run_metadata
4 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "PCR" and experiment.platform = "BGISEQ"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | 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 | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 48054 | 48054 | SRR7008006 | SRX3940581 | SRS3171382 | SRP140462 | PRJNA450341 | Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling | PRJNA450341 | Other | Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs. | MO26h rep1 | MO26h 1 | Sample3 | strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:fsd1morphants 1|BioSampleModel:Model organism or animal | RNA seq of fsd1 morphants1 | MO26h 1 | MO26h 1 | RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform. | RNA-Seq | TRANSCRIPTOMIC | PCR | SINGLE | BGISEQ | BGISEQ-500 | SRP140462 | MO26h_1_1.fq.gz | fastq | 1193983450.0 | 23879669.0 | MO26h 1 1.fq.gz | 0:50 | A:313344068;C:282899939;G:291404437;T:306051122;N:283884 | 50 | 313344068 | 282899939 | 291404437 | 306051122 | 283884 | SRX3940581 | SRS3171382 | SRA690964 | Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology | Institute of Zoology, CHINESE ACADEMY OF SCIENCES | 1 | 0.95658 | 0.07921 | 0.70307 | 0.47586 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2018-04-16 | Pharyngula | Embryo | Trunk | Surface Structure | ||||||||||||||||||||||||||
| 48055 | 48055 | SRR7008007 | SRX3940580 | SRS3171381 | SRP140462 | PRJNA450341 | Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling | PRJNA450341 | Other | Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs. | MO26h rep2 | MO26h 2 | Sample4 | strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:fsd1morphants 2|BioSampleModel:Model organism or animal | RNA seq of fsd1 morphants2 | MO26h 2 | MO26h 2 | RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform. | RNA-Seq | TRANSCRIPTOMIC | PCR | SINGLE | BGISEQ | BGISEQ-500 | SRP140462 | MO26h_2_1.fq.gz | fastq | 1199524600.0 | 23990492.0 | MO26h 2 1.fq.gz | 0:50 | A:318726410;C:282721669;G:287606979;T:310182197;N:287345 | 50 | 318726410 | 282721669 | 287606979 | 310182197 | 287345 | SRX3940580 | SRS3171381 | SRA690964 | Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology | Institute of Zoology, CHINESE ACADEMY OF SCIENCES | 1 | 0.9541 | 0.08695 | 0.70404 | 0.47195 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2018-04-16 | Pharyngula | Embryo | Trunk | Surface Structure | ||||||||||||||||||||||||||
| 48056 | 48056 | SRR7008008 | SRX3940579 | SRS3171379 | SRP140462 | PRJNA450341 | Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling | PRJNA450341 | Other | Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs. | WT26h rep1 | WT26h 1 | Sample1 | strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:normal embryos 1|BioSampleModel:Model organism or animal | RNA seq of normal embryos1 | WT26h 1 | WT26h 1 | RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform. | RNA-Seq | TRANSCRIPTOMIC | PCR | SINGLE | BGISEQ | BGISEQ-500 | SRP140462 | WT26h_1_1.fq.gz | fastq | 1200268650.0 | 24005373.0 | WT26h 1 1.fq.gz | 0:50 | A:315743815;C:284447849;G:295772915;T:303964473;N:339598 | 50 | 315743815 | 284447849 | 295772915 | 303964473 | 339598 | SRX3940579 | SRS3171379 | SRA690964 | Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology | Institute of Zoology, CHINESE ACADEMY OF SCIENCES | 1 | 0.95659 | 0.07726 | 0.70425 | 0.47269 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2018-04-16 | Pharyngula | Embryo | Trunk | Surface Structure | ||||||||||||||||||||||||||
| 48057 | 48057 | SRR7008009 | SRX3940578 | SRS3171380 | SRP140462 | PRJNA450341 | Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling | PRJNA450341 | Other | Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs. | WT26h rep2 | WT26h 2 | Sample2 | strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:normal embryos 2|BioSampleModel:Model organism or animal | RNA seq of normal embryos2 | WT26h 2 | WT26h 2 | RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform. | RNA-Seq | TRANSCRIPTOMIC | PCR | SINGLE | BGISEQ | BGISEQ-500 | SRP140462 | WT26h_2_1.fq.gz | fastq | 1199179850.0 | 23983597.0 | WT26h 2 1.fq.gz | 0:50 | A:316605984;C:281184572;G:292581373;T:308419476;N:388445 | 50 | 316605984 | 281184572 | 292581373 | 308419476 | 388445 | SRX3940578 | SRS3171380 | SRA690964 | Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology | Institute of Zoology, CHINESE ACADEMY OF SCIENCES | 1 | 0.95377 | 0.08617 | 0.70508 | 0.4775 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2018-04-16 | Pharyngula | Embryo | Trunk | Surface Structure |
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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");;