run_metadata: 41601
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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| 41601 | SRR5084079 | SRX2401782 | SRS1841770 | SRP094690 | PRJNA356508 | Ikk2 regulates cytokinesis during vertebrate development Trancriptome profiling from the wild type and Ikk2 maternal zygotic mutant zebrafish | GSE90971 | Transcriptome Analysis | Purpose: The Ikk2 maternal zygotic mutants are the only vertebrates animals completely depleted globally of the Ikk2 function which is expected to block an activity of the canonical NFkB signaling pathway. Transcriptome profiling of embryos before the midblastula transition MBT and post MBT may provide a clean strategy to identify the NFkB target genes. Methods: Zebrafish lines were maintained under standard laboratory procedures. Results: Using an optimized data analysis workflow we identified 54 276 transcripts in the embryos at 2 hpf and 4 hpf. RNA seq data confirmed lack of expression of a number of genes in the mutant both prior to and post the MBT including genes linked to angiogenesis skin development cytokinesis innate immunity and cytoskeletonT and 4 of these were validated with qRT–PCR. M. add here if required. Conclusions: Our study represents the first detailed analysis of transcriptomes of vertebrates globally depleted of activity of Ikk2 with two biologic replicates generated by RNA seq technology.The data reported here should provide a framework for understanding of maternal and zygotic genes which expression is controlled by Ikk2 activity. Our results expands a list of transcripts which expression may be controlled by the canonical NFkB signaling. We conclude that RNA seq based transcriptome characterization improves analysis of NFkB regulated genes. Overall design: Zebrafish Ikk2 mutants were obtained using zinc finger nuclease mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2. | pubmed:28808254 | Ikk2 2h | GSM2418528 | source name:whole embryo|strain:AB|tissue:whole embryo|genotype/variation:ikk2 / | Ikk2 2h | Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome with ensembl annotation 71 using tophat v2.0.9 Mapped reads fragments per kilobase of transcript per million FPKM was calculated and normalized using cuffdiff Cufflinks v2.1.1 with default parameters. Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample ... | whole embryo | No treatment. | Embryos were flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols | Zebrafish Ikk2 mutants were obtained using zinc finger nuclease mediated mutagenesis. Some of the mutant homozygotic embryos grow into fertile adults able to produce embryos totally deplated of maternal and zygotic Ikk2. | strain:AB|tissue:whole embryo|genotype/variation:ikk2 / | GSM2418528 | GSM2418528: Ikk2 2h; Danio rerio; RNA Seq | GSM2418528 | 1 | Embryos were flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM2418528 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP094690 | HS003-SR-R00112_AC2G1KACXX.RZL034_GCCAAT_L005_R1.fastq.gz | fastq | 2599886650.0 | 51997733.0 | GSM2418528 r1 | 0:50 | A:671073263;C:627049298;G:585161091;T:715743575;N:859423 | 50 | 671073263 | 627049298 | 585161091 | 715743575 | 859423 | SRX2401782 | SRS1841770 | SRA501296 | GEO | Computational and Systems Biology, Genome Institute of Singapore | 1 | 0.93765 | 0.03452 | 0.77041 | 0.4773 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Singapore | 2016-12-07 | Adult | Adult | Whole Organism | All anatomical structures |