run_metadata
4 rows where experiment.platform = "DNBSEQ", technology = "10x" and tissue_curation = "Spinal Cord"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 71409 | 71409 | SRR21590947 | SRX17592668 | SRS15130333 | SRP397443 | PRJNA880627 | Single cell sequencing of WT and hb egfaKO zebrafish spinal cord at 1 week post sham or transection injury. | GSE213435 | Transcriptome Analysis | We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total WT 1 wpi WT sham hb egfaKO 1 wpi hb egfaKO sham. | pubmed:37567873 | danRer11 WT 7dpi | GSM6586115 | source name:spinal cord|genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi|geo loc name:missing|collection date:missing | danRer11 WT 7dpi | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table | spinal cord | Samples were processed following the 10X Chromium platform following the manufacturer’s guidelines using 10X Single Cell 3’ v3 chemistry 10X Genomics Pleasanton USA. | genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi | GSM6586115 | GSM6586115: danRer11 WT 7dpi; Danio rerio; RNA Seq | GSM6586115 r1 | GSM6586115 | 1 | Samples were processed following the 10X Chromium platform following the manufacturer's guidelines using 10X Single Cell three prime v3 chemistry 10X Genomics Pleasanton USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP397443 | KP_VC_sample4_S1_L001_R2_001.fastq.gz KP_VC_sample4_S1_L001_R1_001.fastq.gz | fastq fastq | 50454681480.0 | 423988920.0 | GSM6586115 r1 | 0:28 1:91 | A:14159328348;C:10820572193;G:11486998159;T:13985883249;N:1899531 | 28 | 91 | 14159328348 | 10820572193 | 11486998159 | 13985883249 | 1899531 | SRX17592668 | SRS15130333 | SRA1500311 | Cell biology, Duke University | Poss, Cell Biology, Duke University | 2 | 0.00753 | 0.88935 | 0.00224 | 0.18283 | 0.98528 | 0.77656 | 0.24704 | 0.5609 | 28 | 91 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2022-09-15 | Adult | Adult | Spinal Cord | Nervous System | ||||||||||||
| 71410 | 71410 | SRR21590948 | SRX17592667 | SRS15130332 | SRP397443 | PRJNA880627 | Single cell sequencing of WT and hb egfaKO zebrafish spinal cord at 1 week post sham or transection injury. | GSE213435 | Transcriptome Analysis | We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total WT 1 wpi WT sham hb egfaKO 1 wpi hb egfaKO sham. | pubmed:37567873 | danRer11 WT sham | GSM6586114 | source name:spinal cord|genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham|geo loc name:missing|collection date:missing | danRer11 WT sham | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table | spinal cord | Samples were processed following the 10X Chromium platform following the manufacturer’s guidelines using 10X Single Cell 3’ v3 chemistry 10X Genomics Pleasanton USA. | genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham | GSM6586114 | GSM6586114: danRer11 WT sham; Danio rerio; RNA Seq | GSM6586114 r1 | GSM6586114 | 1 | Samples were processed following the 10X Chromium platform following the manufacturer's guidelines using 10X Single Cell three prime v3 chemistry 10X Genomics Pleasanton USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP397443 | KP_VC_sample3_S1_L001_R1_001.fastq.gz KP_VC_sample3_S1_L001_R2_001.fastq.gz | fastq fastq | 49434606578.0 | 415416862.0 | GSM6586114 r1 | 0:28 1:91 | A:13689985840;C:10750469002;G:11165716773;T:13825714788;N:2720175 | 28 | 91 | 13689985840 | 10750469002 | 11165716773 | 13825714788 | 2720175 | SRX17592667 | SRS15130332 | SRA1500311 | Cell biology, Duke University | Poss, Cell Biology, Duke University | 2 | 0.01019 | 0.90181 | 0.00309 | 0.16838 | 0.98522 | 0.78459 | 0.27523 | 0.51926 | 28 | 91 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2022-09-15 | Adult | Adult | Spinal Cord | Nervous System | ||||||||||||
| 71411 | 71411 | SRR21590949 | SRX17592666 | SRS15130331 | SRP397443 | PRJNA880627 | Single cell sequencing of WT and hb egfaKO zebrafish spinal cord at 1 week post sham or transection injury. | GSE213435 | Transcriptome Analysis | We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total WT 1 wpi WT sham hb egfaKO 1 wpi hb egfaKO sham. | pubmed:37567873 | danRer11 hbegfaKO 7dpi | GSM6586113 | source name:spinal cord|genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi|geo loc name:missing|collection date:missing | danRer11 hbegfaKO 7dpi | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table | spinal cord | Samples were processed following the 10X Chromium platform following the manufacturer’s guidelines using 10X Single Cell 3’ v3 chemistry 10X Genomics Pleasanton USA. | genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi | GSM6586113 | GSM6586113: danRer11 hbegfaKO 7dpi; Danio rerio; RNA Seq | GSM6586113 r1 | GSM6586113 | 1 | Samples were processed following the 10X Chromium platform following the manufacturer's guidelines using 10X Single Cell three prime v3 chemistry 10X Genomics Pleasanton USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP397443 | KP_VC_sample2_S1_L001_R1_001.fastq.gz KP_VC_sample2_S1_L001_R2_001.fastq.gz | fastq fastq | 48346471411.0 | 406272869.0 | GSM6586113 r1 | 0:28 1:91 | A:13278513523;C:10826562396;G:11318717473;T:12918171753;N:4506266 | 28 | 91 | 13278513523 | 10826562396 | 11318717473 | 12918171753 | 4506266 | SRX17592666 | SRS15130331 | SRA1500311 | Cell biology, Duke University | Poss, Cell Biology, Duke University | 2 | 0.01379 | 0.89003 | 0.00446 | 0.1909 | 0.97808 | 0.78415 | 0.32888 | 0.6007 | 28 | 91 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2022-09-15 | Adult | Adult | Spinal Cord | Nervous System | ||||||||||||
| 71412 | 71412 | SRR21590950 | SRX17592665 | SRS15130330 | SRP397443 | PRJNA880627 | Single cell sequencing of WT and hb egfaKO zebrafish spinal cord at 1 week post sham or transection injury. | GSE213435 | Transcriptome Analysis | We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total WT 1 wpi WT sham hb egfaKO 1 wpi hb egfaKO sham. | pubmed:37567873 | danRer11 hbegfaKO sham | GSM6586112 | source name:spinal cord|genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham|geo loc name:missing|collection date:missing | danRer11 hbegfaKO sham | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table | spinal cord | Samples were processed following the 10X Chromium platform following the manufacturer’s guidelines using 10X Single Cell 3’ v3 chemistry 10X Genomics Pleasanton USA. | genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham | GSM6586112 | GSM6586112: danRer11 hbegfaKO sham; Danio rerio; RNA Seq | GSM6586112 r1 | GSM6586112 | 1 | Samples were processed following the 10X Chromium platform following the manufacturer's guidelines using 10X Single Cell three prime v3 chemistry 10X Genomics Pleasanton USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | DNBSEQ | DNBSEQ-G400 | SRP397443 | KP_VC_sample1_S1_L001_R1_001.fastq.gz KP_VC_sample1_S1_L001_R2_001.fastq.gz | fastq fastq | 50009919813.0 | 420251427.0 | GSM6586112 r1 | 0:28 1:91 | A:13721824199;C:11296818044;G:11807686254;T:13179637678;N:3953638 | 28 | 91 | 13721824199 | 11296818044 | 11807686254 | 13179637678 | 3953638 | SRX17592665 | SRS15130330 | SRA1500311 | Cell biology, Duke University | Poss, Cell Biology, Duke University | 2 | 0.01254 | 0.83945 | 0.00371 | 0.16358 | 0.98378 | 0.80728 | 0.25895 | 0.57907 | 28 | 91 | T | B | sc-like readlen | bgi | bgi | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2022-09-15 | Adult | Adult | Spinal Cord | Nervous 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");;