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run_metadata

6 rows where experiment.library_selection = "RT-PCR", experiment.library_strategy = "RNA-Seq" and tissue_curation_coarse = "Adipose Tissue"

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tissue_curation_coarse 1

  • Adipose Tissue · 6 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 6 ✖

experiment.library_source 1

experiment.library_selection 1

  • RT-PCR · 6 ✖

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

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
66302 66302 SRR16292398 SRX12571558 SRS10528531 SRP340859 PRJNA770361 Transcriptome analysis of scd5 homologous deficiency zebrafish PRJNA770361 Other Detection of expression changes in zebrafish visceral adipose and subcutaneous adipose tissue transcriptome under homologous deficiency of scd5 and dietary supplement of w3 PUFA.         scd5+DE SAT   strain:scd5 / |isolate:dietary supplement of DHA and EPA|dev stage:4mpf|sex:male|tissue:Subcutaneous adipose tissue|BioSampleModel:Model organism or animal                 RNA seq of scd5 / Danio rario with diet of PUFA: adult male SAT scd5 3 M scd5 3 M RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP340859     scd3_M.R1.fastq.gz scd3_M.R2.fastq.gz fastq fastq 6745182684.0 22335042.0 scd3 M.R1.fastq.gz 0:151 1:151 A:1765346125;C:1595704052;G:1623853268;T:1760176500;N:102739 151 151     1765346125 1595704052 1623853268 1760176500 102739 SRX12571558 SRS10528531     Children's Hospital of Fudan University 2 0.93913 0.93015 0.06513 0.06469 0.63631 0.63824 0.48153 0.48017 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   China 2021-10-11 Adult Adult Adipose Tissue Adipose Tissue
66303 66303 SRR16292399 SRX12571557 SRS10528530 SRP340859 PRJNA770361 Transcriptome analysis of scd5 homologous deficiency zebrafish PRJNA770361 Other Detection of expression changes in zebrafish visceral adipose and subcutaneous adipose tissue transcriptome under homologous deficiency of scd5 and dietary supplement of w3 PUFA.         scd5 SAT   strain:scd5 / |dev stage:4mpf|sex:male|tissue:Subcutaneous adipose tissue|BioSampleModel:Model organism or animal                 RNA seq of scd5 / Danio rario: adult male SAT scd5 0 M scd5 0 M RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP340859     scd0_M.R1.fastq.gz scd0_M.R2.fastq.gz fastq fastq 6609239196.0 21884898.0 scd0 M.R1.fastq.gz 0:151 1:151 A:1727886993;C:1565529312;G:1593133073;T:1722589181;N:100637 151 151     1727886993 1565529312 1593133073 1722589181 100637 SRX12571557 SRS10528530     Children's Hospital of Fudan University 2 0.93103 0.92201 0.05665 0.05579 0.63731 0.63875 0.47603 0.48482 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   China 2021-10-11 Adult Adult Adipose Tissue Adipose Tissue
66304 66304 SRR16292400 SRX12571556 SRS10528529 SRP340859 PRJNA770361 Transcriptome analysis of scd5 homologous deficiency zebrafish PRJNA770361 Other Detection of expression changes in zebrafish visceral adipose and subcutaneous adipose tissue transcriptome under homologous deficiency of scd5 and dietary supplement of w3 PUFA.         ab SAT   strain:ab|dev stage:4mpf|sex:male|tissue:Subcutaneous adipose tissue|BioSampleModel:Model organism or animal                 RNA seq of Danio rario: adult male SAT ab0 M ab0 M RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP340859     ab0_M.R1.fastq.gz ab0_M.R2.fastq.gz fastq fastq 6414355576.0 21239588.0 ab0 M.R1.fastq.gz 0:151 1:151 A:1686199414;C:1513903010;G:1536678772;T:1677477213;N:97167 151 151     1686199414 1513903010 1536678772 1677477213 97167 SRX12571556 SRS10528529     Children's Hospital of Fudan University 2 0.94035 0.93293 0.0647 0.06386 0.6323 0.63341 0.48645 0.48681 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   China 2021-10-11 Adult Adult Adipose Tissue Adipose Tissue
66305 66305 SRR16292401 SRX12571555 SRS10528528 SRP340859 PRJNA770361 Transcriptome analysis of scd5 homologous deficiency zebrafish PRJNA770361 Other Detection of expression changes in zebrafish visceral adipose and subcutaneous adipose tissue transcriptome under homologous deficiency of scd5 and dietary supplement of w3 PUFA.         scd5+DE VAT   strain:scd5 / |isolate:dietary supplement of DHA and EPA|dev stage:4mpf|sex:male|tissue:visceral adipose tissue|BioSampleModel:Model organism or animal                 RNA seq of scd5 / Danio rario with diet of PUFA: adult male VAT scd5 3 L scd5 3 L RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP340859     scd3_L.R1.fastq.gz scd3_L.R2.fastq.gz fastq fastq 6489926244.0 21489822.0 scd3 L.R1.fastq.gz 0:151 1:151 A:1673067907;C:1553308451;G:1582201247;T:1681249645;N:98994 151 151     1673067907 1553308451 1582201247 1681249645 98994 SRX12571555 SRS10528528     Children's Hospital of Fudan University 2 0.94228 0.93373 0.02579 0.02582 0.71047 0.71173 0.50387 0.50723 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   China 2021-10-11 Adult Adult Adipose Tissue Adipose Tissue
66306 66306 SRR16292402 SRX12571554 SRS10528527 SRP340859 PRJNA770361 Transcriptome analysis of scd5 homologous deficiency zebrafish PRJNA770361 Other Detection of expression changes in zebrafish visceral adipose and subcutaneous adipose tissue transcriptome under homologous deficiency of scd5 and dietary supplement of w3 PUFA.         scd5 VAT   strain:scd5 / |dev stage:4mpf|sex:male|tissue:visceral adipose tissue|BioSampleModel:Model organism or animal                 RNA seq of scd5 / Danio rario: adult male VAT scd5 0 L scd5 0 L RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP340859     scd0_L.R1.fastq.gz scd0_L.R2.fastq.gz fastq fastq 6940147542.0 22980621.0 scd0 L.R1.fastq.gz 0:151 1:151 A:1777349154;C:1663070037;G:1697971696;T:1801650476;N:106179 151 151     1777349154 1663070037 1697971696 1801650476 106179 SRX12571554 SRS10528527     Children's Hospital of Fudan University 2 0.94273 0.93332 0.03159 0.03113 0.76753 0.76887 0.56506 0.56717 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   China 2021-10-11 Adult Adult Adipose Tissue Adipose Tissue
66307 66307 SRR16292403 SRX12571553 SRS10528526 SRP340859 PRJNA770361 Transcriptome analysis of scd5 homologous deficiency zebrafish PRJNA770361 Other Detection of expression changes in zebrafish visceral adipose and subcutaneous adipose tissue transcriptome under homologous deficiency of scd5 and dietary supplement of w3 PUFA.         ab VAT   strain:ab|dev stage:4mpf|sex:male|tissue:visceral adipose tissue|BioSampleModel:Model organism or animal                 RNA seq of Danio rario: adult male VAT ab0 L ab0 L RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 4000   SRP340859     ab0_L.R1.fastq.gz ab0_L.R2.fastq.gz fastq fastq 7008737782.0 23207741.0 ab0 L.R1.fastq.gz 0:151 1:151 A:1798749961;C:1683894187;G:1713651140;T:1812336087;N:106407 151 151     1798749961 1683894187 1713651140 1812336087 106407 SRX12571553 SRS10528526     Children's Hospital of Fudan University 2 0.94465 0.9362 0.02302 0.02266 0.7119 0.71238 0.47109 0.4709 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   China 2021-10-11 Adult Adult Adipose Tissue Adipose Tissue

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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");;