run_metadata
3 rows where devstage_curation_coarse = "Multi-stage" and tissue_curation = "Cancer or Tumor"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 71533 | 71533 | SRR21659014 | SRX17658778 | SRS15191045 | SRP398439 | PRJNA882818 | Defining function of wild type and three patient specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma | GSE213869 | Transcriptome Analysis | RNAseq analyses comparing gene expression in zebrafish embryonal rhabdomyosarcoma tumors expressing kRASG12D/tp53 / /GFP or /kRASG12Dtp53 / + TP53 P153?/GFP Overall design: The RNAseq samples being submitted are of zebrafish embryonal rhabdomyosarcoma tumors generated in th CG1 syngeneic background expressing kRASG12D/tp53 / /GFP and /kRASG12Dtp53 / + TP53 P153?/GFP | pubmed:37266578 | ProDel3 c | GSM6595573 | source name:rhabdomyosarcoma tumors in zebrafish|tissue:zebrafish|geo loc name:missing|collection date:missing | ProDel3 c | Illumina Casava v1.8.2 software used for base calling All RNA seq FastQ reads were aligned with the reference genome danRer11 using TopHat2 default settings. The aligned BAM files sorted SAMTools and then processed using HTSeq count to obtain the counts per gene gene count measurements were obtained using HTSeq count Assembly: danRer11 Supplementary files format and content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq count. | rhabdomyosarcoma tumors in zebrafish | post tissue grinding and homogenization in RNA lysis buffer total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia CA according to the manufacturer’s recommendation. post quantification with Nanodrop Thermo Scientific; Rockford IL RNA was stored at 80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit | For expression of mutant human TP53 experiments tumors were generated by injecting XhoI linearized rag2 kRASG12D and rag2 GFP along with Xmn1 linearized rag2 TP53 P153△ 35 ng/ml of rag2 kRASG12D 15 ng/ml rag2 GFP or mutant TP53 and 10 ng/ml of rag2 GFP into the one cell stage of syngeneic zebrafish CG1/tp53 / embryos <1 hpf Ignatius et al. 2012. Animals were monitored for tumor onset beginning at 10 dpf by scoring for GFP fluorescence under an Olympus MVX10 stereomicroscope with an X Cite series 120Q fluorescence illuminator. Scoring for tumor initiation was conducted for 60 days. 3 tumors each expressing kRASG12D/GFP/tp53 / or kRASG12D/GFP/tp53 / +TP53 P153△ were transplanted into secondary CG1 recipients and engrafted tumors were isolated prepared as single cell suspensions and sorted by flowcytometry. Tumor cells were then processed to isolate RNA which was then submitted for RNAseq analyses Ignatius et al. 2012. | tissue:zebrafish|tp53 / + TP53 P153△ | GSM6595573 | GSM6595573: ProDel3 c; Danio rerio; RNA Seq | GSM6595573 r1 | GSM6595573 | 1 | post tissue grinding and homogenization in RNA lysis buffer total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia CA according to the manufacturer's recommendation. post quantification with Nanodrop Thermo Scientific; Rockford IL RNA was stored at 80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | SRP398439 | ProDel3_c_S41_R1.fastq | fastq | 1583531283.0 | 31049633.0 | GSM6595573 r1 | 0:51 1:0 | A:371274884;C:377726847;G:377321846;T:456738328;N:469378 | 51 | 0 | 371274884 | 377726847 | 377321846 | 456738328 | 469378 | SRX17658778 | SRS15191045 | SRA1503133 | Population Health Sciences, UT Health Science Center at San Antonio | Population Health Sciences, UT Health Science Center at San Antonio | 1 | 0.9215 | 0.08584 | 0.73028 | 0.52093 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2022-09-21 | Multi-stage | Multi-stage | Cancer or Tumor | Cancer or Tumor | |||||||||||||||||
| 71534 | 71534 | SRR21659015 | SRX17658777 | SRS15191044 | SRP398439 | PRJNA882818 | Defining function of wild type and three patient specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma | GSE213869 | Transcriptome Analysis | RNAseq analyses comparing gene expression in zebrafish embryonal rhabdomyosarcoma tumors expressing kRASG12D/tp53 / /GFP or /kRASG12Dtp53 / + TP53 P153?/GFP Overall design: The RNAseq samples being submitted are of zebrafish embryonal rhabdomyosarcoma tumors generated in th CG1 syngeneic background expressing kRASG12D/tp53 / /GFP and /kRASG12Dtp53 / + TP53 P153?/GFP | pubmed:37266578 | ProDel2 b | GSM6595572 | source name:rhabdomyosarcoma tumors in zebrafish|tissue:zebrafish|geo loc name:missing|collection date:missing | ProDel2 b | Illumina Casava v1.8.2 software used for base calling All RNA seq FastQ reads were aligned with the reference genome danRer11 using TopHat2 default settings. The aligned BAM files sorted SAMTools and then processed using HTSeq count to obtain the counts per gene gene count measurements were obtained using HTSeq count Assembly: danRer11 Supplementary files format and content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq count. | rhabdomyosarcoma tumors in zebrafish | post tissue grinding and homogenization in RNA lysis buffer total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia CA according to the manufacturer’s recommendation. post quantification with Nanodrop Thermo Scientific; Rockford IL RNA was stored at 80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit | For expression of mutant human TP53 experiments tumors were generated by injecting XhoI linearized rag2 kRASG12D and rag2 GFP along with Xmn1 linearized rag2 TP53 P153△ 35 ng/ml of rag2 kRASG12D 15 ng/ml rag2 GFP or mutant TP53 and 10 ng/ml of rag2 GFP into the one cell stage of syngeneic zebrafish CG1/tp53 / embryos <1 hpf Ignatius et al. 2012. Animals were monitored for tumor onset beginning at 10 dpf by scoring for GFP fluorescence under an Olympus MVX10 stereomicroscope with an X Cite series 120Q fluorescence illuminator. Scoring for tumor initiation was conducted for 60 days. 3 tumors each expressing kRASG12D/GFP/tp53 / or kRASG12D/GFP/tp53 / +TP53 P153△ were transplanted into secondary CG1 recipients and engrafted tumors were isolated prepared as single cell suspensions and sorted by flowcytometry. Tumor cells were then processed to isolate RNA which was then submitted for RNAseq analyses Ignatius et al. 2012. | tissue:zebrafish|tp53 / + TP53 P153△ | GSM6595572 | GSM6595572: ProDel2 b; Danio rerio; RNA Seq | GSM6595572 r1 | GSM6595572 | 1 | post tissue grinding and homogenization in RNA lysis buffer total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia CA according to the manufacturer's recommendation. post quantification with Nanodrop Thermo Scientific; Rockford IL RNA was stored at 80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | SRP398439 | ProDel2_b_S44_R1.fastq | fastq | 2345978580.0 | 45999580.0 | GSM6595572 r1 | 0:51 1:0 | A:552533223;C:559993030;G:552168331;T:680585870;N:698126 | 51 | 0 | 552533223 | 559993030 | 552168331 | 680585870 | 698126 | SRX17658777 | SRS15191044 | SRA1503133 | Population Health Sciences, UT Health Science Center at San Antonio | Population Health Sciences, UT Health Science Center at San Antonio | 1 | 0.92533 | 0.088 | 0.72894 | 0.52635 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2022-09-21 | Multi-stage | Multi-stage | Cancer or Tumor | Cancer or Tumor | |||||||||||||||||
| 71535 | 71535 | SRR21659016 | SRX17658776 | SRS15191043 | SRP398439 | PRJNA882818 | Defining function of wild type and three patient specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma | GSE213869 | Transcriptome Analysis | RNAseq analyses comparing gene expression in zebrafish embryonal rhabdomyosarcoma tumors expressing kRASG12D/tp53 / /GFP or /kRASG12Dtp53 / + TP53 P153?/GFP Overall design: The RNAseq samples being submitted are of zebrafish embryonal rhabdomyosarcoma tumors generated in th CG1 syngeneic background expressing kRASG12D/tp53 / /GFP and /kRASG12Dtp53 / + TP53 P153?/GFP | pubmed:37266578 | ProDel1 a | GSM6595571 | source name:rhabdomyosarcoma tumors in zebrafish|tissue:zebrafish|geo loc name:missing|collection date:missing | ProDel1 a | Illumina Casava v1.8.2 software used for base calling All RNA seq FastQ reads were aligned with the reference genome danRer11 using TopHat2 default settings. The aligned BAM files sorted SAMTools and then processed using HTSeq count to obtain the counts per gene gene count measurements were obtained using HTSeq count Assembly: danRer11 Supplementary files format and content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq count. | rhabdomyosarcoma tumors in zebrafish | post tissue grinding and homogenization in RNA lysis buffer total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia CA according to the manufacturer’s recommendation. post quantification with Nanodrop Thermo Scientific; Rockford IL RNA was stored at 80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit | For expression of mutant human TP53 experiments tumors were generated by injecting XhoI linearized rag2 kRASG12D and rag2 GFP along with Xmn1 linearized rag2 TP53 P153△ 35 ng/ml of rag2 kRASG12D 15 ng/ml rag2 GFP or mutant TP53 and 10 ng/ml of rag2 GFP into the one cell stage of syngeneic zebrafish CG1/tp53 / embryos <1 hpf Ignatius et al. 2012. Animals were monitored for tumor onset beginning at 10 dpf by scoring for GFP fluorescence under an Olympus MVX10 stereomicroscope with an X Cite series 120Q fluorescence illuminator. Scoring for tumor initiation was conducted for 60 days. 3 tumors each expressing kRASG12D/GFP/tp53 / or kRASG12D/GFP/tp53 / +TP53 P153△ were transplanted into secondary CG1 recipients and engrafted tumors were isolated prepared as single cell suspensions and sorted by flowcytometry. Tumor cells were then processed to isolate RNA which was then submitted for RNAseq analyses Ignatius et al. 2012. | tissue:zebrafish|tp53 / + TP53 P153△ | GSM6595571 | GSM6595571: ProDel1 a; Danio rerio; RNA Seq | GSM6595571 r1 | GSM6595571 | 1 | post tissue grinding and homogenization in RNA lysis buffer total RNA was isolated from harvested tumors using the RNAeasy Kit Qiagen; Valencia CA according to the manufacturer's recommendation. post quantification with Nanodrop Thermo Scientific; Rockford IL RNA was stored at 80ºC. Total RNA was used for RNA Seq library preparation by following the KAPA Stranded RNA Seq Kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | SRP398439 | ProDel1_a_S39_R1.fastq | fastq | 1771640397.0 | 34738047.0 | GSM6595571 r1 | 0:51 1:0 | A:416983341;C:417769921;G:421189840;T:515172446;N:524849 | 51 | 0 | 416983341 | 417769921 | 421189840 | 515172446 | 524849 | SRX17658776 | SRS15191043 | SRA1503133 | Population Health Sciences, UT Health Science Center at San Antonio | Population Health Sciences, UT Health Science Center at San Antonio | 1 | 0.91616 | 0.08481 | 0.70435 | 0.51658 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2022-09-21 | Multi-stage | Multi-stage | Cancer or Tumor | Cancer or Tumor |
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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");;