metadata: run_metadata: 4 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "celseq" and tissue

4 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "celseq" and tissue_curation = "Liver"

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.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
70094	70094	SRR19520282	SRX15572798	SRS13275626	SRP378140	PRJNA844556	Loss of pex5 sensitizes zebrafish to fasting due to deregulated mitochondria mTOR and autophagy	GSE205349	Transcriptome Analysis	Animal models have been utilized to understand the pathogenesis of Zellweger spectrum disorders ZSD but the link between the clinical manifestations and molecular pathways has not yet been clearly established. We generated a peroxin 5 homozygous mutant zebrafish pex5 / to gain insight into the molecular pathogenesis of peroxisome dysfunction. pex5 / displays hallmarks of ZSD in humans and die within one month post birth. Fasting rapidly depletes the liver lipids and glycogen in pex5 / and expedites their mortality. Mechanistically abnormal mitochondrial activity and mechanistic target of rapamycin mTOR signaling act together to induce metabolic alterations to deplete the hepatic nutrients and accumulate the damaged mitochondria. Accordingly the use of chemical interventions blocking either the mitochondrial activities or the mechanistic target of rapamycin complex 1 or a combination of both improves the metabolic imbalance shown in the fasted pex5 / livers and extends the survival of the animals. Furthermore the use of an autophagy activator also effectively ameliorated the early mortality of the fasted pex5 / . These results suggest that fasting may be detrimental to patients with peroxisome dysfunction and that modulating the mitochondria mTOR or autophagy activities may provide a therapeutic option to alleviate the symptoms of peroxisomal diseases associated with metabolic dysfunction. Overall design: Total RNAs of whole liver tissues from fasted WT and pex5 homozygous mutant zebrafish at 6 dpf were used to identify differential gene expression between the two genotype under fasting condition	pubmed:36821008	pex5KO 6dpf 2 [N047 06]	GSM6210777	source name:liver\|tissue:liver\|genotype:pex5 KO\|treatment:fasted	pex5KO 6dpf 2 [N047 06]	Quantitative analysis was performed using 51bp of insert reads Read2. Cell barcode and UMI in Read1 was extracted by using UMI tools ver.1.1.1. Four cell barcodes were mixed and used for all samples. Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore ver.0.6.7. Reads were mapped to the GRCz11 reference using HISAT2 ver.2.2.1. Read counts for each gene were obtained by featureCounts ver.2.0.1. UMI duplication was removed by UMI tools. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TMM values for each Sample	liver	Total RNA was extracted by using Direct zol RNA Kit ZYMO RESEARCH according to the manufacture’s instruction. 3’UTR RNA seq was performed using the CEL Seq2 protocol except that Second Strand Synthesis Module NEB was used for double stranded cDNA synthesis and library was amplified by 9 cycles of PCR without xxx sample pooling.	tissue:liver\|genotype:pex5 KO\|treatment:fasted	GSM6210777	GSM6210777: pex5KO 6dpf 2 [N047 06]; Danio rerio; RNA Seq	GSM6210777 r1	GSM6210777	1	Total RNA was extracted by using Direct zol RNA Kit ZYMO RESEARCH according to the manufacture's instruction. three primeUTR RNA seq was performed using the CEL Seq2 protocol except that Second Strand Synthesis Module NEB was used for double stranded cDNA synthesis and library was amplified by 9 cycles of PCR without xxx sample pooling.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiniSeq	SRP378140	N047-06_S6_L001_R1_001.fastq.gz N047-06_S6_L001_R2_001.fastq.gz	fastq fastq	174282570.0	2489751.0	GSM6210777 r1	0:19 1:51	A:44582662;C:35509006;G:39346826;T:54785033;N:59043	19	51	44582662	35509006	39346826	54785033	59043	SRX15572798	SRS13275626	SRA1430748	Sungkyunkwan University	Sungkyunkwan University	2	0.01246	0.9141	0.01046	0.0952	0.99391	0.84159	0.53989	0.66354	19	51	T	B	sc-like readlen	illumina	miseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	South Korea	2022-06-02	Larval	Larval	Liver	Liver and Biliary System
70095	70095	SRR19520283	SRX15572797	SRS13275623	SRP378140	PRJNA844556	Loss of pex5 sensitizes zebrafish to fasting due to deregulated mitochondria mTOR and autophagy	GSE205349	Transcriptome Analysis	Animal models have been utilized to understand the pathogenesis of Zellweger spectrum disorders ZSD but the link between the clinical manifestations and molecular pathways has not yet been clearly established. We generated a peroxin 5 homozygous mutant zebrafish pex5 / to gain insight into the molecular pathogenesis of peroxisome dysfunction. pex5 / displays hallmarks of ZSD in humans and die within one month post birth. Fasting rapidly depletes the liver lipids and glycogen in pex5 / and expedites their mortality. Mechanistically abnormal mitochondrial activity and mechanistic target of rapamycin mTOR signaling act together to induce metabolic alterations to deplete the hepatic nutrients and accumulate the damaged mitochondria. Accordingly the use of chemical interventions blocking either the mitochondrial activities or the mechanistic target of rapamycin complex 1 or a combination of both improves the metabolic imbalance shown in the fasted pex5 / livers and extends the survival of the animals. Furthermore the use of an autophagy activator also effectively ameliorated the early mortality of the fasted pex5 / . These results suggest that fasting may be detrimental to patients with peroxisome dysfunction and that modulating the mitochondria mTOR or autophagy activities may provide a therapeutic option to alleviate the symptoms of peroxisomal diseases associated with metabolic dysfunction. Overall design: Total RNAs of whole liver tissues from fasted WT and pex5 homozygous mutant zebrafish at 6 dpf were used to identify differential gene expression between the two genotype under fasting condition	pubmed:36821008	pex5KO 6dpf 1 [N047 05]	GSM6210776	source name:liver\|tissue:liver\|genotype:pex5 KO\|treatment:fasted	pex5KO 6dpf 1 [N047 05]	Quantitative analysis was performed using 51bp of insert reads Read2. Cell barcode and UMI in Read1 was extracted by using UMI tools ver.1.1.1. Four cell barcodes were mixed and used for all samples. Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore ver.0.6.7. Reads were mapped to the GRCz11 reference using HISAT2 ver.2.2.1. Read counts for each gene were obtained by featureCounts ver.2.0.1. UMI duplication was removed by UMI tools. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TMM values for each Sample	liver	Total RNA was extracted by using Direct zol RNA Kit ZYMO RESEARCH according to the manufacture’s instruction. 3’UTR RNA seq was performed using the CEL Seq2 protocol except that Second Strand Synthesis Module NEB was used for double stranded cDNA synthesis and library was amplified by 9 cycles of PCR without xxx sample pooling.	tissue:liver\|genotype:pex5 KO\|treatment:fasted	GSM6210776	GSM6210776: pex5KO 6dpf 1 [N047 05]; Danio rerio; RNA Seq	GSM6210776 r1	GSM6210776	1	Total RNA was extracted by using Direct zol RNA Kit ZYMO RESEARCH according to the manufacture's instruction. three primeUTR RNA seq was performed using the CEL Seq2 protocol except that Second Strand Synthesis Module NEB was used for double stranded cDNA synthesis and library was amplified by 9 cycles of PCR without xxx sample pooling.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiniSeq	SRP378140	N047-05_S5_L001_R1_001.fastq.gz N047-05_S5_L001_R2_001.fastq.gz	fastq fastq	172133920.0	2459056.0	GSM6210776 r1	0:19 1:51	A:45030545;C:35152439;G:38626479;T:53266372;N:58085	19	51	45030545	35152439	38626479	53266372	58085	SRX15572797	SRS13275623	SRA1430748	Sungkyunkwan University	Sungkyunkwan University	2	0.01077	0.9045	0.00913	0.08354	0.99498	0.85535	0.55921	0.67705	19	51	T	B	sc-like readlen	illumina	miseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	South Korea	2022-06-02	Larval	Larval	Liver	Liver and Biliary System
70096	70096	SRR19520284	SRX15572796	SRS13275624	SRP378140	PRJNA844556	Loss of pex5 sensitizes zebrafish to fasting due to deregulated mitochondria mTOR and autophagy	GSE205349	Transcriptome Analysis	Animal models have been utilized to understand the pathogenesis of Zellweger spectrum disorders ZSD but the link between the clinical manifestations and molecular pathways has not yet been clearly established. We generated a peroxin 5 homozygous mutant zebrafish pex5 / to gain insight into the molecular pathogenesis of peroxisome dysfunction. pex5 / displays hallmarks of ZSD in humans and die within one month post birth. Fasting rapidly depletes the liver lipids and glycogen in pex5 / and expedites their mortality. Mechanistically abnormal mitochondrial activity and mechanistic target of rapamycin mTOR signaling act together to induce metabolic alterations to deplete the hepatic nutrients and accumulate the damaged mitochondria. Accordingly the use of chemical interventions blocking either the mitochondrial activities or the mechanistic target of rapamycin complex 1 or a combination of both improves the metabolic imbalance shown in the fasted pex5 / livers and extends the survival of the animals. Furthermore the use of an autophagy activator also effectively ameliorated the early mortality of the fasted pex5 / . These results suggest that fasting may be detrimental to patients with peroxisome dysfunction and that modulating the mitochondria mTOR or autophagy activities may provide a therapeutic option to alleviate the symptoms of peroxisomal diseases associated with metabolic dysfunction. Overall design: Total RNAs of whole liver tissues from fasted WT and pex5 homozygous mutant zebrafish at 6 dpf were used to identify differential gene expression between the two genotype under fasting condition	pubmed:36821008	WT 6dpf 4 [N047 04]	GSM6210775	source name:liver\|tissue:liver\|genotype:Wild type\|treatment:fasted	WT 6dpf 4 [N047 04]	Quantitative analysis was performed using 51bp of insert reads Read2. Cell barcode and UMI in Read1 was extracted by using UMI tools ver.1.1.1. Four cell barcodes were mixed and used for all samples. Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore ver.0.6.7. Reads were mapped to the GRCz11 reference using HISAT2 ver.2.2.1. Read counts for each gene were obtained by featureCounts ver.2.0.1. UMI duplication was removed by UMI tools. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TMM values for each Sample	liver	Total RNA was extracted by using Direct zol RNA Kit ZYMO RESEARCH according to the manufacture’s instruction. 3’UTR RNA seq was performed using the CEL Seq2 protocol except that Second Strand Synthesis Module NEB was used for double stranded cDNA synthesis and library was amplified by 9 cycles of PCR without xxx sample pooling.	tissue:liver\|genotype:Wild type\|treatment:fasted	GSM6210775	GSM6210775: WT 6dpf 4 [N047 04]; Danio rerio; RNA Seq	GSM6210775 r1	GSM6210775	1	Total RNA was extracted by using Direct zol RNA Kit ZYMO RESEARCH according to the manufacture's instruction. three primeUTR RNA seq was performed using the CEL Seq2 protocol except that Second Strand Synthesis Module NEB was used for double stranded cDNA synthesis and library was amplified by 9 cycles of PCR without xxx sample pooling.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiniSeq	SRP378140	N047-04_S4_L001_R1_001.fastq.gz N047-04_S4_L001_R2_001.fastq.gz	fastq fastq	147083090.0	2101187.0	GSM6210775 r1	0:19 1:51	A:37975239;C:30348934;G:33184532;T:45523625;N:50760	19	51	37975239	30348934	33184532	45523625	50760	SRX15572796	SRS13275624	SRA1430748	Sungkyunkwan University	Sungkyunkwan University	2	0.01149	0.91123	0.00998	0.0933	0.99515	0.84928	0.51408	0.66541	19	51	T	B	sc-like readlen	illumina	miseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	South Korea	2022-06-02	Larval	Larval	Liver	Liver and Biliary System
70097	70097	SRR19520285	SRX15572795	SRS13275625	SRP378140	PRJNA844556	Loss of pex5 sensitizes zebrafish to fasting due to deregulated mitochondria mTOR and autophagy	GSE205349	Transcriptome Analysis	Animal models have been utilized to understand the pathogenesis of Zellweger spectrum disorders ZSD but the link between the clinical manifestations and molecular pathways has not yet been clearly established. We generated a peroxin 5 homozygous mutant zebrafish pex5 / to gain insight into the molecular pathogenesis of peroxisome dysfunction. pex5 / displays hallmarks of ZSD in humans and die within one month post birth. Fasting rapidly depletes the liver lipids and glycogen in pex5 / and expedites their mortality. Mechanistically abnormal mitochondrial activity and mechanistic target of rapamycin mTOR signaling act together to induce metabolic alterations to deplete the hepatic nutrients and accumulate the damaged mitochondria. Accordingly the use of chemical interventions blocking either the mitochondrial activities or the mechanistic target of rapamycin complex 1 or a combination of both improves the metabolic imbalance shown in the fasted pex5 / livers and extends the survival of the animals. Furthermore the use of an autophagy activator also effectively ameliorated the early mortality of the fasted pex5 / . These results suggest that fasting may be detrimental to patients with peroxisome dysfunction and that modulating the mitochondria mTOR or autophagy activities may provide a therapeutic option to alleviate the symptoms of peroxisomal diseases associated with metabolic dysfunction. Overall design: Total RNAs of whole liver tissues from fasted WT and pex5 homozygous mutant zebrafish at 6 dpf were used to identify differential gene expression between the two genotype under fasting condition	pubmed:36821008	WT 6dpf 1 [N047 01]	GSM6210774	source name:liver\|tissue:liver\|genotype:Wild type\|treatment:fasted	WT 6dpf 1 [N047 01]	Quantitative analysis was performed using 51bp of insert reads Read2. Cell barcode and UMI in Read1 was extracted by using UMI tools ver.1.1.1. Four cell barcodes were mixed and used for all samples. Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore ver.0.6.7. Reads were mapped to the GRCz11 reference using HISAT2 ver.2.2.1. Read counts for each gene were obtained by featureCounts ver.2.0.1. UMI duplication was removed by UMI tools. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TMM values for each Sample	liver	Total RNA was extracted by using Direct zol RNA Kit ZYMO RESEARCH according to the manufacture’s instruction. 3’UTR RNA seq was performed using the CEL Seq2 protocol except that Second Strand Synthesis Module NEB was used for double stranded cDNA synthesis and library was amplified by 9 cycles of PCR without xxx sample pooling.	tissue:liver\|genotype:Wild type\|treatment:fasted	GSM6210774	GSM6210774: WT 6dpf 1 [N047 01]; Danio rerio; RNA Seq	GSM6210774 r1	GSM6210774	1	Total RNA was extracted by using Direct zol RNA Kit ZYMO RESEARCH according to the manufacture's instruction. three primeUTR RNA seq was performed using the CEL Seq2 protocol except that Second Strand Synthesis Module NEB was used for double stranded cDNA synthesis and library was amplified by 9 cycles of PCR without xxx sample pooling.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina MiniSeq	SRP378140	N047-01_S1_L001_R1_001.fastq.gz N047-01_S1_L001_R2_001.fastq.gz	fastq fastq	174019160.0	2485988.0	GSM6210774 r1	0:19 1:51	A:44401044;C:36220148;G:39239552;T:54096960;N:61456	19	51	44401044	36220148	39239552	54096960	61456	SRX15572795	SRS13275625	SRA1430748	Sungkyunkwan University	Sungkyunkwan University	2	0.01132	0.90822	0.00976	0.09386	0.99504	0.84118	0.54452	0.66722	19	51	T	B	sc-like readlen	illumina	miseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	South Korea	2022-06-02	Larval	Larval	Liver	Liver and Biliary 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");;