metadata: run_metadata: 8 rows where technology = "10x" and tissue_curation

8 rows where technology = "10x" and tissue_curation_coarse = "Muscular System"

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.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.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
66846	66846	SRR16681977	SRX12882565	SRS10825217	SRP344071	PRJNA776888	Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts	GSE186957	Transcriptome Analysis	Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation w…	pubmed:39741296	runx2b / scRNA seq	GSM5664293	source name:muscle and IB\|strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:runx2b /	runx2b / scRNA seq	Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample	muscle and IB	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:runx2b /	GSM5664293	GSM5664293: runx2b / scRNA seq; Danio rerio; RNA Seq	GSM5664293	1	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	GEO Accession:GSM5664293	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP344071	loader:fastq load.py	MU_S2_L003_R2_001.fastq MU_S2_L003_R1_001.fastq	fastq fastq	112565768100.0	375219227.0	GSM5664293 r1	0:150 1:150	A:34329910863;C:17430450121;G:18090145246;T:42713500460;N:1761410	150	150	34329910863	17430450121	18090145246	42713500460	1761410	SRX12882565	SRS10825217	SRA1320685	GEO	huazhong agricultural university	2	0.34718	0.92478	0.05085	0.09377	0.98545	0.82375	0.7209	0.73759	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	small_rna	trueseq	sc	single_cell_droplet	10x	China	2021-11-01	Juvenile	Juvenile	Muscle	Muscular System
66847	66847	SRR16681976	SRX12882564	SRS10825216	SRP344071	PRJNA776888	Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts	GSE186957	Transcriptome Analysis	Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation w…	pubmed:39741296	runx2b+/+ scRNA seq	GSM5664292	source name:muscle and IB\|strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:wild type	runx2b+/+ scRNA seq	Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample	muscle and IB	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:wild type	GSM5664292	GSM5664292: runx2b+/+ scRNA seq; Danio rerio; RNA Seq	GSM5664292	1	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	GEO Accession:GSM5664292	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP344071	loader:fastq load.py\|options: doNotUseSharq	WT_S1_L003_R1_001.fastq WT_S1_L003_R2_001.fastq	fastq fastq	99838157100.0	332793857.0	GSM5664292 r1	0:150 1:150	A:30283010374;C:15529232903;G:16181518775;T:37842782328;N:1612720	150	150	30283010374	15529232903	16181518775	37842782328	1612720	SRX12882564	SRS10825216	SRA1320685	GEO	huazhong agricultural university	2	0.34316	0.92608	0.04623	0.09467	0.98701	0.83644	0.72084	0.76059	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	small_rna	trueseq	sc	single_cell_droplet	10x	China	2021-11-01	Juvenile	Juvenile	Muscle	Muscular System
66848	66848	SRR16681984	SRX12882563	SRS10825218	SRP344071	PRJNA776888	Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts	GSE186957	Transcriptome Analysis	Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation w…	pubmed:39741296	runx2b / bulk RNA seq rep3	GSM5664299	source name:muscle and IB\|strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:runx2b /	runx2b / bulk RNA seq rep3	Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample	muscle and IB	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:runx2b /	GSM5664299	GSM5664299: runx2b / bulk RNA seq rep3; Danio rerio; RNA Seq	GSM5664299	1	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	GEO Accession:GSM5664299	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP344071	loader:fastq load.py	MUT_3_60dpf.R1.fq MUT_3_60dpf.R2.fq	fastq fastq	7358370600.0	24527902.0	GSM5664299 r1	0:150 1:150	A:1781646726;C:1790446433;G:2025455441;T:1760804227;N:17773	150	150	1781646726	1790446433	2025455441	1760804227	17773	SRX12882563	SRS10825218	SRA1320685	GEO	huazhong agricultural university	2	0.92553	0.92182	0.01196	0.01201	0.86239	0.86348	0.70266	0.63893	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	trueseq	sc	single_cell_droplet	10x	China	2021-11-01	Juvenile	Juvenile	Muscle	Muscular System
66849	66849	SRR16681983	SRX12882562	SRS10825219	SRP344071	PRJNA776888	Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts	GSE186957	Transcriptome Analysis	Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation w…	pubmed:39741296	runx2b / bulk RNA seq rep2	GSM5664298	source name:muscle and IB\|strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:runx2b /	runx2b / bulk RNA seq rep2	Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample	muscle and IB	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:runx2b /	GSM5664298	GSM5664298: runx2b / bulk RNA seq rep2; Danio rerio; RNA Seq	GSM5664298	1	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	GEO Accession:GSM5664298	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP344071	loader:fastq load.py	MUT_2_60dpf.R2.fq MUT_2_60dpf.R1.fq	fastq fastq	5983046100.0	19943487.0	GSM5664298 r1	0:150 1:150	A:1456794159;C:1460953692;G:1613536834;T:1451747111;N:14304	150	150	1456794159	1460953692	1613536834	1451747111	14304	SRX12882562	SRS10825219	SRA1320685	GEO	huazhong agricultural university	2	0.9349	0.92939	0.01147	0.01123	0.85488	0.85687	0.69455	0.61732	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	trueseq	sc	single_cell_droplet	10x	China	2021-11-01	Juvenile	Juvenile	Muscle	Muscular System
66850	66850	SRR16681982	SRX12882561	SRS10825215	SRP344071	PRJNA776888	Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts	GSE186957	Transcriptome Analysis	Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation w…	pubmed:39741296	runx2b / bulk RNA seq rep1	GSM5664297	source name:muscle and IB\|strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:runx2b /	runx2b / bulk RNA seq rep1	Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample	muscle and IB	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:runx2b /	GSM5664297	GSM5664297: runx2b / bulk RNA seq rep1; Danio rerio; RNA Seq	GSM5664297	1	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	GEO Accession:GSM5664297	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP344071	loader:fastq load.py	MUT_1_60dpf.R1.fq MUT_1_60dpf.R2.fq	fastq fastq	6876053100.0	22920177.0	GSM5664297 r1	0:150 1:150	A:1683687632;C:1665466650;G:1862910858;T:1663971371;N:16589	150	150	1683687632	1665466650	1862910858	1663971371	16589	SRX12882561	SRS10825215	SRA1320685	GEO	huazhong agricultural university	2	0.9327	0.92802	0.01178	0.0113	0.84861	0.84987	0.62221	0.67729	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	trueseq	sc	single_cell_droplet	10x	China	2021-11-01	Juvenile	Juvenile	Muscle	Muscular System
66851	66851	SRR16681981	SRX12882560	SRS10825214	SRP344071	PRJNA776888	Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts	GSE186957	Transcriptome Analysis	Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation w…	pubmed:39741296	runx2b+/+ bulk RNA seq rep3	GSM5664296	source name:muscle and IB\|strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:wild type	runx2b+/+ bulk RNA seq rep3	Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample	muscle and IB	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:wild type	GSM5664296	GSM5664296: runx2b+/+ bulk RNA seq rep3; Danio rerio; RNA Seq	GSM5664296	1	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	GEO Accession:GSM5664296	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP344071	loader:fastq load.py	WT_3_60dpf.R1.fq WT_3_60dpf.R2.fq	fastq fastq	6834033900.0	22780113.0	GSM5664296 r1	0:150 1:150	A:1665713519;C:1660512523;G:1864685424;T:1643106338;N:16096	150	150	1665713519	1660512523	1864685424	1643106338	16096	SRX12882560	SRS10825214	SRA1320685	GEO	huazhong agricultural university	2	0.92969	0.92347	0.01017	0.01012	0.85807	0.86001	0.63698	0.67717	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	trueseq	sc	single_cell_droplet	10x	China	2021-11-01	Juvenile	Juvenile	Muscle	Muscular System
66852	66852	SRR16681980	SRX12882559	SRS10825212	SRP344071	PRJNA776888	Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts	GSE186957	Transcriptome Analysis	Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation w…	pubmed:39741296	runx2b+/+ bulk RNA seq rep2	GSM5664295	source name:muscle and IB\|strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:wild type	runx2b+/+ bulk RNA seq rep2	Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample	muscle and IB	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:wild type	GSM5664295	GSM5664295: runx2b+/+ bulk RNA seq rep2; Danio rerio; RNA Seq	GSM5664295	1	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	GEO Accession:GSM5664295	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP344071	loader:fastq load.py	WT_2_60dpf.R1.fq WT_2_60dpf.R2.fq	fastq fastq	7007750400.0	23359168.0	GSM5664295 r1	0:150 1:150	A:1714498514;C:1702913716;G:1897215939;T:1693105532;N:16699	150	150	1714498514	1702913716	1897215939	1693105532	16699	SRX12882559	SRS10825212	SRA1320685	GEO	huazhong agricultural university	2	0.93182	0.92608	0.01221	0.01171	0.8478	0.85023	0.67158	0.65917	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	trueseq	sc	single_cell_droplet	10x	China	2021-11-01	Juvenile	Juvenile	Muscle	Muscular System
66853	66853	SRR16681979	SRX12882558	SRS10825213	SRP344071	PRJNA776888	Single cell transcriptomes and runx2b / mutants reveal the genetic signatures of intermuscular bone formation in teleosts	GSE186957	Transcriptome Analysis	Purpose: Intermuscular bones IBs are hard spicules mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using the 10X Genomics Chromium system. The bulk RNA seq profiles of 60 dpf wild type zebrafish and 60 dpf runx2b / zebrafish were generated using mirVana™ miRNA ISOlation Kit. The scRNA seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRT–PCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin HE Alizarin red masson trichrome staining and mico CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large scale gene function analysis using CRISPR Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation w…	pubmed:39741296	runx2b+/+ bulk RNA seq rep1	GSM5664294	source name:muscle and IB\|strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:wild type	runx2b+/+ bulk RNA seq rep1	Illumina PE150 machine and Illumina HiSeq 2000 used for basecalling. Using Cell Ranger to identify and count the barcode sequence for scRNA seq 6 transcriptome sequencing libraries were generated using TruSeq Stranded mRNA LTSample Prep Kit Illumina USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Genome build: GRCz11 Supplementary files format and content: [scRNA seq samples] Cell Ranger ouput files barcodes.tsv features.tsv matrix.mtx Supplementary files format and content: [bulkRNA seq samples] Matrix table with raw gene counts for every gene and every sample	muscle and IB	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	strain:Tg sp7/eGFP transgenic line\|tissue:muscle and IB\|age:60 dpf\|genotype:wild type	GSM5664294	GSM5664294: runx2b+/+ bulk RNA seq rep1; Danio rerio; RNA Seq	GSM5664294	1	tail muscles with IBs were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit Illumina USA was used with 1 ug of total RNA for the construction of sequencing libraries. The single cell suspensions of tail muscles with IBs were prepared by Personalbio company and the 10X Genomics Chromium system was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols and 10X Genomics Chromium system.	GEO Accession:GSM5664294	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP344071	loader:fastq load.py	WT_1_60dpf.R1.fq WT_1_60dpf.R2.fq	fastq fastq	6785203800.0	22617346.0	GSM5664294 r1	0:150 1:150	A:1660992152;C:1637869425;G:1843210897;T:1643114944;N:16382	150	150	1660992152	1637869425	1843210897	1643114944	16382	SRX12882558	SRS10825213	SRA1320685	GEO	huazhong agricultural university	2	0.92763	0.92196	0.00968	0.00949	0.84295	0.84593	0.65456	0.65914	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	trueseq	sc	single_cell_droplet	10x	China	2021-11-01	Juvenile	Juvenile	Muscle	Muscular 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");;