metadata: run_metadata: 3 rows where experiment.library_layout = "SINGLE", technology = "scirnaseq" and tissue

3 rows where experiment.library_layout = "SINGLE", technology = "scirnaseq" and tissue_curation = "Fin"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
67811	67811	SRR17312072	SRX13488771	SRS11384713	SRP352163	PRJNA791663	Single cell resolution of MET and EMT like programs in osteoblasts during zebrafish fin regeneration	GSE192498	Transcriptome Analysis	We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump and in differentiating osteoblastic cells in the regenerate the latter of which are enriched in EMT signatures. We also show that esrp1 a regulator of alternative splicing in epithelial cells that is associated with MET is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration and supports the contribution of MET and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3	pubmed:35169687	5 dpa	GSM5747967	source name:adult caudal fin\|strain:AB\|tissue:caudal fin\|timepoint:5 dy post amputation\|molecule subtype:nuclear RNA	5 dpa	Base calls were converted to fastq format using Illumina's bcl2fastq v2.20 tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information while the R2 reads contain the transcriptome sequence. In the demultiplexing process the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted and duplicates were removed using the UMI sequence reverse transcription RT index and read 2 end coordinate tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes gene annotations and a gene count sparse matrix for each Sample	adult caudal fin	Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.	strain:AB\|tissue:caudal fin\|timepoint:5 dy post amputation\|molecule subtype:nuclear RNA	GSM5747967	GSM5747967: 5 dpa; Danio rerio; RNA Seq	GSM5747967 r1	GSM5747967	1	Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP352163	loader:fastq load.py\|options: appendBCtoName	RK6.fq.gz	fastq	10033219500.0	100332195.0	GSM5747967 r1	0:100	A:3474987443;C:1873037986;G:1979251566;T:2705812216;N:130289	100	3474987443	1873037986	1979251566	2705812216	130289	SRX13488771	SRS11384713	SRA1347953	Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington	Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington	1	0.71399	0.43822	0.84161	0.72626	100	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_plate	scirnaseq	United States	2021-12-22	Adult	Adult	Fin	Surface Structure
67812	67812	SRR17312073	SRX13488770	SRS11384711	SRP352163	PRJNA791663	Single cell resolution of MET and EMT like programs in osteoblasts during zebrafish fin regeneration	GSE192498	Transcriptome Analysis	We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump and in differentiating osteoblastic cells in the regenerate the latter of which are enriched in EMT signatures. We also show that esrp1 a regulator of alternative splicing in epithelial cells that is associated with MET is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration and supports the contribution of MET and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3	pubmed:35169687	3 dpa	GSM5747966	source name:adult caudal fin\|strain:AB\|tissue:caudal fin\|timepoint:3 dy post amputation\|molecule subtype:nuclear RNA	3 dpa	Base calls were converted to fastq format using Illumina's bcl2fastq v2.20 tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information while the R2 reads contain the transcriptome sequence. In the demultiplexing process the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted and duplicates were removed using the UMI sequence reverse transcription RT index and read 2 end coordinate tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes gene annotations and a gene count sparse matrix for each Sample	adult caudal fin	Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.	strain:AB\|tissue:caudal fin\|timepoint:3 dy post amputation\|molecule subtype:nuclear RNA	GSM5747966	GSM5747966: 3 dpa; Danio rerio; RNA Seq	GSM5747966 r1	GSM5747966	1	Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP352163	loader:fastq load.py\|options: appendBCtoName	RK5.fq.gz	fastq	7765549400.0	77655494.0	GSM5747966 r1	0:100	A:2667279419;C:1502480624;G:1625734956;T:1969954499;N:99902	100	2667279419	1502480624	1625734956	1969954499	99902	SRX13488770	SRS11384711	SRA1347953	Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington	Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington	1	0.65628	0.27575	0.84918	0.73771	100	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_plate	scirnaseq	United States	2021-12-22	Adult	Adult	Fin	Surface Structure
67813	67813	SRR17312074	SRX13488769	SRS11384712	SRP352163	PRJNA791663	Single cell resolution of MET and EMT like programs in osteoblasts during zebrafish fin regeneration	GSE192498	Transcriptome Analysis	We performed single cell RNA sequencing scRNA seq to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial to mesenchymal transition EMT and its reverse mesenchymal to epithelial transition MET. Trajectory analyses indicate osteoblastic cells solely expressed EMT components or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co expressed in dedifferentiating cells at the amputation stump and in differentiating osteoblastic cells in the regenerate the latter of which are enriched in EMT signatures. We also show that esrp1 a regulator of alternative splicing in epithelial cells that is associated with MET is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration and supports the contribution of MET and EMT associated components to this process. Overall design: Single cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci RNA seq3	pubmed:35169687	3 dpa pilot	GSM5747965	source name:adult caudal fin\|strain:AB\|tissue:caudal fin\|timepoint:3 dy post amputation\|molecule subtype:nuclear RNA	3 dpa pilot	Base calls were converted to fastq format using Illumina's bcl2fastq v2.20 tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.: https://github.com/bbi lab/bbi dmux Demultiplexed reads were then adaptor clipped using trim galore with default settings cutadapt/1.18:trim galore/0.6.5. Reads were originally paired end. R1 contained cell barcodes and sample information while the R2 reads contain the transcriptome sequence. In the demultiplexing process the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted. Trimmed reads were mapped to the three primeUTR extended reference STAR index generated above with default settings STAR v.2.5.2b. Uniquely mapping reads were extracted and duplicates were removed using the UMI sequence reverse transcription RT index and read 2 end coordinate tolerating 1bp mismatches in UMIs samtools v1.9. To generate expression matrices the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format. Genome build: GRCz11.96 Supplementary files format and content: tab delimited text files containing cell barcodes gene annotations and a gene count sparse matrix for each Sample	adult caudal fin	Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.	strain:AB\|tissue:caudal fin\|timepoint:3 dy post amputation\|molecule subtype:nuclear RNA	GSM5747965	GSM5747965: 3 dpa pilot; Danio rerio; RNA Seq	GSM5747965 r1	GSM5747965	1	Fin tissues were collected and immediately frozen at 80C. Nuclei were extracted fixed in 4% paraformaldehyde and prepared for sci RNA seq3 please see details at http://atlas.gs.washington.edu/mouse rna. The library preparation scheme for sci RNA seq3 on paraformaldehyde fixed nuclei was followed with the following modifications: 2 uL of oligo dT primers were added to each well with 80 000 nuclei for reverse transcription the Quick Ligation kit New England Biolabs was used in place of T4 ligase and tagmentation was performed using 1/40th uL per well of i7 loaded TDE1 enzyme prepared at the University of Washington following published protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP352163	loader:fastq load.py\|options: appendBCtoName	RK.1.fq.gz	fastq	4869714300.0	48697143.0	GSM5747965 r1	0:100	A:1531034092;C:971890195;G:1007416432;T:1359257595;N:115986	100	1531034092	971890195	1007416432	1359257595	115986	SRX13488769	SRS11384712	SRA1347953	Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington	Kwon Lab, Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine, University of Washington	1	0.60845	0.32412	0.84916	0.72554	100	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_plate	scirnaseq	United States	2021-12-22	Adult	Adult	Fin	Surface Structure

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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");;