metadata: run_metadata: 12 rows where experiment.platform = "DNBSEQ", technology = "unknown" and tissue

12 rows where experiment.platform = "DNBSEQ", technology = "unknown" and tissue_curation = "Kidney"

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.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	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.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
68121	68121	SRR17606004	SRX13774802	SRS11654800	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN Homo Kidney RNAseq rep3	GSM5815265	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	CEN Homo Kidney RNAseq rep3	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815265	GSM5815265: CEN Homo Kidney RNAseq rep3; Danio rerio; RNA Seq	GSM5815265 r1	GSM5815265	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	CENHOMO3_2.fq.gz CENHOMO3_1.fq.gz	fastq fastq	7215517200.0	72155172.0	GSM5815265 r1	0:100 1:100	A:1927134950;C:1661322135;G:1683841967;T:1943218148;N:0	100	100	1927134950	1661322135	1683841967	1943218148	SRX13774802	SRS11654800	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94062	0.07183	0.72596	0.55426	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68122	68122	SRR17606005	SRX13774801	SRS11654799	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN Homo Kidney RNAseq rep2	GSM5815264	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	CEN Homo Kidney RNAseq rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815264	GSM5815264: CEN Homo Kidney RNAseq rep2; Danio rerio; RNA Seq	GSM5815264 r1	GSM5815264	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	CENHOMO2_2.fq.gz CENHOMO2_1.fq.gz	fastq fastq	7207596800.0	72075968.0	GSM5815264 r1	0:100 1:100	A:1913835378;C:1670319627;G:1686651138;T:1936790657;N:0	100	100	1913835378	1670319627	1686651138	1936790657	SRX13774801	SRS11654799	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94306	0.06924	0.72376	0.56145	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68123	68123	SRR17606006	SRX13774800	SRS11654798	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN Homo Kidney RNAseq rep1	GSM5815263	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	CEN Homo Kidney RNAseq rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:CEN homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815263	GSM5815263: CEN Homo Kidney RNAseq rep1; Danio rerio; RNA Seq	GSM5815263 r1	GSM5815263	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	CENHOMO1_1.fq.gz CENHOMO1_2.fq.gz	fastq fastq	7204062600.0	72040626.0	GSM5815263 r1	0:100 1:100	A:1902216192;C:1680493255;G:1696367176;T:1924985977;N:0	100	100	1902216192	1680493255	1696367176	1924985977	SRX13774800	SRS11654798	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.9408	0.06772	0.71545	0.53936	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68124	68124	SRR17606007	SRX13774799	SRS11654797	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN WT Kidney RNAseq rep3	GSM5815262	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	CEN WT Kidney RNAseq rep3	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815262	GSM5815262: CEN WT Kidney RNAseq rep3; Danio rerio; RNA Seq	GSM5815262 r1	GSM5815262	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	CENWT3_2.fq.gz CENWT3_1.fq.gz	fastq fastq	7205589000.0	72055890.0	GSM5815262 r1	0:100 1:100	A:1892937448;C:1690826558;G:1711136694;T:1910688300;N:0	100	100	1892937448	1690826558	1711136694	1910688300	SRX13774799	SRS11654797	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94358	0.06548	0.72336	0.54655	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68125	68125	SRR17606008	SRX13774798	SRS11654796	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN WT Kidney RNAseq rep2	GSM5815261	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	CEN WT Kidney RNAseq rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815261	GSM5815261: CEN WT Kidney RNAseq rep2; Danio rerio; RNA Seq	GSM5815261 r1	GSM5815261	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	CENWT2_1.fq.gz CENWT2_2.fq.gz	fastq fastq	7219678800.0	72196788.0	GSM5815261 r1	0:100 1:100	A:1908750065;C:1680876268;G:1700533938;T:1929518529;N:0	100	100	1908750065	1680876268	1700533938	1929518529	SRX13774798	SRS11654796	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94561	0.06821	0.71792	0.54803	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68126	68126	SRR17606009	SRX13774797	SRS11654795	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	CEN WT Kidney RNAseq rep1	GSM5815260	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	CEN WT Kidney RNAseq rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815260	GSM5815260: CEN WT Kidney RNAseq rep1; Danio rerio; RNA Seq	GSM5815260 r1	GSM5815260	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	CENWT1_1.fq.gz CENWT1_2.fq.gz	fastq fastq	7213577400.0	72135774.0	GSM5815260 r1	0:100 1:100	A:1899760333;C:1688268609;G:1705140400;T:1920408058;N:0	100	100	1899760333	1688268609	1705140400	1920408058	SRX13774797	SRS11654795	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94364	0.06593	0.71796	0.55315	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68127	68127	SRR17606010	SRX13774796	SRS11654794	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd Homo Kidney RNAseq rep3	GSM5815259	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	cebpd Homo Kidney RNAseq rep3	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815259	GSM5815259: cebpd Homo Kidney RNAseq rep3; Danio rerio; RNA Seq	GSM5815259 r1	GSM5815259	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	cebpdHomo3_1.fq.gz cebpdHomo3_2.fq.gz	fastq fastq	7279069400.0	72790694.0	GSM5815259 r1	0:100 1:100	A:1930406096;C:1690658505;G:1705808112;T:1952196687;N:0	100	100	1930406096	1690658505	1705808112	1952196687	SRX13774796	SRS11654794	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94225	0.05895	0.74353	0.55835	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68128	68128	SRR17606011	SRX13774795	SRS11654793	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd Homo Kidney RNAseq rep2	GSM5815258	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	cebpd Homo Kidney RNAseq rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815258	GSM5815258: cebpd Homo Kidney RNAseq rep2; Danio rerio; RNA Seq	GSM5815258 r1	GSM5815258	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	cebpdHomo2_2.fq.gz cebpdHomo2_1.fq.gz	fastq fastq	7264240800.0	72642408.0	GSM5815258 r1	0:100 1:100	A:1907893057;C:1703728991;G:1717658793;T:1934959959;N:0	100	100	1907893057	1703728991	1717658793	1934959959	SRX13774795	SRS11654793	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94566	0.06391	0.72417	0.5235	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68129	68129	SRR17606012	SRX13774794	SRS11654791	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd Homo Kidney RNAseq rep1	GSM5815257	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	cebpd Homo Kidney RNAseq rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:cebpd homozygous knockout\|treatment:cardiomyocyte ablation	GSM5815257	GSM5815257: cebpd Homo Kidney RNAseq rep1; Danio rerio; RNA Seq	GSM5815257 r1	GSM5815257	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	cebpdHomo1_2.fq.gz cebpdHomo1_1.fq.gz	fastq fastq	7192873200.0	71928732.0	GSM5815257 r1	0:100 1:100	A:1905599298;C:1665589905;G:1707980534;T:1913703463;N:0	100	100	1905599298	1665589905	1707980534	1913703463	SRX13774794	SRS11654791	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.92744	0.062	0.72393	0.55384	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68130	68130	SRR17606013	SRX13774793	SRS11654792	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd WT Kidney RNAseq rep3	GSM5815256	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	cebpd WT Kidney RNAseq rep3	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815256	GSM5815256: cebpd WT Kidney RNAseq rep3; Danio rerio; RNA Seq	GSM5815256 r1	GSM5815256	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	cebpdWT3_1.fq.gz cebpdWT3_2.fq.gz	fastq fastq	7280350400.0	72803504.0	GSM5815256 r1	0:100 1:100	A:1925119485;C:1698344141;G:1714885029;T:1942001745;N:0	100	100	1925119485	1698344141	1714885029	1942001745	SRX13774793	SRS11654792	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94212	0.05877	0.73446	0.54431	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68131	68131	SRR17606014	SRX13774792	SRS11654802	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd WT Kidney RNAseq rep2	GSM5815255	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	cebpd WT Kidney RNAseq rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815255	GSM5815255: cebpd WT Kidney RNAseq rep2; Danio rerio; RNA Seq	GSM5815255 r1	GSM5815255	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	cebpdWT2_1.fq.gz cebpdWT2_2.fq.gz	fastq fastq	7264980400.0	72649804.0	GSM5815255 r1	0:100 1:100	A:1953740321;C:1658035501;G:1681062257;T:1972142321;N:0	100	100	1953740321	1658035501	1681062257	1972142321	SRX13774792	SRS11654802	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.93531	0.06698	0.73499	0.56385	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System
68132	68132	SRR17606015	SRX13774791	SRS11654790	SRP354915	PRJNA796975	Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish	GSE193630	Transcriptome Analysis	In previous studies we identified and demonstrated that a 1.2kb cebpd downstream element CEN is capable and neccessary for the induction of cebpd in the kidney post cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer CEN mutant fish zebrafish to massive injuries of the heart. Overall design: cebpd+/+ and cebpd / kidney RNA seq profiling post cardiac injury; CEN+/+ and CEN / kidney RNA seq profiling post cardiac injury;	pubmed:35513710	cebpd WT Kidney RNAseq rep1	GSM5815254	source name:Kidney\|strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	cebpd WT Kidney RNAseq rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	Kidney	animals were incubated in 0.50.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 412 mpf were used in this study.	strain:EK\|tissue:Kidney\|genotype:Wild type\|treatment:cardiomyocyte ablation	GSM5815254	GSM5815254: cebpd WT Kidney RNAseq rep1; Danio rerio; RNA Seq	GSM5815254 r1	GSM5815254	1	Whole kidney were snap freezed. Total RNA was extracted using TRI reagent T9424 Sigma Aldrich and treated with DNase1 to degrade genomic DNA. Samples were purified with Quick RNA Miniprep kit R1054 Zymo Research. RNA libraries were prepared for sequencing using standard Illumina protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP354915	cebpdWT1_1.fq.gz cebpdWT1_2.fq.gz	fastq fastq	7256843800.0	72568438.0	GSM5815254 r1	0:100 1:100	A:1920544243;C:1687420610;G:1707252526;T:1941626421;N:0	100	100	1920544243	1687420610	1707252526	1941626421	SRX13774791	SRS11654790	SRA1356624	Cell biology, Duke University	Poss, Cell Biology, Duke University	1	0.94388	0.06494	0.7265	0.54419	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-01-13	Larval	Larval	Kidney	Renal System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;