run_metadata
2 rows where experiment.library_selection = "unspecified" and experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 25302 | 25302 | SRR25793493 | SRX21515745 | SRS18742910 | SRP457465 | PRJNA1010662 | The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. | PRJNA1010662 | Other | Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation. | Single cell Pr1phros ADULT miR 144 mutant Danio rerio | miR 144 | isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal | Single cell Pr1phros ADULT miR 144 mutant Danio rerio | CD 144 1 | CD 144 1 | Single cell library cloning was done with 10X Genomics | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | unspecified | PAIRED | ILLUMINA | NextSeq 2000 | SRP457465 | CD_144_1_S3_R1.fastq CD_144_1_S3_R2.fastq | fastq fastq | 12899093774.0 | 108395746.0 | CD 144 1 S3 R1.fastq | 0:28 1:91 | A:3225260764;C:3211986177;G:3151471558;T:3308055659;N:2319616 | 28 | 91 | 3225260764 | 3211986177 | 3151471558 | 3308055659 | 2319616 | SRX21515745 | SRS18742910 | SRA1701829 | University of East Anglia|Biological Sciences | University of East Anglia | 2 | 0.00483 | 0.97382 | 0.00157 | 0.05913 | 0.99439 | 0.86815 | 0.46634 | 0.45907 | 28 | 91 | T | B | sc-like readlen | illumina | nextseq_v2 | unknown | unknown | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-08-30 | Adult | Adult | Blood | Hematopoietic System | ||||||||||||||||||||
| 25303 | 25303 | SRR25793494 | SRX21515744 | SRS18742909 | SRP457465 | PRJNA1010662 | The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. | PRJNA1010662 | Other | Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation. | Single cell Pr1phros ADULT Wild type Danio rerio | WT | isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal | Single cell Pr1phros ADULT Wild type Danio rerio | CD wt 1 | CD wt 1 | Single cell library cloning was done with 10X Genomics | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | unspecified | PAIRED | ILLUMINA | NextSeq 2000 | SRP457465 | CD_wt_1_S2_R1.fastq CD_wt_1_S2_R2.fastq | fastq fastq | 12715533299.0 | 106853221.0 | CD wt 1 S2 R1.fastq | 0:28 1:91 | A:3324705878;C:3042843364;G:3105568183;T:3240105528;N:2310346 | 28 | 91 | 3324705878 | 3042843364 | 3105568183 | 3240105528 | 2310346 | SRX21515744 | SRS18742909 | SRA1701829 | University of East Anglia|Biological Sciences | University of East Anglia | 2 | 0.00593 | 0.93177 | 0.00191 | 0.09596 | 0.99257 | 0.84394 | 0.42447 | 0.4869 | 28 | 91 | T | B | sc-like readlen | illumina | nextseq_v2 | unknown | unknown | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-08-30 | Adult | Adult | Blood | Hematopoietic 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");;