run_metadata: 39635
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 39635 | SRR1974165 | SRX994290 | SRS907736 | SRP057116 | PRJNA280983 | Danio rerio strain:CG2 Transcriptome or Gene expression | PRJNA280983 | Other | CG2 homozygous diploid zebrafish line. | Model organism or animal sample from Danio rerio CG2 | CG2 immune related tissues | strain:CG2|dev stage:adult|sex:not determined|tissue:kidney intestine gills and spleen|BioSampleModel:Model organism or animal | CG2 normalized RNA seq pooled kidney intestine gills and spleen | CG2 Normalized | CG2 | A single adult CG2 zebrafish was euthanized and the kidney intestine gills and spleen were dissected and combined for RNA extraction Trizol Life Technologies. RNA was prepared for sequencing with the TruSeq RNA kit Illumina and sequenced 2 x 100 bp paired end reads on a single lane of a HiSeq2000 Illumina.In an effort to detect rare transcripts a normalization procedure also was employed. Normalized cDNA was achieved with the MINT Universal cDNA synthesis and TRIMMER DIRECT cDNA normalization kits Evrogen which was then prepared for sequencing with the TruSeq DNA kit Illumina. Average insert size of 200 bps. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><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_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP057116 | 130508_I1089_FCC1VKUACXX_L1_NCSU-GSL-0099_2.fq.gz 130508_I1089_FCC1VKUACXX_L1_NCSU-GSL-0099_1.fq.gz | fastq fastq | 32265477800.0 | 161327389.0 | CG2 Normalized | 0:100 1:100 | A:9100821450;C:6628233467;G:7212252211;T:9279872090;N:44298582 | 100 | 100 | 9100821450 | 6628233467 | 7212252211 | 9279872090 | 44298582 | SRX994290 | SRS907736 | SRA258497 | North Carolina State University | North Carolina State University | 2 | 0.83842 | 0.78503 | 0.19412 | 0.17922 | 0.69704 | 0.71959 | 0.48624 | 0.4789 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | random_priming | trueseq | bulk | unknown | unknown | United States | 2015-04-18 | Adult | Adult | Multi-tissue | Multi-system |