run_metadata: 15046
This data as json
| 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 |
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| 15046 | ERR594439 | ERX552410 | ERS539974 | ERP006866 | PRJEB7172 | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E-MTAB-2886 | Transcriptome Analysis | Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system. | Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | MM01 T | SAMEA2747166 | Iowa State University | ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | E MTAB 2886:McGrail T MM01 007 | MM01 T | Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. | Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP006866 | Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line | ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 | McGrail_T_MM01_007_R1.fastq.gz McGrail_T_MM01_007_R2.fastq.gz | fastq fastq | 3200000000.0 | 16000000.0 | E MTAB 2886:McGrail T MM01 007 R | 0:100 1:100 | A:850777874;C:752786693;G:741650641;T:854268527;N:516265 | 100 | 100 | 850777874 | 752786693 | 741650641 | 854268527 | 516265 | ERX552410 | ERS539974 | ERA356220 | Iowa State University | Iowa State University | 2 | 0.93398 | 0.93264 | 0.0917 | 0.09232 | 0.67878 | 0.68172 | 0.48311 | 0.48417 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2014-12-11 | Adult | Adult | Multi-tissue | Multi-system |