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run_metadata

6 rows where experiment.library_selection = "unspecified", experiment.platform = "ILLUMINA" and tissue_curation_coarse = "Embryo Imprecise"

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tissue_curation_coarse 1

  • Embryo Imprecise · 6 ✖

tissue_curation 1

technology 1

experiment.platform 1

  • ILLUMINA · 6 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • unspecified · 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
66222 66222 SRR16148348 SRX12433220 SRS10400589 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 3 RNAseq Gli3 /   RNAseq Gli3KO 3   strain:Gli3 / ex5 3|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: Gli3 / EGFP cells 6 6 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 Gli3KO3_aligned.sorted.bam bam 5067915101.0 25431299.0 Gli3KO3 aligned.sorted.bam 0:99.63 1:99.65 A:1368455893;C:1172445678;G:1173478123;T:1353535407;N:0 99 99     1368455893 1172445678 1173478123 1353535407 0 SRX12433220 SRS10400589 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.95469 0.95749 0.09504 0.09606 0.73951 0.73963 0.54439 0.54442 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise
66223 66223 SRR16148349 SRX12433219 SRS10400587 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 2 RNAseq Gli3 /   RNAseq Gli3KO 2   strain:Gli3 / ex5 2|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: Gli3 / EGFP cells 5 5 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 V300059050_Gli3KO2_aligned.cordinatesort.bam bam 10961381631.0 54976705.0 V300059050 Gli3KO2 aligned.cordinatesort.bam 0:99.70 1:99.68 A:2988819475;C:2499700971;G:2467906402;T:3004531404;N:423379 99 99     2988819475 2499700971 2467906402 3004531404 423379 SRX12433219 SRS10400587 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.94015 0.9439 0.12356 0.12485 0.75315 0.75304 0.51072 0.50897 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise
66224 66224 SRR16148350 SRX12433218 SRS10400586 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 1 RNAseq Gli3 /   RNAseq Gli3KO 1   strain:Gli3 / ex5 1|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: Gli3 / EGFP cells 4 4 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 V300059050_Gli3KO1_aligned.cordinatesort.bam bam 10204176056.0 51177828.0 V300059050 Gli3KO1 aligned.cordinatesort.bam 0:99.68 1:99.71 A:2761524632;C:2342024573;G:2322758345;T:2777476126;N:392380 99 99     2761524632 2342024573 2322758345 2777476126 392380 SRX12433218 SRS10400586 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.94248 0.9466 0.11206 0.11246 0.73634 0.73582 0.50038 0.49971 100 91 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise
66225 66225 SRR16148351 SRX12433217 SRS10400585 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 3 RNAseq WT   RNAseq WT 3   strain:WT3|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: WT EGFP cells 3 3 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 Gli3WT3_aligned.sorted.bam bam 6055778800.0 30391313.0 Gli3WT3 aligned.sorted.bam 0:99.60 1:99.66 A:1632778751;C:1402895889;G:1402788250;T:1617315910;N:0 99 99     1632778751 1402895889 1402788250 1617315910 0 SRX12433217 SRS10400585 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.95971 0.96273 0.09206 0.09219 0.72458 0.72391 0.55162 0.55278 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise
66226 66226 SRR16148353 SRX12433215 SRS10400584 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 2 RNAseq WT   RNAseq WT 2   strain:WT2|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: WT EGFP cells 2 2 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 Gli3WT2_aligned.sorted.bam bam 6030526704.0 30274232.0 Gli3WT2 aligned.sorted.bam 0:99.58 1:99.62 A:1627670320;C:1395587022;G:1395639693;T:1611629669;N:0 99 99     1627670320 1395587022 1395639693 1611629669 0 SRX12433215 SRS10400584 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.95942 0.96186 0.08632 0.08652 0.72671 0.72732 0.53408 0.55623 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise
66227 66227 SRR16148354 SRX12433214 SRS10400582 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 1 RNAseq WT   RNAseq WT 1   strain:WT1|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: WT EGFP cells 1 1 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 V300059050_Gli3WT_aligned.cordinatesort.bam bam 8907848854.0 44671741.0 V300059050 Gli3WT aligned.cordinatesort.bam 0:99.68 1:99.73 A:2444869517;C:2007841709;G:1991672704;T:2463143463;N:321461 99 99     2444869517 2007841709 1991672704 2463143463 321461 SRX12433214 SRS10400582 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.94004 0.94329 0.13907 0.13978 0.74943 0.74897 0.507 0.5105 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise

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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");;