metadata: run_metadata: 7 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation

7 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation_coarse = "Cardiovascular System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	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.r3_length	run.r4_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
72120	72120	SRR22366730	SRX18337367	SRS15826352	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.	single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post injured zebrafish heart with CL condition	single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post injured zebrafish heart with CL condition	sc CL 7dpci	strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|cell type:macrophage and neutrophil\|treatment:7day post cryoinjured heart with CL condition\|BioSampleModel:Model organism or animal	single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post zebrafish injured heart in CL condition	HS19157 1	HS19157 1	7 day post cryoinjured CL	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292	HS19157-1_S1_L001_I1_001.fastq.gz HS19157-1_S1_L001_R1_001.fastq.gz HS19157-1_S1_L001_R2_001.fastq.gz	fastq fastq fastq	29030208386.0	228584318.0	HS19157 1 S1 L001 I1 001.fastq.gz	0:8 1:28 2:91	A:6001335918;C:4374546179;G:4652617189;T:5772031621;N:642031	8	28	91		6001335918	4374546179	4652617189	5772031621	642031	SRX18337367	SRS15826352	SRA1544923	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	1	0.90785		0.14887		0.80955		0.54438		91		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	bulk	bulk	Taiwan	2022-11-22	Adult	Adult	Heart	Cardiovascular System
72121	72121	SRR22366731	SRX18337366	SRS15826351	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.	single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post injured zebrafish heart with CL condition	single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post injured zebrafish heart with CL condition	sc CL 3dpci	strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|cell type:macrophage and neutrophil\|treatment:3day post cryoinjured heart with CL condition\|BioSampleModel:Model organism or animal	single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post zebrafish injured heart in CL condition	KO 10X GEX ZBNM CL	KO 10X GEX ZBNM CL	3 day post cryoinjured CL	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292	KO_10X_GEX_ZBNM_CL_S1_L002_I1_001.fastq.gz KO_10X_GEX_ZBNM_CL_S1_L002_I2_001.fastq.gz KO_10X_GEX_ZBNM_CL_S1_L002_R1_001.fastq.gz KO_10X_GEX_ZBNM_CL_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	136386569076.0	428888582.0	KO 10X GEX ZBNM CL S1 L002 I1 001.fastq.gz	0:8 1:8 2:151 3:151	A:55416348531;C:22858620140;G:22320883224;T:28927596919;N:902950	8	8	151	151	55416348531	22858620140	22320883224	28927596919	902950	SRX18337366	SRS15826351	SRA1544923	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	5e-05	0.91197	4e-05	0.16298	1.0	0.81531		0.6066	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	bulk	bulk	Taiwan	2022-11-23	Adult	Adult	Heart	Cardiovascular System
72122	72122	SRR22366732	SRX18337365	SRS15826349	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.	single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post injured zebrafish heart with CL condition	single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post injured zebrafish heart with CL condition	sc CL 1dpci	strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|cell type:macrophage and neutrophil\|treatment:1day post cryoinjured heart with CL condition\|BioSampleModel:Model organism or animal	single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post zebrafish injured heart in CL condition	KO 10X GEX ZBNMCL1dpci	KO 10X GEX ZBNMCL1dpci	1 day post cryoinjured CL	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292	KO_10X_GEX_ZBNMCL1dpci_S6_L002_R2_001.fastq.gz KO_10X_GEX_ZBNMCL1dpci_S6_L002_R1_001.fastq.gz KO_10X_GEX_ZBNMCL1dpci_S6_L002_I2_001.fastq.gz KO_10X_GEX_ZBNMCL1dpci_S6_L002_I1_001.fastq.gz	fastq fastq fastq fastq	116701252260.0	366985070.0	KO 10X GEX ZBNMCL1dpci S6 L002 I1 001.fastq.gz	0:8 1:8 2:151 3:151	A:47399839020;C:19285022403;G:18825392415;T:25318468073;N:769229	8	8	151	151	47399839020	19285022403	18825392415	25318468073	769229	SRX18337365	SRS15826349	SRA1544923	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.0	0.91164	0.0	0.16285	1.0	0.82132		0.60109	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	bulk	bulk	Taiwan	2022-11-23	Adult	Adult	Heart	Cardiovascular System
72123	72123	SRR22366733	SRX18337364	SRS15826350	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.	single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post injured zebrafish heart with PBS condition	single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post injured zebrafish heart with PBS condition	sc PBS 7dpci	strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|cell type:macrophage and neutrophil\|treatment:7day post cryoinjured heart with PBS condition\|BioSampleModel:Model organism or animal	single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post zebrafish injured heart in PBS condition	HS19157 2	HS19157 2	7 day post cryoinjured PBS	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292	HS19157-2_S2_L001_I1_001.fastq.gz HS19157-2_S2_L001_R1_001.fastq.gz HS19157-2_S2_L001_R2_001.fastq.gz	fastq fastq fastq	27285141518.0	214843634.0	HS19157 2 S2 L001 I1 001.fastq.gz	0:8 1:28 2:91	A:5601997478;C:4186239866;G:4438635185;T:5323299767;N:598398	8	28	91		5601997478	4186239866	4438635185	5323299767	598398	SRX18337364	SRS15826350	SRA1544923	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	1	0.91295		0.12796		0.81917		0.54156		91		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	sc	bulk	bulk	Taiwan	2022-11-22	Adult	Adult	Heart	Cardiovascular System
72124	72124	SRR22366734	SRX18337363	SRS15826348	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.	single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post injured zebrafish heart with PBS condition	single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post injured zebrafish heart with PBS condition	sc PBS 3dpci	strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|cell type:macrophage and neutrophil\|treatment:3day post cryoinjured heart with PBS condition\|BioSampleModel:Model organism or animal	single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post zebrafish injured heart in PBS condition	KO 10X GEX ZBNM PBS	KO 10X GEX ZBNM PBS	3 day post cryoinjured PBS	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292	KO_10X_GEX_ZBNM_PBS_S2_L002_I1_001.fastq.gz KO_10X_GEX_ZBNM_PBS_S2_L002_I2_001.fastq.gz KO_10X_GEX_ZBNM_PBS_S2_L002_R1_001.fastq.gz KO_10X_GEX_ZBNM_PBS_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	90678465744.0	285152408.0	KO 10X GEX ZBNM PBS S2 L002 I1 001.fastq.gz	0:8 1:8 2:151 3:151	A:36925379975;C:14988640095;G:14661131954;T:19540280259;N:594933	8	8	151	151	36925379975	14988640095	14661131954	19540280259	594933	SRX18337363	SRS15826348	SRA1544923	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.0	0.91472	0.0	0.14149	1.0	0.82369		0.59397	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	bulk	bulk	Taiwan	2022-11-22	Adult	Adult	Heart	Cardiovascular System
72125	72125	SRR22366735	SRX18337362	SRS15826347	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.	single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post injured zebrafish heart with PBS condition	single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post injured zebrafish heart with PBS condition	sc PBS 1dpci	strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|cell type:macrophage and neutrophil\|treatment:1day post cryoinjured heart with PBS condition\|BioSampleModel:Model organism or animal	single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post zebrafish injured heart in PBS condition	KO 10X GEX ZBNMPBS1dpci	KO 10X GEX ZBNMPBS1dpci	1 day post cryoinjured PBS	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292	KO_10X_GEX_ZBNMPBS1dpci_S7_L002_I1_001.fastq.gz KO_10X_GEX_ZBNMPBS1dpci_S7_L002_I2_001.fastq.gz KO_10X_GEX_ZBNMPBS1dpci_S7_L002_R1_001.fastq.gz KO_10X_GEX_ZBNMPBS1dpci_S7_L002_R2_001.fastq.gz	fastq fastq fastq fastq	124280694174.0	390819793.0	KO 10X GEX ZBNMPBS1dpci S7 L002 I1 001.fastq.gz	0:8 1:8 2:151 3:151	A:50504338257;C:20602333071;G:20112647801;T:26807443112;N:815245	8	8	151	151	50504338257	20602333071	20112647801	26807443112	815245	SRX18337362	SRS15826347	SRA1544923	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.0	0.9161	0.0	0.14822	1.0	0.81891		0.59781	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	bulk	bulk	Taiwan	2022-11-23	Adult	Adult	Heart	Cardiovascular System
72126	72126	SRR22366736	SRX18337361	SRS15826346	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.	single cell RNA seq of macrophage and neutrophil cells sorted from untouched zebrafish heart	single cell RNA seq of macrophage and neutrophil cells sorted from untouched zebrafish heart	sc UT	strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|cell type:macrophage and neutrophil\|treatment:wild type heart\|BioSampleModel:Model organism or animal	single cell RNA seq of macrophage and neutrophil cells sorted from zebrafish wild type heart	KO 10X GEX ZBNM WT	KO 10X GEX ZBNM WT	wild type	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292	KO_10X_GEX_ZBNM_WT_S5_L002_I1_001.fastq.gz KO_10X_GEX_ZBNM_WT_S5_L002_I2_001.fastq.gz KO_10X_GEX_ZBNM_WT_S5_L002_R1_001.fastq.gz KO_10X_GEX_ZBNM_WT_S5_L002_R2_001.fastq.gz	fastq fastq fastq fastq	146800238142.0	461635969.0	KO 10X GEX ZBNM WT S5 L002 I1 001.fastq.gz	0:8 1:8 2:151 3:151	A:60009342670;C:24155451853;G:23489314793;T:31758989136;N:964186	8	8	151	151	60009342670	24155451853	23489314793	31758989136	964186	SRX18337361	SRS15826346	SRA1544923	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.0	0.90338	0.0	0.17611	1.0	0.83189		0.53987	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	bulk	bulk	Taiwan	2022-11-23	Adult	Adult	Heart	Cardiovascular 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");;