run_metadata
1 row where experiment.library_selection = "RANDOM PCR", technology = "unknown" and tissue_curation_coarse = "Cardiovascular System"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 44933 | 44933 | SRR6308291 | SRX3408681 | SRS2701477 | SRP125291 | PRJNA419036 | Danio rerio strain:ASWT Transcriptome or Gene expression | PRJNA419036 | Other | A genome wide map of circular RNA in adult zebrafish. | Zf heart | Zf heart | strain:ASWT|age:1year|sex:male|tissue:Heart|BioSampleModel:Model organism or animal | A genome wide map of circular RNA in adult zebrafish | Zf heart | Zf heart | Tissue were isolated from adult zebrafish anaesthetized using 0.004% Tricaine Sigma USA. Extreme care was taken to avoid contamination to obtain pure homogenous tissue samples. The tissues were repeatedly washed in PBS to remove contaminating debris. The tissue samples were homogenized in Trizol for cell lysis Invitrogen USA. RNA was isolated from the homogenized tissue samples using RNeasy kit Qiagen USA. Sample preparation for sequencing was carried out using Truseq stranded RNA sample preparation kit Illumina USA as per supplier's instructions. In order to remove the ribosomal RNA rRNA one microgram of total RNA was hybridised with Ribo zero gold rRNA removal probe. Upon removing rRNA the samples were processed for fragmentation in the presence of ionic cations at 37 degree Celcius. First stranded complementary DNA cDNA was prepared by random hexamers and superscript II reverse transcriptase Invitrogen USA in presence of Actinomycin D to facilitate RNA dependent synthesis for improving strand specificity. The second strand was synthesised with second strand cDNA mix containing dUTP instead of dTTP and subjected to A base addition followed by adapter ligation. Final libraries were prepared by amplifying adapter ligated double strand cDNA. Clusters were generated on Hiseq flow cell v3 Illumina in cBot according to standard protocol Illumina USA. | RNA-Seq | TRANSCRIPTOMIC | RANDOM PCR | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP125291 | loader:fastq load.py | Zf_heart_R1.fastq Zf_heart_R2.fastq | fastq fastq | 5118546291.0 | 51531220.0 | Zf heart R2.fastq | 0:99.33 | A:1442538320;C:1100438227;G:1124766301;T:1450751919;N:51524 | 99 | 1442538320 | 1100438227 | 1124766301 | 1450751919 | 51524 | SRX3408681 | SRS2701477 | SRA631861 | CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine | CSIR-Institute of Genomics and Integrative Biology | 1 | 0.84707 | 0.40863 | 0.69037 | 0.43672 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | ribozero | bulk | unknown | unknown | India | 2017-11-22 | 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");;