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

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

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.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.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
30204	30204	SRR27715729	SRX23381950	SRS20243484	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.	pubmed:39147275	Ko 3	GSM8033238	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout\|geo loc name:missing\|collection date:missing	Ko 3	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout	GSM8033238	GSM8033238: Ko 3; Danio rerio; RNA Seq	GSM8033238 r1	GSM8033238	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714	15_1.fq.gz 15_2.fq.gz	fastq fastq	5020450600.0	25102253.0	GSM8033238 r1	0:100 1:100	A:1371660785;C:1125396855;G:1130384333;T:1393008627;N:0	100	100	1371660785	1125396855	1130384333	1393008627	0	SRX23381950	SRS20243484	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.9229	0.92453	0.12667	0.12674	0.65143	0.65232	0.48379	0.48431	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
30205	30205	SRR27715730	SRX23381949	SRS20243483	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.	pubmed:39147275	control 3	GSM8033237	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control\|geo loc name:missing\|collection date:missing	control 3	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control	GSM8033237	GSM8033237: control 3; Danio rerio; RNA Seq	GSM8033237 r1	GSM8033237	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714	14_1.fq.gz 14_2.fq.gz	fastq fastq	5020525200.0	25102626.0	GSM8033237 r1	0:100 1:100	A:1366975716;C:1129522599;G:1135845277;T:1388181608;N:0	100	100	1366975716	1129522599	1135845277	1388181608	0	SRX23381949	SRS20243483	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.92923	0.93091	0.11899	0.11908	0.65117	0.651	0.48861	0.48085	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
30206	30206	SRR27715731	SRX23381948	SRS20243485	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.	pubmed:39147275	Ko 2	GSM8033236	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout\|geo loc name:missing\|collection date:missing	Ko 2	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout	GSM8033236	GSM8033236: Ko 2; Danio rerio; RNA Seq	GSM8033236 r1	GSM8033236	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714	13_1.fq.gz 13_2.fq.gz	fastq fastq	5016980000.0	25084900.0	GSM8033236 r1	0:100 1:100	A:1362095542;C:1131485761;G:1140659655;T:1382739042;N:0	100	100	1362095542	1131485761	1140659655	1382739042	0	SRX23381948	SRS20243485	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.92867	0.92952	0.12009	0.11989	0.64989	0.65129	0.48735	0.48822	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
30207	30207	SRR27715732	SRX23381947	SRS20243482	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.	pubmed:39147275	control 2	GSM8033235	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control\|geo loc name:missing\|collection date:missing	control 2	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control	GSM8033235	GSM8033235: control 2; Danio rerio; RNA Seq	GSM8033235 r1	GSM8033235	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714	12_1.fq.gz 12_2.fq.gz	fastq fastq	5014043600.0	25070218.0	GSM8033235 r1	0:100 1:100	A:1365729811;C:1126481057;G:1137205154;T:1384627578;N:0	100	100	1365729811	1126481057	1137205154	1384627578	0	SRX23381947	SRS20243482	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.92582	0.92658	0.11419	0.11406	0.65173	0.65257	0.48606	0.48533	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
30208	30208	SRR27715733	SRX23381946	SRS20243480	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.	pubmed:39147275	Ko 1	GSM8033234	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout\|geo loc name:missing\|collection date:missing	Ko 1	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout	GSM8033234	GSM8033234: Ko 1; Danio rerio; RNA Seq	GSM8033234 r1	GSM8033234	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714	11_1.fq.gz 11_2.fq.gz	fastq fastq	5245066800.0	26225334.0	GSM8033234 r1	0:100 1:100	A:1440549629;C:1168536590;G:1175698878;T:1460281703;N:0	100	100	1440549629	1168536590	1175698878	1460281703	0	SRX23381946	SRS20243480	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.92279	0.92105	0.13454	0.13464	0.65238	0.65291	0.47828	0.48217	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
30209	30209	SRR27715734	SRX23381945	SRS20243481	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.	pubmed:39147275	control 1	GSM8033233	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control\|geo loc name:missing\|collection date:missing	control 1	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control	GSM8033233	GSM8033233: control 1; Danio rerio; RNA Seq	GSM8033233 r1	GSM8033233	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714	10_1.fq.gz 10_2.fq.gz	fastq fastq	5460961000.0	27304805.0	GSM8033233 r1	0:100 1:100	A:1485370839;C:1228940953;G:1237868479;T:1508780729;N:0	100	100	1485370839	1228940953	1237868479	1508780729	0	SRX23381945	SRS20243481	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.92598	0.92555	0.12074	0.12035	0.65731	0.6577	0.46497	0.47306	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
76526	76526	SRR25007131	SRX20762489	SRS18050783	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.	pubmed:38542412	T3 1	GSM7507240	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:36hpf\|geo loc name:missing\|collection date:missing	T3 1	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:36hpf	GSM7507240	GSM7507240: T3 1; Danio rerio; RNA Seq	GSM7507240 r1	GSM7507240	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520	T3_1.R1.fq.gz T3_1.R2.fq.gz	fastq fastq	15316392300.0	51054641.0	GSM7507240 r1	0:150 1:150	A:3880671888;C:3784758050;G:3856071137;T:3794810224;N:81001	150	150	3880671888	3784758050	3856071137	3794810224	81001	SRX20762489	SRS18050783	SRA1661372	henan normal university	henan normal university	2	0.41572	0.57842	0.09076	0.13329	0.79385	0.76142	0.43528	0.43567	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
76527	76527	SRR25007132	SRX20762488	SRS18050782	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.	pubmed:38542412	T1 1	GSM7507236	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:10hpf\|geo loc name:missing\|collection date:missing	T1 1	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:10hpf	GSM7507236	GSM7507236: T1 1; Danio rerio; RNA Seq	GSM7507236 r1	GSM7507236	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520	T1_1.R1.fq.gz T1_1.R2.fq.gz	fastq fastq	13484033700.0	44946779.0	GSM7507236 r1	0:150 1:150	A:3415746428;C:3329088326;G:3392039530;T:3347088129;N:71287	150	150	3415746428	3329088326	3392039530	3347088129	71287	SRX20762488	SRS18050782	SRA1661372	henan normal university	henan normal university	2	0.40423	0.57514	0.07655	0.11873	0.80308	0.77092	0.46754	0.46803	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76528	76528	SRR25007133	SRX20762487	SRS18050781	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.	pubmed:38542412	T1 2	GSM7507237	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:10hpf\|geo loc name:missing\|collection date:missing	T1 2	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:10hpf	GSM7507237	GSM7507237: T1 2; Danio rerio; RNA Seq	GSM7507237 r1	GSM7507237	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520	T1_2.R1.fq.gz T1_2.R2.fq.gz	fastq fastq	13733190600.0	45777302.0	GSM7507237 r1	0:150 1:150	A:3445382955;C:3412918499;G:3490188153;T:3384626806;N:74187	150	150	3445382955	3412918499	3490188153	3384626806	74187	SRX20762487	SRS18050781	SRA1661372	henan normal university	henan normal university	2	0.43011	0.59623	0.08158	0.13068	0.80288	0.77544	0.47026	0.47364	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76529	76529	SRR25007134	SRX20762486	SRS18050778	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.	pubmed:38542412	T2 1	GSM7507238	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:24hpf\|geo loc name:missing\|collection date:missing	T2 1	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:24hpf	GSM7507238	GSM7507238: T2 1; Danio rerio; RNA Seq	GSM7507238 r1	GSM7507238	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520	T2_1.R2.fq.gz T2_1.R1.fq.gz	fastq fastq	14649880200.0	48832934.0	GSM7507238 r1	0:150 1:150	A:3695224943;C:3636149584;G:3688479871;T:3629948859;N:76943	150	150	3695224943	3636149584	3688479871	3629948859	76943	SRX20762486	SRS18050778	SRA1661372	henan normal university	henan normal university	2	0.43452	0.60496	0.08789	0.13132	0.7862	0.7528	0.44881	0.45341	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
76530	76530	SRR25007135	SRX20762485	SRS18050780	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.	pubmed:38542412	T2 2	GSM7507239	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:24hpf\|geo loc name:missing\|collection date:missing	T2 2	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:24hpf	GSM7507239	GSM7507239: T2 2; Danio rerio; RNA Seq	GSM7507239 r1	GSM7507239	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520	T2_2.R1.fq.gz T2_2.R2.fq.gz	fastq fastq	14696199900.0	48987333.0	GSM7507239 r1	0:150 1:150	A:3735683721;C:3615176348;G:3714335362;T:3630926317;N:78152	150	150	3735683721	3615176348	3714335362	3630926317	78152	SRX20762485	SRS18050780	SRA1661372	henan normal university	henan normal university	2	0.42139	0.57658	0.08829	0.1292	0.78831	0.75617	0.44949	0.45776	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
76531	76531	SRR25007136	SRX20762484	SRS18050779	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.	pubmed:38542412	T3 2	GSM7507241	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:36hpf\|geo loc name:missing\|collection date:missing	T3 2	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:36hpf	GSM7507241	GSM7507241: T3 2; Danio rerio; RNA Seq	GSM7507241 r1	GSM7507241	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520	T3_2.R2.fq.gz T3_2.R1.fq.gz	fastq fastq	15346908000.0	51156360.0	GSM7507241 r1	0:150 1:150	A:3937027213;C:3752697817;G:3796118846;T:3860983131;N:80993	150	150	3937027213	3752697817	3796118846	3860983131	80993	SRX20762484	SRS18050779	SRA1661372	henan normal university	henan normal university	2	0.4823	0.64213	0.10848	0.15245	0.77966	0.74752	0.43616	0.43697	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures

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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");;