY version 1.4.4. Genome build: not provided Supplementary files format and content: barcodes.tsv.gz: cell barcodes Supplementary files format and content: features.tsv.gz: gene names Supplementary files format and content: matrix.mtx.gz: expression matrix Supplementary files format and content: filtered feature bc matrix.h5: expression matrix in HDF5 format	P4 zebrafish hair cell	n/a	Zebrafish larvae Tgmyo6b: RiboTag at 4 dpf were dissected to remove the head which included the ear. Approximately 400 dissected bodies in batches of 50 were dissociated by adding 0.5 ml of 0.5% trypsin Gibco cat# 15400054 and triturated with 1 ml pipette tip for 30 seconds at 30°C. The dissociated cells were filtered with 40 μm strainer Pluriselect cat# 43 50040 50 and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C. Cells were resuspended and kept in DMEM before processing for FACS. scRNA seq was carried out with 10X Genomics single cell platform 10X Genomics Pleasanton CA. USA. Approximately 5000 live cells post FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller 10x Genomics. Chromium Single Cell three prime Library and Gel Bead Kit v2 10X Genomics was used for libraries preparation according to manufacturer’s instructions. Quality of the libraries was evaluated on a Fragment Analyzer instrument Agilent and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1 8 bp I7 Index and 98 bp Read 2.	n/a	genotype/variation:Tgmyo6b:RiboTag\|developmental stage:4 dpf\|cell type:Neuromast hair cells	GSM4628143	GSM4628143: scRNA seq zebrafish 4dpf neuromast hair cells; Danio rerio; RNA Seq	GSM4628143		1	Zebrafish larvae Tgmyo6b: RiboTag at 4 dpf were dissected to remove the head which included the ear. Approximately 400 dissected bodies in batches of 50 were dissociated by adding 0.5 ml of 0.5% trypsin Gibco cat# 15400054 and triturated with 1 ml pipette tip for 30 seconds at 30°C. The dissociated cells were filtered with 40 μm strainer Pluriselect cat# 43 50040 50 and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C. Cells were resuspended and kept in DMEM before processing for FACS. scRNA seq was carried out with 10X Genomics single cell platform 10X Genomics Pleasanton CA. USA. Approximately 5000 live cells post FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller 10x Genomics. Chromium Single Cell three prime Library and Gel Bead Kit v2 10X Genomics was used for libraries preparation according to manufacturer's instructions. Quality of the libraries was evaluated on a Fragment Analyzer instrument Agilent and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1 8 bp I7 Index and 98 bp Read 2.	GEO Accession:GSM4628143	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268040	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ZM4 S1 L002 I1 001.fastq.gz read2PairFiles=ZM4 S1 L002 R1 001.fastq.gz read3PairFiles=ZM4 S1 L002 R2 001.fastq.gz	ZM4_S1_L002_I1_001.fastq.gz ZM4_S1_L002_R1_001.fastq.gz ZM4_S1_L002_R2_001.fastq.gz	fastq fastq fastq	5480072136.0	41515698.0	GSM4628143 r2	0:8 1:26 2:98	A:1556115839;C:1180006462;G:1189325251;T:1553616619;N:1007965	8	26	98		1556115839	1180006462	1189325251	1553616619	1007965	SRX8584378	SRS6875885	SRA1089164	GEO	Molecular Biology, NIDCD	1	0.93811		0.12465		0.8227		0.42538		98		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Larval	Larval	Multi-tissue	Multi-system
59872	59872	SRR12055987	SRX8584378	SRS6875885	SRP268040	PRJNA640655	Emx2 defines bidirectional polarity of neuromasts by changing hair bundle orientation and not hair cell positions	GSE152859	Other	The bidirectional sensitivity of neuromasts to water flow in the zebrafish lateral line system is attributed to the opposite orientation of the hair bundles on top of sensory hair cells HC within a neuromast. post each HC precursor divides to form two nascent HCs HCs of the same bundle orientation are positioned on one side of the neuromast across from HCs with opposite bundle orientation. The transcription factor emx2 is expressed in only one of the sibling HCs. Loss or gain of function of emx2 in HCs causes unidirectional hair bundle orientation in neuromasts. It is not clear whether Emx2 is required specifically in establishing hair bundle orientation post HC formation or Emx2 has an earlier role in HC fate and/or positioning which indirectly changes hair bundle orientation. A phenomenon in which nascent sibling HCs exchange positions with each other has been postulated to be the mechanism for HCs to acquire their designated positions within the neuromast. We asked whether Emx2 is involved in positional acquisition of HCs within the neuromast. Using live imaging and our emx2 reporter we find that the HC rearrangement redefined as two processes named Rock & Roll are required for HCs to acquire their positions. Although Emx2 regulates the duration of the Rock and the frequency of Roll of nascent HCs it is not required for their positional acquisition. Instead Emx2 regulates the morphology of nascent HCs which facilitates the rearrangement process. Overall design: Single cell RNA sequencing on FACS sorted Hair Cells from zebrafish neuromast in 4dpf wild type larvae.		pubmed:33377867	scRNA seq zebrafish 4dpf neuromast hair cells	GSM4628143	tissue:P4 zebrafish hair cell\|genotype/variation:Tgmyo6b:RiboTag\|developmental stage:4 dpf\|cell type:Neuromast hair cells	scRNA seq zebrafish 4dpf neuromast hair cells	Basecalls performed using Illumina’s RTA 2.0.12. Sample demultiplexing alignment and gene counts were performed using the 10X Genomics CellRanger v3.0.1 pipeline using default settings. Secondary analysis was performed using SCANPY version 1.4.4. Genome build: not provided Supplementary files format and content: barcodes.tsv.gz: cell barcodes Supplementary files format and content: features.tsv.gz: gene names Supplementary files format and content: matrix.mtx.gz: expression matrix Supplementary files format and content: filtered feature bc matrix.h5: expression matrix in HDF5 format	P4 zebrafish hair cell	n/a	Zebrafish larvae Tgmyo6b: RiboTag at 4 dpf were dissected to remove the head which included the ear. Approximately 400 dissected bodies in batches of 50 were dissociated by adding 0.5 ml of 0.5% trypsin Gibco cat# 15400054 and triturated with 1 ml pipette tip for 30 seconds at 30°C. The dissociated cells were filtered with 40 μm strainer Pluriselect cat# 43 50040 50 and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C. Cells were resuspended and kept in DMEM before processing for FACS. scRNA seq was carried out with 10X Genomics single cell platform 10X Genomics Pleasanton CA. USA. Approximately 5000 live cells post FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller 10x Genomics. Chromium Single Cell three prime Library and Gel Bead Kit v2 10X Genomics was used for libraries preparation according to manufacturer’s instructions. Quality of the libraries was evaluated on a Fragment Analyzer instrument Agilent and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1 8 bp I7 Index and 98 bp Read 2.	n/a	genotype/variation:Tgmyo6b:RiboTag\|developmental stage:4 dpf\|cell type:Neuromast hair cells	GSM4628143	GSM4628143: scRNA seq zebrafish 4dpf neuromast hair cells; Danio rerio; RNA Seq	GSM4628143		1	Zebrafish larvae Tgmyo6b: RiboTag at 4 dpf were dissected to remove the head which included the ear. Approximately 400 dissected bodies in batches of 50 were dissociated by adding 0.5 ml of 0.5% trypsin Gibco cat# 15400054 and triturated with 1 ml pipette tip for 30 seconds at 30°C. The dissociated cells were filtered with 40 μm strainer Pluriselect cat# 43 50040 50 and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C. Cells were resuspended and kept in DMEM before processing for FACS. scRNA seq was carried out with 10X Genomics single cell platform 10X Genomics Pleasanton CA. USA. Approximately 5000 live cells post FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller 10x Genomics. Chromium Single Cell three prime Library and Gel Bead Kit v2 10X Genomics was used for libraries preparation according to manufacturer's instructions. Quality of the libraries was evaluated on a Fragment Analyzer instrument Agilent and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1 8 bp I7 Index and 98 bp Read 2.	GEO Accession:GSM4628143	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268040	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ZM4 S1 L003 I1 001.fastq.gz read2PairFiles=ZM4 S1 L003 R1 001.fastq.gz read3PairFiles=ZM4 S1 L003 R2 001.fastq.gz	ZM4_S1_L003_I1_001.fastq.gz ZM4_S1_L003_R1_001.fastq.gz ZM4_S1_L003_R2_001.fastq.gz	fastq fastq fastq	5589739452.0	42346511.0	GSM4628143 r3	0:8 1:26 2:98	A:1586134828;C:1202961360;G:1215543516;T:1584245728;N:854020	8	26	98		1586134828	1202961360	1215543516	1584245728	854020	SRX8584378	SRS6875885	SRA1089164	GEO	Molecular Biology, NIDCD	1	0.93749		0.12195		0.82286		0.41205		98		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Larval	Larval	Multi-tissue	Multi-system
59873	59873	SRR12055988	SRX8584378	SRS6875885	SRP268040	PRJNA640655	Emx2 defines bidirectional polarity of neuromasts by changing hair bundle orientation and not hair cell positions	GSE152859	Other	The bidirectional sensitivity of neuromasts to water flow in the zebrafish lateral line system is attributed to the opposite orientation of the hair bundles on top of sensory hair cells HC within a neuromast. post each HC precursor divides to form two nascent HCs HCs of the same bundle orientation are positioned on one side of the neuromast across from HCs with opposite bundle orientation. The transcription factor emx2 is expressed in only one of the sibling HCs. Loss or gain of function of emx2 in HCs causes unidirectional hair bundle orientation in neuromasts. It is not clear whether Emx2 is required specifically in establishing hair bundle orientation post HC formation or Emx2 has an earlier role in HC fate and/or positioning which indirectly changes hair bundle orientation. A phenomenon in which nascent sibling HCs exchange positions with each other has been postulated to be the mechanism for HCs to acquire their designated positions within the neuromast. We asked whether Emx2 is involved in positional acquisition of HCs within the neuromast. Using live imaging and our emx2 reporter we find that the HC rearrangement redefined as two processes named Rock & Roll are required for HCs to acquire their positions. Although Emx2 regulates the duration of the Rock and the frequency of Roll of nascent HCs it is not required for their positional acquisition. Instead Emx2 regulates the morphology of nascent HCs which facilitates the rearrangement process. Overall design: Single cell RNA sequencing on FACS sorted Hair Cells from zebrafish neuromast in 4dpf wild type larvae.		pubmed:33377867	scRNA seq zebrafish 4dpf neuromast hair cells	GSM4628143	tissue:P4 zebrafish hair cell\|genotype/variation:Tgmyo6b:RiboTag\|developmental stage:4 dpf\|cell type:Neuromast hair cells	scRNA seq zebrafish 4dpf neuromast hair cells	Basecalls performed using Illumina’s RTA 2.0.12. Sample demultiplexing alignment and gene counts were performed using the 10X Genomics CellRanger v3.0.1 pipeline using default settings. Secondary analysis was performed using SCANPY version 1.4.4. Genome build: not provided Supplementary files format and content: barcodes.tsv.gz: cell barcodes Supplementary files format and content: features.tsv.gz: gene names Supplementary files format and content: matrix.mtx.gz: expression matrix Supplementary files format and content: filtered feature bc matrix.h5: expression matrix in HDF5 format	P4 zebrafish hair cell	n/a	Zebrafish larvae Tgmyo6b: RiboTag at 4 dpf were dissected to remove the head which included the ear. Approximately 400 dissected bodies in batches of 50 were dissociated by adding 0.5 ml of 0.5% trypsin Gibco cat# 15400054 and triturated with 1 ml pipette tip for 30 seconds at 30°C. The dissociated cells were filtered with 40 μm strainer Pluriselect cat# 43 50040 50 and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C. Cells were resuspended and kept in DMEM before processing for FACS. scRNA seq was carried out with 10X Genomics single cell platform 10X Genomics Pleasanton CA. USA. Approximately 5000 live cells post FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller 10x Genomics. Chromium Single Cell three prime Library and Gel Bead Kit v2 10X Genomics was used for libraries preparation according to manufacturer’s instructions. Quality of the libraries was evaluated on a Fragment Analyzer instrument Agilent and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1 8 bp I7 Index and 98 bp Read 2.	n/a	genotype/variation:Tgmyo6b:RiboTag\|developmental stage:4 dpf\|cell type:Neuromast hair cells	GSM4628143	GSM4628143: scRNA seq zebrafish 4dpf neuromast hair cells; Danio rerio; RNA Seq	GSM4628143		1	Zebrafish larvae Tgmyo6b: RiboTag at 4 dpf were dissected to remove the head which included the ear. Approximately 400 dissected bodies in batches of 50 were dissociated by adding 0.5 ml of 0.5% trypsin Gibco cat# 15400054 and triturated with 1 ml pipette tip for 30 seconds at 30°C. The dissociated cells were filtered with 40 μm strainer Pluriselect cat# 43 50040 50 and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C. Cells were resuspended and kept in DMEM before processing for FACS. scRNA seq was carried out with 10X Genomics single cell platform 10X Genomics Pleasanton CA. USA. Approximately 5000 live cells post FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller 10x Genomics. Chromium Single Cell three prime Library and Gel Bead Kit v2 10X Genomics was used for libraries preparation according to manufacturer's instructions. Quality of the libraries was evaluated on a Fragment Analyzer instrument Agilent and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1 8 bp I7 Index and 98 bp Read 2.	GEO Accession:GSM4628143	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268040	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ZM4 S1 L004 I1 001.fastq.gz read2PairFiles=ZM4 S1 L004 R1 001.fastq.gz read3PairFiles=ZM4 S1 L004 R2 001.fastq.gz	ZM4_S1_L004_I1_001.fastq.gz ZM4_S1_L004_R1_001.fastq.gz ZM4_S1_L004_R2_001.fastq.gz	fastq fastq fastq	5495099808.0	41629544.0	GSM4628143 r4	0:8 1:26 2:98	A:1559732557;C:1183298748;G:1193530338;T:1557803123;N:735042	8	26	98		1559732557	1183298748	1193530338	1557803123	735042	SRX8584378	SRS6875885	SRA1089164	GEO	Molecular Biology, NIDCD	1	0.93891		0.12244		0.82181		0.42894		98		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-19	Larval	Larval	Multi-tissue	Multi-system
62679	62679	SRR13311744	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_1_S21_L001_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_1_S21_L001_R2_001.fastq.gz	fastq fastq	23474658448.0	77935654.0	GSM4990514 r1	0:150.58 1:150.62	A:5315661572;C:4260464374;G:7908155075;T:5989858000;N:519427	150	150			5315661572	4260464374	7908155075	5989858000	519427	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90618	0.0	0.11433	1.0	0.80178		0.51559	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62680	62680	SRR13311745	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_1_S21_L002_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_1_S21_L002_R2_001.fastq.gz	fastq fastq	23453047207.0	77864343.0	GSM4990514 r2	0:150.58 1:150.62	A:5353428042;C:4272250712;G:7801502473;T:6025426926;N:439054	150	150			5353428042	4272250712	7801502473	6025426926	439054	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90571	0.0	0.11445	1.0	0.80326		0.51014	149	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62681	62681	SRR13311746	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_2_S22_L001_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_2_S22_L001_R2_001.fastq.gz	fastq fastq	18693961077.0	62064026.0	GSM4990514 r3	0:150.58 1:150.62	A:4223627306;C:3394276969;G:6298948837;T:4776692177;N:415788	150	150			4223627306	3394276969	6298948837	4776692177	415788	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90754	0.0	0.11555	1.0	0.8018		0.50793	150	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62682	62682	SRR13311747	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_2_S22_L002_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_2_S22_L002_R2_001.fastq.gz	fastq fastq	18650610191.0	61920476.0	GSM4990514 r4	0:150.58 1:150.62	A:4248232322;C:3398942457;G:6205002760;T:4798080435;N:352217	150	150			4248232322	3398942457	6205002760	4798080435	352217	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90621	0.0	0.11451	1.0	0.80223		0.51751	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62683	62683	SRR13311748	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_3_S23_L001_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_3_S23_L001_R2_001.fastq.gz	fastq fastq	21139583045.0	70183976.0	GSM4990514 r5	0:150.58 1:150.62	A:4766130433;C:3847270802;G:7123755600;T:5401957528;N:468682	150	150			4766130433	3847270802	7123755600	5401957528	468682	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90939	0.0	0.11373	1.0	0.80044		0.51922	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62684	62684	SRR13311749	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_3_S23_L002_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_3_S23_L002_R2_001.fastq.gz	fastq fastq	21127496209.0	70144256.0	GSM4990514 r6	0:150.58 1:150.62	A:4801779342;C:3857990471;G:7030522815;T:5436808841;N:394740	150	150			4801779342	3857990471	7030522815	5436808841	394740	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90941	0.0	0.11435	1.0	0.80087		0.51663	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62685	62685	SRR13311750	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_4_S24_L001_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_4_S24_L001_R2_001.fastq.gz	fastq fastq	19213599440.0	63789538.0	GSM4990514 r7	0:150.58 1:150.62	A:4332795032;C:3494053982;G:6477323231;T:4908999176;N:428019	150	150			4332795032	3494053982	6477323231	4908999176	428019	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.9086	0.0	0.11426	1.0	0.80257		0.51017	151	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62686	62686	SRR13311751	SRX9739651	SRS7936985	SRP299375	PRJNA688157	Single cell RNA analysis of trunk neural crest cells in zebrafish	GSE163907	Other	Single cell RNA seq data of tgsox10:GFP cells from 20 hpf 24 hpf zebrafish. Sequenced with 10x genomics. Overall design: tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		pubmed:34397384	tgsox10:GFP	GSM4990514	source name:zebrafish trunk tgsox10:GFP positive cells\|genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	tgsox10:GFP	cellranger v3.2 seurat v3.2.2 Genome build: GRCz11 Supplementary files format and content: features barcodes counts matrix for scRNAseq Supplementary files format and content: Cluster assignments	zebrafish trunk tgsox10:GFP positive cells		tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing		genotype:tgsox10:GFP ba2\|tissue:trunk neural crest cells\|developmental stage:24 hpf	GSM4990514	GSM4990514: tgsox10:GFP; Danio rerio; RNA Seq	GSM4990514		1	tgsox10:GFP cells were isolated by FACS from dissociated trunks of 20 24hpf zebrafish and submitted to 10x Sequencing	GEO Accession:GSM4990514	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299375		Cut_Sox10_GFP_24hpf_12142018_4_S24_L002_R1_001.fastq.gz Cut_Sox10_GFP_24hpf_12142018_4_S24_L002_R2_001.fastq.gz	fastq fastq	19195135075.0	63728553.0	GSM4990514 r8	0:150.58 1:150.62	A:4363501238;C:3503247240;G:6390188740;T:4937837783;N:360074	150	150			4363501238	3503247240	6390188740	4937837783	360074	SRX9739651	SRS7936985	SRA1178122	GEO	Artinger Laboratory, Craniofacial Biology, University of Colorado Denver \| Anschutz	2	0.0	0.90626	0.0	0.11537	1.0	0.8032		0.50845	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-28	Pharyngula	Embryo	Multi-tissue	Multi-system
62904	62904	SRR13429041	SRX9843973	SRS8025681	SRP301615	PRJNA691919	A single cell transcriptomic atlas identifies synapse associated microglia in the developing zebrafish single cells	GSE164772	Transcriptome Analysis	This study profiles developing and adult zebrafish macrophages and defines regional and functional microglial subtypes. Overall design: Macrophages Mpeg+ and CD45+ cells were sorted and sequenced from 28 dpf and 6 mpf zebrafish		pubmed:34625548	Adult A	GSM5018536	tissue:Brain and Spinal Cord Mpeg+ and CD45+\|age:6 mpf A\|cell type:Mpeg+ myeloid cells and CD45+ immune cells	Adult A	Cell Ranger 3.1.0 STAR alignment with Danio rerio zebrafish transcriptome z11 Quality control to select cells with <10% mitochondrial RNA 500 3 000 unique genes and 1 200 15 000 unique mRNA counts [scaledata only] Log normalization Seurat v3.2 with scale factor 10 000 [scaledata only] most variable genes scaled with "vst" algorithm and #genes/cell regressed out Seurat v3.2 Genome build: z11 Supplementary files format and content: Counts: unnormalized count data for all cells included in the manuscript Supplementary files format and content: Metadata: file containing age individual and cluster assignment for each cell Supplementary files format and content: sc dr Silva2021Counts.txt: All cells in paper Supplementary files format and content: sc dr Silva2021 metadata.csv: All cells in paper Supplementary files format and content: sc dr Silva2021 JMscaledata.txt: Juvenile Mpeg+ cells Supplementary files format and content: sc dr Silva2021 Jscaledata.txt: All Juvenile cells Supplementary files format and content: sc dr Silva2021 Ascaledata.txt: Adult and Juvenile Mpeg+ cells	Brain and Spinal Cord Mpeg+ and CD45+		Zebrafish brains from mpeg:GFP; CD45:DsRed fish were homogenized and sorted to isolate single CD45:DsRed+ and double mpeg:GFP+/CD45:DsRed+ positive cells 10x Genomics v3.1 three prime Single Index Chip Kit B was used to make a single cell suspension in gel beads and the v3 three prime Library Kit was used to prepare cDNA		age:6 mpf A\|cell type:Mpeg+ myeloid cells and CD45+ immune cells	GSM5018536	GSM5018536: Adult A; Danio rerio; RNA Seq	GSM5018536		1	Zebrafish brains from mpeg:GFP; CD45:DsRed fish were homogenized and sorted to isolate single CD45:DsRed+ and double mpeg:GFP+/CD45:DsRed+ positive cells 10x Genomics v3.1 three prime Single Index Chip Kit B was used to make a single cell suspension in gel beads and the v3 three prime Library Kit was used to prepare cDNA	GEO Accession:GSM5018536	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP301615	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Sample3 A1 S2 L001 I1 001.fastq.gz read2PairFiles=Sample3 A1 S2 L001 R1 001.fastq.gz read3PairFiles=Sample3 A1 S2 L001 R2 001.fastq.gz	Sample3-_A1__S2_L001_I1_001.fastq.gz Sample3-_A1__S2_L001_R1_001.fastq.gz Sample3-_A1__S2_L001_R2_001.fastq.gz	fastq fastq fastq	5863809770.0	45106229.0	GSM5018536 r1	0:8 1:28 2:94	A:1686208936;C:1248351000;G:1297163723;T:1629033266;N:3052845	8	28	94		1686208936	1248351000	1297163723	1629033266	3052845	SRX9843973	SRS8025681	SRA1183553	GEO	Anna Molofsky Lab, Psychiatry, UCSF	1	0.89063		0.3045		0.79632		0.57216		94		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-01-13	Adult	Adult	Multi-tissue	Multi-system
62905	62905	SRR13429040	SRX9843972	SRS8025678	SRP301615	PRJNA691919	A single cell transcriptomic atlas identifies synapse associated microglia in the developing zebrafish single cells	GSE164772	Transcriptome Analysis	This study profiles developing and adult zebrafish macrophages and defines regional and functional microglial subtypes. Overall design: Macrophages Mpeg+ and CD45+ cells were sorted and sequenced from 28 dpf and 6 mpf zebrafish		pubmed:34625548	Juvenile B	GSM5018535	tissue:Brain and Spinal Cord Mpeg+ and CD45+\|age:28 dpf B\|cell type:Mpeg+ myeloid cells and CD45+ immune cells	Juvenile B	Cell Ranger 3.1.0 STAR alignment with Danio rerio zebrafish transcriptome z11 Quality control to select cells with <10% mitochondrial RNA 500 3 000 unique genes and 1 200 15 000 unique mRNA counts [scaledata only] Log normalization Seurat v3.2 with scale factor 10 000 [scaledata only] most variable genes scaled with "vst" algorithm and #genes/cell regressed out Seurat v3.2 Genome build: z11 Supplementary files format and content: Counts: unnormalized count data for all cells included in the manuscript Supplementary files format and content: Metadata: file containing age individual and cluster assignment for each cell Supplementary files format and content: sc dr Silva2021Counts.txt: All cells in paper Supplementary files format and content: sc dr Silva2021 metadata.csv: All cells in paper Supplementary files format and content: sc dr Silva2021 JMscaledata.txt: Juvenile Mpeg+ cells Supplementary files format and content: sc dr Silva2021 Jscaledata.txt: All Juvenile cells Supplementary files format and content: sc dr Silva2021 Ascaledata.txt: Adult and Juvenile Mpeg+ cells	Brain and Spinal Cord Mpeg+ and CD45+		Zebrafish brains from mpeg:GFP; CD45:DsRed fish were homogenized and sorted to isolate single CD45:DsRed+ and double mpeg:GFP+/CD45:DsRed+ positive cells 10x Genomics v3.1 three prime Single Index Chip Kit B was used to make a single cell suspension in gel beads and the v3 three prime Library Kit was used to prepare cDNA		age:28 dpf B\|cell type:Mpeg+ myeloid cells and CD45+ immune cells	GSM5018535	GSM5018535: Juvenile B; Danio rerio; RNA Seq	GSM5018535		1	Zebrafish brains from mpeg:GFP; CD45:DsRed fish were homogenized and sorted to isolate single CD45:DsRed+ and double mpeg:GFP+/CD45:DsRed+ positive cells 10x Genomics v3.1 three prime Single Index Chip Kit B was used to make a single cell suspension in gel beads and the v3 three prime Library Kit was used to prepare cDNA	GEO Accession:GSM5018535	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP301615	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Sample2 L2 S4 L001 I1 001.fastq.gz read2PairFiles=Sample2 L2 S4 L001 R1 001.fastq.gz read3PairFiles=Sample2 L2 S4 L001 R2 001.fastq.gz	Sample2-_L2__S4_L001_I1_001.fastq.gz Sample2-_L2__S4_L001_R1_001.fastq.gz Sample2-_L2__S4_L001_R2_001.fastq.gz	fastq fastq fastq	20625538440.0	158657988.0	GSM5018535 r1	0:8 1:28 2:94	A:5854974563;C:4547250454;G:4552388689;T:5660267648;N:10657086	8	28	94		5854974563	4547250454	4552388689	5660267648	10657086	SRX9843972	SRS8025678	SRA1183553	GEO	Anna Molofsky Lab, Psychiatry, UCSF	1	0.90631		0.26392		0.78407		0.56464		94		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-01-13	Larval	Larval	Multi-tissue	Multi-system
62906	62906	SRR13429039	SRX9843971	SRS8025680	SRP301615	PRJNA691919	A single cell transcriptomic atlas identifies synapse associated microglia in the developing zebrafish single cells	GSE164772	Transcriptome Analysis	This study profiles developing and adult zebrafish macrophages and defines regional and functional microglial subtypes. Overall design: Macrophages Mpeg+ and CD45+ cells were sorted and sequenced from 28 dpf and 6 mpf zebrafish		pubmed:34625548	Juvenile A	GSM5018534	tissue:Brain and Spinal Cord Mpeg+ and CD45+\|age:28 dpf A\|cell type:Mpeg+ myeloid cells and CD45+ immune cells	Juvenile A	Cell Ranger 3.1.0 STAR alignment with Danio rerio zebrafish transcriptome z11 Quality control to select cells with <10% mitochondrial RNA 500 3 000 unique genes and 1 200 15 000 unique mRNA counts [scaledata only] Log normalization Seurat v3.2 with scale factor 10 000 [scaledata only] most variable genes scaled with "vst" algorithm and #genes/cell regressed out Seurat v3.2 Genome build: z11 Supplementary files format and content: Counts: unnormalized count data for all cells included in the manuscript Supplementary files format and content: Metadata: file containing age individual and cluster assignment for each cell Supplementary files format and content: sc dr Silva2021Counts.txt: All cells in paper Supplementary files format and content: sc dr Silva2021 metadata.csv: All cells in paper Supplementary files format and content: sc dr Silva2021 JMscaledata.txt: Juvenile Mpeg+ cells Supplementary files format and content: sc dr Silva2021 Jscaledata.txt: All Juvenile cells Supplementary files format and content: sc dr Silva2021 Ascaledata.txt: Adult and Juvenile Mpeg+ cells	Brain and Spinal Cord Mpeg+ and CD45+		Zebrafish brains from mpeg:GFP; CD45:DsRed fish were homogenized and sorted to isolate single CD45:DsRed+ and double mpeg:GFP+/CD45:DsRed+ positive cells 10x Genomics v3.1 three prime Single Index Chip Kit B was used to make a single cell suspension in gel beads and the v3 three prime Library Kit was used to prepare cDNA		age:28 dpf A\|cell type:Mpeg+ myeloid cells and CD45+ immune cells	GSM5018534	GSM5018534: Juvenile A; Danio rerio; RNA Seq	GSM5018534		1	Zebrafish brains from mpeg:GFP; CD45:DsRed fish were homogenized and sorted to isolate single CD45:DsRed+ and double mpeg:GFP+/CD45:DsRed+ positive cells 10x Genomics v3.1 three prime Single Index Chip Kit B was used to make a single cell suspension in gel beads and the v3 three prime Library Kit was used to prepare cDNA	GEO Accession:GSM5018534	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP301615	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Sample1 L1 S1 L001 I1 001.fastq.gz read2PairFiles=Sample1 L1 S1 L001 R1 001.fastq.gz read3PairFiles=Sample1 L1 S1 L001 R2 001.fastq.gz	Sample1-_L1__S1_L001_I1_001.fastq.gz Sample1-_L1__S1_L001_R1_001.fastq.gz Sample1-_L1__S1_L001_R2_001.fastq.gz	fastq fastq fastq	12770179370.0	98232149.0	GSM5018534 r1	0:8 1:28 2:94	A:3657439948;C:2724528296;G:2851650695;T:3529904486;N:6655945	8	28	94		3657439948	2724528296	2851650695	3529904486	6655945	SRX9843971	SRS8025680	SRA1183553	GEO	Anna Molofsky Lab, Psychiatry, UCSF	1	0.89472		0.26792		0.78837		0.55341		94		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-01-13	Larval	Larval	Multi-tissue	Multi-system
63226	63226	SRR13660516	SRX10052201	SRS8215327	SRP305389	PRJNA700672	Endothelial progenitor migration and differentiation is regulated by distinct transcriptional effectors of Cloche/Npas4l	GSE166396	Transcriptome Analysis	Embryonic cells including endothelial progenitors undergo extensive migration and differentiation events; however whether and how these processes are interrelated remains unclear. The transcription factor Npas4l is necessary for endothelial specification in zebrafish by inducing the expression of the transcription factor genes etsrp tal1 and lmo2. We generated a knock in reporter in the npas4l locus to visualize endothelial progenitors and their derivatives in wild type and mutant embryos. We find that in npas4l mutants npas4l reporter expressing cells do not migrate to the midline and instead contribute to skeletal muscle and pronephric tubules. Investigating the Npas4l transcriptional effectors we find that npas4l reporter expressing cells in tal1 mutants fail to migrate while those in etsrp mutants migrate but fail to differentiate. In lmo2 mutants npas4l reporter expressing cells migrate and differentiate but many express pronephric tubule markers. Altogether these data reveal the complex regulation of endothelial progenitor migration differentiation and fate restriction. Overall design: Comparison of npas4l reporter positive cells from heterozygous and homozygous npas4l mutant embryos using single cell RNAseq on sorted cells.			npas4l mut	GSM5070576	tissue:npas4l reporter positive cells\|cell type:sorted npas4l reporter positive cells\|Stage:20 hpf	npas4l mut	Reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed only 16 cells in total that did not express between 1000 and 7000 genes or had an mitochondrial content less than 6%. Further we filtered genes if they were detected in less than 30 cells <0.3%. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding and cell clustering via community detection were based on the initial PCA. Final data visualization was done by scVelo and cellxgene packages. Genome build: DanRer11 Supplementary files format and content: Mattonet adata obs.csv: basic anndata observations Sample n genes by counts log1p total counts pct counts is mito n genes detected leiden clustering Supplementary files format and content: Mattonet udata obs.csv: velocity anmdata observations initial size unspliced initial size spliced initial size n counts velocity self transition root cells end points velocity pseudotime	npas4l reporter positive cells		Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.		cell type:sorted npas4l reporter positive cells\|Stage:20 hpf	GSM5070576	GSM5070576: npas4l mut; Danio rerio; RNA Seq	GSM5070576		1	Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.	GEO Accession:GSM5070576	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP305389		Kenny_scRNA_Mut_BC.fastq.gz Kenny_scRNA_Mut_cDNA.fastq.gz	fastq fastq	15859812024.0	188807286.0	GSM5070576 r1	0:28 1:56	A:4422689365;C:3447909764;G:3545664942;T:4438912669;N:4635284	28	56			4422689365	3447909764	3545664942	4438912669	4635284	SRX10052201	SRS8215327	SRA1193720	GEO	MPI for heart and lung research	2	0.00208	0.92256	0.00079	0.14522	0.99602	0.81554	0.38888	0.49915	28	56	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2021-02-08	Segmentation	Embryo	Multi-tissue	Multi-system
63227	63227	SRR13660515	SRX10052200	SRS8215328	SRP305389	PRJNA700672	Endothelial progenitor migration and differentiation is regulated by distinct transcriptional effectors of Cloche/Npas4l	GSE166396	Transcriptome Analysis	Embryonic cells including endothelial progenitors undergo extensive migration and differentiation events; however whether and how these processes are interrelated remains unclear. The transcription factor Npas4l is necessary for endothelial specification in zebrafish by inducing the expression of the transcription factor genes etsrp tal1 and lmo2. We generated a knock in reporter in the npas4l locus to visualize endothelial progenitors and their derivatives in wild type and mutant embryos. We find that in npas4l mutants npas4l reporter expressing cells do not migrate to the midline and instead contribute to skeletal muscle and pronephric tubules. Investigating the Npas4l transcriptional effectors we find that npas4l reporter expressing cells in tal1 mutants fail to migrate while those in etsrp mutants migrate but fail to differentiate. In lmo2 mutants npas4l reporter expressing cells migrate and differentiate but many express pronephric tubule markers. Altogether these data reveal the complex regulation of endothelial progenitor migration differentiation and fate restriction. Overall design: Comparison of npas4l reporter positive cells from heterozygous and homozygous npas4l mutant embryos using single cell RNAseq on sorted cells.			npas4l het	GSM5070575	tissue:npas4l reporter positive cells\|cell type:sorted npas4l reporter positive cells\|Stage:20 hpf	npas4l het	Reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed only 16 cells in total that did not express between 1000 and 7000 genes or had an mitochondrial content less than 6%. Further we filtered genes if they were detected in less than 30 cells <0.3%. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding and cell clustering via community detection were based on the initial PCA. Final data visualization was done by scVelo and cellxgene packages. Genome build: DanRer11 Supplementary files format and content: Mattonet adata obs.csv: basic anndata observations Sample n genes by counts log1p total counts pct counts is mito n genes detected leiden clustering Supplementary files format and content: Mattonet udata obs.csv: velocity anmdata observations initial size unspliced initial size spliced initial size n counts velocity self transition root cells end points velocity pseudotime	npas4l reporter positive cells		Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.		cell type:sorted npas4l reporter positive cells\|Stage:20 hpf	GSM5070575	GSM5070575: npas4l het; Danio rerio; RNA Seq	GSM5070575		1	Tails from 150 npas4l heterozygous npas4lbns423/+ and trans heterozygous npas4lbns423/bns297 mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP fluorescence using an AriaIII sorter and DAPI as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Single cell RNAseq library preparation was done using standard protocol.	GEO Accession:GSM5070575	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP305389		Kenny_scRNA_Het_BC.fastq.gz Kenny_scRNA_Het_cDNA.fastq.gz	fastq fastq	21384880020.0	254581905.0	GSM5070575 r1	0:28 1:56	A:5828925615;C:4816199698;G:4885826464;T:5847660976;N:6267267	28	56			5828925615	4816199698	4885826464	5847660976	6267267	SRX10052200	SRS8215328	SRA1193720	GEO	MPI for heart and lung research	2	0.00213	0.9288	0.00071	0.11864	0.99559	0.8312	0.43162	0.47914	28	56	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2021-02-08	Segmentation	Embryo	Multi-tissue	Multi-system
63253	63253	SRR13693851	SRX10083149	SRS8241165	SRP305927	PRJNA701473	Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors	GSE166646	Transcriptome Analysis	Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.	parent bioproject:PRJNA701471	pubmed:35504924	Normal cells Control scRNA Seq	GSM5076939	source name:Zebrafish cells control\|tissue:normal cells\|sorted cells:mCherry sorted cells\|genotype:Control	Normal cells Control scRNA Seq	Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze	Zebrafish cells control	No treatment	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control.	tissue:normal cells\|sorted cells:mCherry sorted cells\|genotype:Control	GSM5076939	GSM5076939: Normal cells Control scRNA Seq; Danio rerio; RNA Seq	GSM5076939		1	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq	GEO Accession:GSM5076939	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP305927	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=PC8 I1.fastq.gz read2PairFiles=PC8 R1.fastq.gz read3PairFiles=PC8 R2.fastq.gz	PC8_I1.fastq.gz PC8_R1.fastq.gz PC8_R2.fastq.gz	fastq fastq fastq	27368502216.0	207337138.0	GSM5076939 r1	0:8 1:26 2:98	A:7549832339;C:6248269949;G:6287147333;T:7274505713;N:8746882	8	26	98		7549832339	6248269949	6287147333	7274505713	8746882	SRX10083149	SRS8241165	SRA1195246	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.89463		0.1714		0.81093		0.53939		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Singapore	2021-02-11	Undetermined	Undetermined	Multi-tissue	Multi-system
63865	63865	SRR14143478	SRX10512841	SRS8636598	SRP313475	PRJNA719789	scRNA seq of tailbud development in zebrafish	GSE171482	Other	We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.			Tailbud single cells at 16 hpf	GSM5226215	source name:Dissociated tailbuds from 30 hpf 16 hpf embryos\|transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	Tailbud single cells at 16 hpf	FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds	Dissociated tailbuds from 30 hpf 16 hpf embryos		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3		transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	GSM5226215	GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq	GSM5226215		1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3	GEO Accession:GSM5226215	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP313475	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S1 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S1 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S1 L003 R2 001.fastq.gz			31286394882.0	246349566.0	GSM5226215 r1	0:8 1:28 2:91	A:8483875403;C:6562544452;G:7703313223;T:8535328683;N:1333121	8	28	91		8483875403	6562544452	7703313223	8535328683	1333121	SRX10512841	SRS8636598	SRA1215249	GEO	Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine	1	0.94915		0.12419		0.79411		0.48155		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-05	Segmentation	Embryo	Tail	Multi-system
63866	63866	SRR14143479	SRX10512841	SRS8636598	SRP313475	PRJNA719789	scRNA seq of tailbud development in zebrafish	GSE171482	Other	We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.			Tailbud single cells at 16 hpf	GSM5226215	source name:Dissociated tailbuds from 30 hpf 16 hpf embryos\|transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	Tailbud single cells at 16 hpf	FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds	Dissociated tailbuds from 30 hpf 16 hpf embryos		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3		transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	GSM5226215	GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq	GSM5226215		1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3	GEO Accession:GSM5226215	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP313475	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S2 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S2 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S2 L003 R2 001.fastq.gz	WT_tailbud_S2_L003_I1_001.fastq.gz WT_tailbud_S2_L003_R1_001.fastq.gz WT_tailbud_S2_L003_R2_001.fastq.gz	fastq fastq fastq	34222167268.0	269465884.0	GSM5226215 r2	0:8 1:28 2:91	A:10380791879;C:7173180527;G:7598116520;T:9068620061;N:1458281	8	28	91		10380791879	7173180527	7598116520	9068620061	1458281	SRX10512841	SRS8636598	SRA1215249	GEO	Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine	1	0.94862		0.1236		0.79322		0.50153		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-05	Segmentation	Embryo	Tail	Multi-system
63867	63867	SRR14143480	SRX10512841	SRS8636598	SRP313475	PRJNA719789	scRNA seq of tailbud development in zebrafish	GSE171482	Other	We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.			Tailbud single cells at 16 hpf	GSM5226215	source name:Dissociated tailbuds from 30 hpf 16 hpf embryos\|transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	Tailbud single cells at 16 hpf	FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds	Dissociated tailbuds from 30 hpf 16 hpf embryos		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3		transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	GSM5226215	GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq	GSM5226215		1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3	GEO Accession:GSM5226215	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP313475	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S3 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S3 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S3 L003 R2 001.fastq.gz	WT_tailbud_S3_L003_I1_001.fastq.gz WT_tailbud_S3_L003_R1_001.fastq.gz WT_tailbud_S3_L003_R2_001.fastq.gz	fastq fastq fastq	33676411438.0	265168594.0	GSM5226215 r3	0:8 1:28 2:91	A:9145545141;C:7581198882;G:7228819079;T:9719412772;N:1435564	8	28	91		9145545141	7581198882	7228819079	9719412772	1435564	SRX10512841	SRS8636598	SRA1215249	GEO	Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine	1	0.94728		0.12372		0.79366		0.49386		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-05	Segmentation	Embryo	Tail	Multi-system
63868	63868	SRR14143481	SRX10512841	SRS8636598	SRP313475	PRJNA719789	scRNA seq of tailbud development in zebrafish	GSE171482	Other	We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.			Tailbud single cells at 16 hpf	GSM5226215	source name:Dissociated tailbuds from 30 hpf 16 hpf embryos\|transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	Tailbud single cells at 16 hpf	FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds	Dissociated tailbuds from 30 hpf 16 hpf embryos		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3		transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	GSM5226215	GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq	GSM5226215		1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3	GEO Accession:GSM5226215	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP313475	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S4 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S4 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S4 L003 R2 001.fastq.gz	WT_tailbud_S4_L003_I1_001.fastq.gz WT_tailbud_S4_L003_R1_001.fastq.gz WT_tailbud_S4_L003_R2_001.fastq.gz	fastq fastq fastq	30944524598.0	243657674.0	GSM5226215 r4	0:8 1:28 2:91	A:8382983101;C:6979019830;G:7383731031;T:8197465285;N:1325351	8	28	91		8382983101	6979019830	7383731031	8197465285	1325351	SRX10512841	SRS8636598	SRA1215249	GEO	Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine	1	0.94927		0.12443		0.79316		0.48307		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-05	Segmentation	Embryo	Tail	Multi-system
63887	63887	SRR14202114	SRX10569027	SRS8675160	SRP314271	PRJNA720970	Single cell transcriptional profiles of islet1 derived ECs and the other ECs in the tail of 48 hpf zebrafish embryos	GSE171822	Transcriptome Analysis	We report transcriptional heterogeneity of venous endothelial cells ECs in the tail of zebrafish embryos which consist of HSPC niche constituting ECs and caudal vessel CV constituting ECs. To characterize isl1 derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue CHT we performed single cell RNA sequencing scRNA seq of isl1 derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. Our analyses revealed that tail venous ECs were split into 5 distinct sub clusters where isl1 derived ECs and the other ECs were similarly distributed to all venous EC clusters and further revealed that genes whose expression levels are different between isl1 derived ECs and the other ECs tend to show similar changes across all of the clusters even post their diversification. Overall design: We isolated live TagRFP+/EGFP+ cells for isl1 derived ECs and TagRFP /EGFP+ cells for the other ECs separately by FACS sorting from the tails of TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf. Then barcoded single cell cDNA libraries were prepared using the Chromium Single Cell three prime Reagents Kits v3.1 and were then sequenced using Illumina NovaSeq6000.		pubmed:36693371	RNA seq the other ECs	GSM5235246	source name:resected tails posterior to the yolk end\|strain:AB\|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP\|developmental stage:48 hpf\|tissue:Tail\|cell type:other ECs TagRFP /EGFP+	RNA seq the other ECs	The 10x Genomics Cell Ranger pipeline version 5.0.0 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 and reporter sequences EGFP and RFP with the gene annotation file Danio rerio.GRCz11.99.chr.gtf.gz barcode/UMI processing and gene counting for each cell. Genome build: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI counts for each sample.	resected tails posterior to the yolk end		Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco’s modified Eagle’s medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.		strain:AB\|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP\|developmental stage:48 hpf\|tissue:Tail\|cell type:other ECs TagRFP /EGFP+	GSM5235246	GSM5235246: RNA seq the other ECs; Danio rerio; RNA Seq	GSM5235246		1	Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco's modified Eagle's medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.	GEO Accession:GSM5235246	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP314271	loader:fastq load.py\|options: platform=Illumina readTypes=TTTB read1PairFiles=ZebEmb GFP RFP I1.fastq.gz read2PairFiles=ZebEmb GFP RFP I2.fastq.gz read3PairFiles=ZebEmb GFP RFP R1.fastq.gz read4PairFiles=ZebEmb GFP RFP R2.fastq.gz	ZebEmb_GFP_RFP_I1.fastq.gz ZebEmb_GFP_RFP_I2.fastq.gz ZebEmb_GFP_RFP_R1.fastq.gz ZebEmb_GFP_RFP_R2.fastq.gz	fastq fastq fastq fastq	46144044078.0	334377131.0	GSM5235246 r1	0:10 1:10 2:28 3:90	A:12365801825;C:10786766050;G:11098071597;T:11890763395;N:2641211	10	10	28	90	12365801825	10786766050	11098071597	11890763395	2641211	SRX10569027	SRS8675160	SRA1217192	GEO	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.93604		0.14513		0.79038		0.50811		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2021-04-09	Hatching	Embryo	Tail	Multi-system
63888	63888	SRR14202113	SRX10569026	SRS8675161	SRP314271	PRJNA720970	Single cell transcriptional profiles of islet1 derived ECs and the other ECs in the tail of 48 hpf zebrafish embryos	GSE171822	Transcriptome Analysis	We report transcriptional heterogeneity of venous endothelial cells ECs in the tail of zebrafish embryos which consist of HSPC niche constituting ECs and caudal vessel CV constituting ECs. To characterize isl1 derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue CHT we performed single cell RNA sequencing scRNA seq of isl1 derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. Our analyses revealed that tail venous ECs were split into 5 distinct sub clusters where isl1 derived ECs and the other ECs were similarly distributed to all venous EC clusters and further revealed that genes whose expression levels are different between isl1 derived ECs and the other ECs tend to show similar changes across all of the clusters even post their diversification. Overall design: We isolated live TagRFP+/EGFP+ cells for isl1 derived ECs and TagRFP /EGFP+ cells for the other ECs separately by FACS sorting from the tails of TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf. Then barcoded single cell cDNA libraries were prepared using the Chromium Single Cell three prime Reagents Kits v3.1 and were then sequenced using Illumina NovaSeq6000.		pubmed:36693371	RNA seq isl1 derived ECs	GSM5235245	source name:resected tails posterior to the yolk end\|strain:AB\|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP\|developmental stage:48 hpf\|tissue:Tail\|cell type:isl1 derived ECs TagRFP+/EGFP+	RNA seq isl1 derived ECs	The 10x Genomics Cell Ranger pipeline version 5.0.0 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 and reporter sequences EGFP and RFP with the gene annotation file Danio rerio.GRCz11.99.chr.gtf.gz barcode/UMI processing and gene counting for each cell. Genome build: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI counts for each sample.	resected tails posterior to the yolk end		Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco’s modified Eagle’s medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.		strain:AB\|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP\|developmental stage:48 hpf\|tissue:Tail\|cell type:isl1 derived ECs TagRFP+/EGFP+	GSM5235245	GSM5235245: RNA seq isl1 derived ECs; Danio rerio; RNA Seq	GSM5235245		1	Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco's modified Eagle's medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.	GEO Accession:GSM5235245	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP314271	loader:fastq load.py\|options: platform=Illumina readTypes=TTTB read1PairFiles=ZebEmb GFP I1.fastq.gz read2PairFiles=ZebEmb GFP I2.fastq.gz read3PairFiles=ZebEmb GFP R1.fastq.gz read4PairFiles=ZebEmb GFP R2.fastq.gz	ZebEmb_GFP_I1.fastq.gz ZebEmb_GFP_I2.fastq.gz ZebEmb_GFP_R1.fastq.gz ZebEmb_GFP_R2.fastq.gz	fastq fastq fastq fastq	53036547366.0	384322807.0	GSM5235245 r1	0:10 1:10 2:28 3:90	A:14610188978;C:12169986421;G:12283689207;T:13969658178;N:3024582	10	10	28	90	14610188978	12169986421	12283689207	13969658178	3024582	SRX10569026	SRS8675161	SRA1217192	GEO	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.94469		0.10454		0.79133		0.51214		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2021-04-09	Hatching	Embryo	Tail	Multi-system
64263	64263	SRR14428602	SRX10779739	SRS8866172	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354	scRNA seq of notum 1 treatment embryo replicate 4	GSM5282506	tissue:tail\|treatment:notum 1	scRNA seq of notum 1 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:notum 1	GSM5282506	GSM5282506: scRNA seq of notum 1 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282506		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282506	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543		WNT_MG2_S40_L006_R1_001.fastq.gz WNT_MG2_S40_L006_R2_001.fastq.gz	fastq fastq	59309016800.0	296545084.0	GSM5282506 r1	0:100 1:100	A:13101652467;C:9053865386;G:9914199388;T:27226829088;N:12470471	100	100			13101652467	9053865386	9914199388	27226829088	12470471	SRX10779739	SRS8866172	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	2	0.00907	0.91374	0.00232	0.07221	0.99293	0.82822	0.5	0.50749	100	100	T	B	mate1 technical by mapping diff	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64264	64264	SRR14428601	SRX10779738	SRS8866171	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354	scRNA seq of notum 1 treatment embryo replicate 3	GSM5282505	tissue:tail\|treatment:notum 1	scRNA seq of notum 1 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:notum 1	GSM5282505	GSM5282505: scRNA seq of notum 1 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282505		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282505	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543		WNT_MG1_S39_L005_R1_001.fastq.gz WNT_MG1_S39_L005_R2_001.fastq.gz	fastq fastq	75003307800.0	375016539.0	GSM5282505 r1	0:100 1:100	A:17011122660;C:12505646501;G:12322737410;T:33144126985;N:19674244	100	100			17011122660	12505646501	12322737410	33144126985	19674244	SRX10779738	SRS8866171	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	2	0.0068	0.94221	0.00175	0.08258	0.99608	0.82473	0.49289	0.52202	100	100	T	B	mate1 technical by mapping diff	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64265	64265	SRR14428600	SRX10779737	SRS8866170	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354	scRNA seq of notum 1 treatment embryo replicate 2	GSM5282504	tissue:tail\|treatment:notum 1	scRNA seq of notum 1 treatment embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:notum 1	GSM5282504	GSM5282504: scRNA seq of notum 1 treatment embryo replicate 2; Danio rerio; RNA Seq	GSM5282504		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282504	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543		WNT_DJ2_S42_L008_R1_001.fastq.gz WNT_DJ2_S42_L008_R2_001.fastq.gz	fastq fastq	73921649200.0	369608246.0	GSM5282504 r1	0:100 1:100	A:16691509262;C:12147679273;G:12179457462;T:32881202116;N:21801087	100	100			16691509262	12147679273	12179457462	32881202116	21801087	SRX10779737	SRS8866170	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	2	0.00683	0.92595	0.00109	0.08047	0.99531	0.82558	0.5017	0.48675	100	100	T	B	mate1 technical by mapping diff	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64266	64266	SRR14428599	SRX10779736	SRS8866169	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354	scRNA seq of notum 1 treatment embryo replicate 1	GSM5282503	tissue:tail\|treatment:notum 1	scRNA seq of notum 1 treatment embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:notum 1	GSM5282503	GSM5282503: scRNA seq of notum 1 treatment embryo replicate 1; Danio rerio; RNA Seq	GSM5282503		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282503	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543		WNT_DJ1_S41_L007_R1_001.fastq.gz WNT_DJ1_S41_L007_R2_001.fastq.gz	fastq fastq	72873756000.0	364368780.0	GSM5282503 r1	0:100 1:100	A:16621508845;C:12254073814;G:11510875104;T:32473791832;N:13506405	100	100			16621508845	12254073814	11510875104	32473791832	13506405	SRX10779736	SRS8866169	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	2	0.00358	0.94302	0.0008	0.08218	0.99803	0.82181	0.50485	0.51251	100	100	T	B	mate1 technical by mapping diff	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64267	64267	SRR14428593	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L001 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L001 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L001 R2 001.fastq.gz	SU4_DRT_S2_L001_I1_001.fastq.gz SU4_DRT_S2_L001_R1_001.fastq.gz SU4_DRT_S2_L001_R2_001.fastq.gz	fastq fastq fastq	6902983527.0	54354201.0	GSM5282502 r1	0:8 1:28 2:91	A:1904129671;C:1528133826;G:1597676497;T:1870308784;N:2734749	8	28	91		1904129671	1528133826	1597676497	1870308784	2734749	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93834		0.14712		0.80097		0.53464		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64268	64268	SRR14428594	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L002 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L002 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L002 R2 001.fastq.gz	SU4_DRT_S2_L002_I1_001.fastq.gz SU4_DRT_S2_L002_R1_001.fastq.gz SU4_DRT_S2_L002_R2_001.fastq.gz	fastq fastq fastq	7355984272.0	57921136.0	GSM5282502 r2	0:8 1:28 2:91	A:2029150464;C:1629831151;G:1703134376;T:1991639472;N:2228809	8	28	91		2029150464	1629831151	1703134376	1991639472	2228809	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93751		0.14654		0.80048		0.53568		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64269	64269	SRR14428595	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L003 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L003 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L003 R2 001.fastq.gz	SU4_DRT_S2_L003_I1_001.fastq.gz SU4_DRT_S2_L003_R1_001.fastq.gz SU4_DRT_S2_L003_R2_001.fastq.gz	fastq fastq fastq	6915051321.0	54449223.0	GSM5282502 r3	0:8 1:28 2:91	A:1907859125;C:1531399983;G:1600723047;T:1872767703;N:2301463	8	28	91		1907859125	1531399983	1600723047	1872767703	2301463	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93859		0.14759		0.80075		0.53726		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64270	64270	SRR14428596	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L004 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L004 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L004 R2 001.fastq.gz	SU4_DRT_S2_L004_I1_001.fastq.gz SU4_DRT_S2_L004_R1_001.fastq.gz SU4_DRT_S2_L004_R2_001.fastq.gz	fastq fastq fastq	6496116929.0	51150527.0	GSM5282502 r4	0:8 1:28 2:91	A:1791207713;C:1438082538;G:1503927125;T:1760463486;N:2436067	8	28	91		1791207713	1438082538	1503927125	1760463486	2436067	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93855		0.14517		0.80142		0.51836		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64271	64271	SRR14428597	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L005 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L005 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L005 R2 001.fastq.gz	SU4_DRT_S2_L005_I1_001.fastq.gz SU4_DRT_S2_L005_R1_001.fastq.gz SU4_DRT_S2_L005_R2_001.fastq.gz	fastq fastq fastq	6925225545.0	54529335.0	GSM5282502 r5	0:8 1:28 2:91	A:1908749610;C:1534337999;G:1604298047;T:1874791459;N:3048430	8	28	91		1908749610	1534337999	1604298047	1874791459	3048430	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93705		0.14527		0.79811		0.49961		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64272	64272	SRR14428598	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L006 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L006 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L006 R2 001.fastq.gz	SU4_DRT_S2_L006_I1_001.fastq.gz SU4_DRT_S2_L006_R1_001.fastq.gz SU4_DRT_S2_L006_R2_001.fastq.gz	fastq fastq fastq	5772764553.0	45454839.0	GSM5282502 r6	0:8 1:28 2:91	A:1592079310;C:1277414314;G:1335013911;T:1565676607;N:2580411	8	28	91		1592079310	1277414314	1335013911	1565676607	2580411	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93895		0.1477		0.79772		0.52786		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64273	64273	SRR14428587	SRX10779734	SRS8866167	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.		pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 3	GSM5282501	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282501	GSM5282501: scRNA seq of SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282501		1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282501	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU3 DRT S1 L001 I1 001.fastq.gz read2PairFiles=SU3 DRT S1 L001 R1 001.fastq.gz read3PairFiles=SU3 DRT S1 L001 R2 001.fastq.gz	SU3_DRT_S1_L001_I1_001.fastq.gz SU3_DRT_S1_L001_R1_001.fastq.gz SU3_DRT_S1_L001_R2_001.fastq.gz	fastq fastq fastq	8251078748.0	64969124.0	GSM5282501 r1	0:8 1:28 2:91	A:2304710369;C:1797342936;G:1900704244;T:2245059790;N:3261409	8	28	91		2304710369	1797342936	1900704244	2245059790	3261409	SRX10779734	SRS8866167	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92754		0.16532		0.81462		0.52604		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-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");;