run_metadata: 48781
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 48781 | SRR7299198 | SRX4201632 | SRS3411866 | SRP150379 | PRJNA475808 | Transcriptome analysis of wildtype and rb1 / zebrafish larval head tissue by RNA Seq | GSE115720 | Transcriptome Analysis | The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1 embryonal brain tumor transcriptome to identify molecular pathways that distinguish transformed rb1 tumor cells from non transformed rb1 / mutant cells. Overall design: 3 pools of 5 zebrafish 5 dpf larval heads were used to prepare 3 wild type +/+ and 3 rb1 / homozygous mutant barcoded indexed RNA Seq libraries. | parent bioproject:PRJNA475805 | pubmed:29914980 | WT1a | GSM3188314 | source name:Wildtype head|strain/background:WIK|genotype/variation:wildtype +/+|age:5 dpf larva|tissue:5 pooled dissected heads | WT1a | Reads were aligned to the GRCz10 zebrafish reference genome using GSNAP version 20150723 with the following parameters “ N 1 t 8 B 4 m 5 A sam split output”. Count data was generated from HT Seq. Differential gene expression analysis was conducted using DESeq2. FPKM was calculated using the following equation: FPKM = 10^9 x Number of mapped reads to a gene/Gene exonic length x Total mapped reads in the experiment. Genome build: GRCz10 using GMAP. Supplementary files format and content: Mutant raw count.txt: Tab delimited text file includes raw expression values. Supplementary files format and content: Mutant FPKM.txt: Tab delimited text file includes normalized expression values. Supplementary files format and content: Mutant DGE.txt: Tab delimited text file includes differential gene expression statistics. | Wildtype head | Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA. | strain/background:WIK|genotype/variation:wildtype +/+|age:5 dpf larva|tissue:5 pooled dissected heads | GSM3188314 | GSM3188314: WT1a; Danio rerio; RNA Seq | GSM3188314 | 1 | Dissected zebrafish larval head tissue was used for total RNA isolation with TRIzol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used for library preparation starting with 1ug total RNA. | GEO Accession:GSM3188314 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP150379 | 1_WT_ACAGTG_L001_R1_001.fastq.gz | fastq | 1538497671.0 | 30166621.0 | GSM3188314 r1 | 0:51 1:0 | A:400221457;C:372214397;G:362764636;T:403260458;N:36723 | 51 | 0 | 400221457 | 372214397 | 362764636 | 403260458 | 36723 | SRX4201632 | SRS3411866 | SRA720942 | GEO | Maura McGrail, GDCB, Iowa State University | 1 | 0.91885 | 0.09093 | 0.65529 | 0.45611 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2018-06-12 | Larval | Larval | Head | Nervous System |