metadata: run_metadata: 4 rows where experiment.library_selection = "RACE", experiment.library_strategy = "RNA-Seq" and tissue

4 rows where experiment.library_selection = "RACE", experiment.library_strategy = "RNA-Seq" 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.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
31687	31687	SRR28490625	SRX24092863	SRS20882184	SRP498456	PRJNA1093028	Effect of depletion of Sas10 in pre rRNA processing	GSE262698	Transcriptome Analysis	Ribosome small subunit SSU is assembled by the SSU processome which contains approximately 70 non ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied however how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. For the remaining 25 proteins we find that UTP3/SAS10 assists the nucleolar localization of five proteins namely MPP10 UTP25 EMG1 and two UTP B components UTP12 and UTP13 and this ferry function of UTP3 is conserved in zebrafish. We also find that knockdown of human UTP3 impairs the cleavage at A0 site while loss of function of either utp3/sas10 or utp13/tbl3 in zebrafish causes an accumulation of the processed products containing the five primeETS supporting the crucial role of UTP3 in mediating the five primeETS processing and degradation. Moreover UTP3 directly interacts with and delivers EXOSC10 into the nucleolus suggesting that UTP3 may play a direct role in recruiting the nuclear exosome to the SSU processome for degradation of the processed five primeETS. These findings lay the ground for studying the mechanism of cytoplasm to nucleolus trafficking of the SSU processome components and the multifaceted roles of UTP3 during pre rRNA processing. Overall design: To validate pre rRNA processing defect in zebrafish sas10 tbl3 mutants and human UTP3 knock down cells we performed three primeRACE seq of these samples.	pubmed:39036955	zebrafish embryo 5dpf sas10 mutant rep 2	GSM8174002	source name:embryo\|tissue:embryo\|genotype:sas10 mutant\|geo loc name:missing\|collection date:missing	zebrafish embryo 5dpf sas10 mutant rep 2	Sequence reads were trimmed of adapter sequences and low quality sequences using Cutadpat. Trimmed sequences were deduplicated zebrafish five primeETS sequence searched and mapped to zebrafish pre rRNA reference sequence to analyze the three prime end of each read. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including each read's relative postion in pre rRNA corresponding sequence modification status and modification size.	embryo	Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.	tissue:embryo\|genotype:sas10 mutant	GSM8174002	GSM8174002: zebrafish embryo 5dpf sas10 mutant rep 2; Danio rerio; RNA Seq	GSM8174002 r1	GSM8174002	1	Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.	RNA-Seq	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498456	RACE_S_2_R2.fq.gz RACE_S_2_R1.fq.gz	fastq fastq	2676884700.0	8922949.0	GSM8174002 r1	0:150 1:150	A:386375545;C:575923603;G:1262958328;T:451548053;N:79171	150	150	386375545	575923603	1262958328	451548053	79171	SRX24092863	SRS20882184	SRA1835384	MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University	MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University	2	0.19638	0.00802	0.19587	0.00751	0.99937	0.99941	0.67088	0.57731	150	150	B	T	mate2 technical by mapping diff	illumina	novaseq_era	3prime	other	unknown	bulk	unknown	unknown	China	2024-03-28	Larval	Larval	Embryo Imprecise	All anatomical structures
31688	31688	SRR28490626	SRX24092862	SRS20882183	SRP498456	PRJNA1093028	Effect of depletion of Sas10 in pre rRNA processing	GSE262698	Transcriptome Analysis	Ribosome small subunit SSU is assembled by the SSU processome which contains approximately 70 non ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied however how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. For the remaining 25 proteins we find that UTP3/SAS10 assists the nucleolar localization of five proteins namely MPP10 UTP25 EMG1 and two UTP B components UTP12 and UTP13 and this ferry function of UTP3 is conserved in zebrafish. We also find that knockdown of human UTP3 impairs the cleavage at A0 site while loss of function of either utp3/sas10 or utp13/tbl3 in zebrafish causes an accumulation of the processed products containing the five primeETS supporting the crucial role of UTP3 in mediating the five primeETS processing and degradation. Moreover UTP3 directly interacts with and delivers EXOSC10 into the nucleolus suggesting that UTP3 may play a direct role in recruiting the nuclear exosome to the SSU processome for degradation of the processed five primeETS. These findings lay the ground for studying the mechanism of cytoplasm to nucleolus trafficking of the SSU processome components and the multifaceted roles of UTP3 during pre rRNA processing. Overall design: To validate pre rRNA processing defect in zebrafish sas10 tbl3 mutants and human UTP3 knock down cells we performed three primeRACE seq of these samples.	pubmed:39036955	zebrafish embryo 5dpf sas10 mutant rep 1	GSM8174001	source name:embryo\|tissue:embryo\|genotype:sas10 mutant\|geo loc name:missing\|collection date:missing	zebrafish embryo 5dpf sas10 mutant rep 1	Sequence reads were trimmed of adapter sequences and low quality sequences using Cutadpat. Trimmed sequences were deduplicated zebrafish five primeETS sequence searched and mapped to zebrafish pre rRNA reference sequence to analyze the three prime end of each read. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including each read's relative postion in pre rRNA corresponding sequence modification status and modification size.	embryo	Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.	tissue:embryo\|genotype:sas10 mutant	GSM8174001	GSM8174001: zebrafish embryo 5dpf sas10 mutant rep 1; Danio rerio; RNA Seq	GSM8174001 r1	GSM8174001	1	Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.	RNA-Seq	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498456	RACE_S_1_R2.fq.gz RACE_S_1_R1.fq.gz	fastq fastq	4094487600.0	13648292.0	GSM8174001 r1	0:150 1:150	A:548452011;C:815932223;G:2109931363;T:620046982;N:125021	150	150	548452011	815932223	2109931363	620046982	125021	SRX24092862	SRS20882183	SRA1835384	MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University	MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University	2	0.17506	0.00958	0.17451	0.00908	0.99937	0.99933	0.66326	0.70212	150	150	B	T	mate2 technical by mapping diff	illumina	novaseq_era	3prime	other	unknown	bulk	unknown	unknown	China	2024-03-28	Larval	Larval	Embryo Imprecise	All anatomical structures
31689	31689	SRR28490627	SRX24092861	SRS20882182	SRP498456	PRJNA1093028	Effect of depletion of Sas10 in pre rRNA processing	GSE262698	Transcriptome Analysis	Ribosome small subunit SSU is assembled by the SSU processome which contains approximately 70 non ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied however how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. For the remaining 25 proteins we find that UTP3/SAS10 assists the nucleolar localization of five proteins namely MPP10 UTP25 EMG1 and two UTP B components UTP12 and UTP13 and this ferry function of UTP3 is conserved in zebrafish. We also find that knockdown of human UTP3 impairs the cleavage at A0 site while loss of function of either utp3/sas10 or utp13/tbl3 in zebrafish causes an accumulation of the processed products containing the five primeETS supporting the crucial role of UTP3 in mediating the five primeETS processing and degradation. Moreover UTP3 directly interacts with and delivers EXOSC10 into the nucleolus suggesting that UTP3 may play a direct role in recruiting the nuclear exosome to the SSU processome for degradation of the processed five primeETS. These findings lay the ground for studying the mechanism of cytoplasm to nucleolus trafficking of the SSU processome components and the multifaceted roles of UTP3 during pre rRNA processing. Overall design: To validate pre rRNA processing defect in zebrafish sas10 tbl3 mutants and human UTP3 knock down cells we performed three primeRACE seq of these samples.	pubmed:39036955	zebrafish embryo 5dpf wild type rep 2	GSM8174000	source name:embryo\|tissue:embryo\|genotype:wild type\|geo loc name:missing\|collection date:missing	zebrafish embryo 5dpf wild type rep 2	Sequence reads were trimmed of adapter sequences and low quality sequences using Cutadpat. Trimmed sequences were deduplicated zebrafish five primeETS sequence searched and mapped to zebrafish pre rRNA reference sequence to analyze the three prime end of each read. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including each read's relative postion in pre rRNA corresponding sequence modification status and modification size.	embryo	Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.	tissue:embryo\|genotype:wild type	GSM8174000	GSM8174000: zebrafish embryo 5dpf wild type rep 2; Danio rerio; RNA Seq	GSM8174000 r1	GSM8174000	1	Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.	RNA-Seq	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498456	RACE_AB_2_R1.fq.gz RACE_AB_2_R2.fq.gz	fastq fastq	4279654200.0	14265514.0	GSM8174000 r1	0:150 1:150	A:664011716;C:1017127170;G:1816549931;T:781834743;N:130640	150	150	664011716	1017127170	1816549931	781834743	130640	SRX24092861	SRS20882182	SRA1835384	MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University	MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University	2	0.10741	0.00626	0.10706	0.00596	0.99939	0.99943	0.65454	0.73684	150	150	B	T	mate2 technical by mapping diff	illumina	novaseq_era	3prime	other	unknown	bulk	unknown	unknown	China	2024-03-28	Larval	Larval	Embryo Imprecise	All anatomical structures
31690	31690	SRR28490628	SRX24092860	SRS20882181	SRP498456	PRJNA1093028	Effect of depletion of Sas10 in pre rRNA processing	GSE262698	Transcriptome Analysis	Ribosome small subunit SSU is assembled by the SSU processome which contains approximately 70 non ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied however how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. For the remaining 25 proteins we find that UTP3/SAS10 assists the nucleolar localization of five proteins namely MPP10 UTP25 EMG1 and two UTP B components UTP12 and UTP13 and this ferry function of UTP3 is conserved in zebrafish. We also find that knockdown of human UTP3 impairs the cleavage at A0 site while loss of function of either utp3/sas10 or utp13/tbl3 in zebrafish causes an accumulation of the processed products containing the five primeETS supporting the crucial role of UTP3 in mediating the five primeETS processing and degradation. Moreover UTP3 directly interacts with and delivers EXOSC10 into the nucleolus suggesting that UTP3 may play a direct role in recruiting the nuclear exosome to the SSU processome for degradation of the processed five primeETS. These findings lay the ground for studying the mechanism of cytoplasm to nucleolus trafficking of the SSU processome components and the multifaceted roles of UTP3 during pre rRNA processing. Overall design: To validate pre rRNA processing defect in zebrafish sas10 tbl3 mutants and human UTP3 knock down cells we performed three primeRACE seq of these samples.	pubmed:39036955	zebrafish embryo 5dpf wild type rep 1	GSM8173999	source name:embryo\|tissue:embryo\|genotype:wild type\|geo loc name:missing\|collection date:missing	zebrafish embryo 5dpf wild type rep 1	Sequence reads were trimmed of adapter sequences and low quality sequences using Cutadpat. Trimmed sequences were deduplicated zebrafish five primeETS sequence searched and mapped to zebrafish pre rRNA reference sequence to analyze the three prime end of each read. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including each read's relative postion in pre rRNA corresponding sequence modification status and modification size.	embryo	Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.	tissue:embryo\|genotype:wild type	GSM8173999	GSM8173999: zebrafish embryo 5dpf wild type rep 1; Danio rerio; RNA Seq	GSM8173999 r1	GSM8173999	1	Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent Aidlab RN0102 with three independent biological repeats each and was treated with DNase I New England Biolabs M0303S to remove genomic DNA contamination. Total RNA for each sample was ligated with three primeRACE adapter followed by three primeRACE adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish five primeETS sequence and reverse primers Illumina RPIs.	RNA-Seq	TRANSCRIPTOMIC	RACE	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP498456	RACE_AB_1_R2.fq.gz RACE_AB_1_R1.fq.gz	fastq fastq	4575871800.0	15252906.0	GSM8173999 r1	0:150 1:150	A:718107616;C:1095325729;G:1919360747;T:842938887;N:138821	150	150	718107616	1095325729	1919360747	842938887	138821	SRX24092860	SRS20882181	SRA1835384	MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University	MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University	2	0.14402	0.00584	0.14352	0.00565	0.99935	0.99955	0.60273	0.77777	150	150	B	T	mate2 technical by mapping diff	illumina	novaseq_era	3prime	other	unknown	bulk	unknown	unknown	China	2024-03-28	Larval	Larval	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");;