run_metadata
3 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "indrops" and tissue_curation_coarse = "Renal System"
This data as json, CSV (advanced)
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 74455 | 74455 | SRR23804140 | SRX19635460 | SRS17004492 | SRP426651 | PRJNA943248 | Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney] | GSE227115 | Transcriptome Analysis | We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected homogenized filtered and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing. | parent bioproject:PRJNA510836 | kdrl:GFP+ adult kidney | GSM7091842 | source name:kdrl:GFP transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney | kdrl:GFP+ adult kidney | the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode | kdrl:GFP transgenic zebrafish adult kidney wild type | No treatments | Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops | Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer. Adult kidneys were dissected then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells. | developmental stage:adult|genotype:wild type|tissue:kidney | GSM7091842 | GSM7091842: kdrl:GFP+ adult kidney; Danio rerio; RNA Seq | GSM7091842 r1 | GSM7091842 | 1 | Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP426651 | FLK-G_Single_Cell_ACTCTAGG.fastq.sorted.fastq.gz | fastq | 10648313404.0 | 80407702.0 | GSM7091842 r1 | 0:132.43 | A:3393628100;C:2087372845;G:1953079760;T:3213786135;N:446564 | 132 | 3393628100 | 2087372845 | 1953079760 | 3213786135 | 446564 | SRX19635460 | SRS17004492 | Oncology/Hematology, Boston Children's Hospital | 1 | 0.60891 | 0.10525 | 0.81903 | 0.52577 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | indrops | United States | 2023-03-10 | Adult | Adult | Kidney | Renal System | |||||||||||||||||||
| 74456 | 74456 | SRR23804141 | SRX19635459 | SRS17004491 | SRP426651 | PRJNA943248 | Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney] | GSE227115 | Transcriptome Analysis | We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected homogenized filtered and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing. | parent bioproject:PRJNA510836 | kdrl:mCherry+ adult kidney rep2 | GSM7091841 | source name:kdrl:mCherry transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney | kdrl:mCherry+ adult kidney rep2 | the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode | kdrl:mCherry transgenic zebrafish adult kidney wild type | No treatments | Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops | Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer. Adult kidneys were dissected then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells. | developmental stage:adult|genotype:wild type|tissue:kidney | GSM7091841 | GSM7091841: kdrl:mCherry+ adult kidney rep2; Danio rerio; RNA Seq | GSM7091841 r1 | GSM7091841 | 1 | Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP426651 | FLK-R_Single_Cell_CTAGTCGA.fastq.sorted.fastq.gz | fastq | 13922952441.0 | 105098464.0 | GSM7091841 r1 | 0:132.48 | A:4341235438;C:2807868369;G:2579519980;T:4193742000;N:586654 | 132 | 4341235438 | 2807868369 | 2579519980 | 4193742000 | 586654 | SRX19635459 | SRS17004491 | Oncology/Hematology, Boston Children's Hospital | 1 | 0.64512 | 0.12315 | 0.81712 | 0.52922 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | indrops | United States | 2023-03-10 | Adult | Adult | Kidney | Renal System | |||||||||||||||||||
| 74457 | 74457 | SRR23804142 | SRX19635458 | SRS17004490 | SRP426651 | PRJNA943248 | Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney] | GSE227115 | Transcriptome Analysis | We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected homogenized filtered and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing. | parent bioproject:PRJNA510836 | kdrl:mCherry+ adult kidney rep1 | GSM7091840 | source name:kdrl:mCherry transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney | kdrl:mCherry+ adult kidney rep1 | the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode | kdrl:mCherry transgenic zebrafish adult kidney wild type | No treatments | Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops | Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer. Adult kidneys were dissected then homogenized filtered and sorted using FACS into PBS collecting at least 25 000 cells. | developmental stage:adult|genotype:wild type|tissue:kidney | GSM7091840 | GSM7091840: kdrl:mCherry+ adult kidney rep1; Danio rerio; RNA Seq | GSM7091840 r1 | GSM7091840 | 1 | Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP426651 | KLR_Single_Cell_ATTAGACG.fastq.sorted.fastq.gz | fastq | 8774502682.0 | 64692571.0 | GSM7091840 r1 | 0:135.63 | A:2791773089;C:1725088037;G:1633088372;T:2624197073;N:356111 | 135 | 2791773089 | 1725088037 | 1633088372 | 2624197073 | 356111 | SRX19635458 | SRS17004490 | Oncology/Hematology, Boston Children's Hospital | 1 | 0.66981 | 0.10372 | 0.81357 | 0.5394 | 38 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | indrops | United States | 2023-03-10 | Adult | Adult | Kidney | Renal System |
Advanced export
JSON shape: default, array, newline-delimited
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");;