run_metadata: 61612
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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| 61612 | SRR12877273 | SRX9343285 | SRS7566337 | SRP288161 | PRJNA670669 | Critical Role for a Subset of Intestinal Macrophages in Shaping Gut Microbiota in Adult Zebrafish | GSE159845 | Transcriptome Analysis | We conducted a whole genome transcriptome analysis to examine significant gene expression changes in the gut tissue of macrophage deficient irf8 mutants compared with their heterozygous sibling guts. Overall design: RNAseq dataset of mRNA libraries made from whole gut total RNA isolated from adult zebrafish: two irf8 heterozyous animals and two irf8 homozygous mutants. | pubmed:30304682 | whole gut total RNA st95 mut1 | GSM4848258 | source name:whole gut total RNA st95 mut|age:adult|genotype/variation:irf8 homozygous mutant|tissue:intestine | whole gut total RNA st95 mut1 | Alignment of reads to the UCSC GRCz10/danRer10 genome build using BBmap v37.99 assigning ambiguous reads randomly Calculating gene counts using the featureCounts tool in the Subread suite v1.5.2 with UCSC annotations Analysis of differential gene expressions with DESeq2 R v3.3.1 Genome build: GRCz10/danRer10 Supplementary files format and content: gene counts using featureCounts tool; genes short list from analysis using CLC Genomics Workbench 9 | whole gut total RNA st95 mut | no treatment | Toal RNA extracted by using the RNAqueous Micro Total RNA Isolation Kit Ambion. Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA seq kit. Magnetic oligo dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity low bias PCR. | for details see Earley et al. 2018 Cell Reports | age:adult|genotype/variation:irf8 homozygous mutant|tissue:intestine | GSM4848258 | GSM4848258: whole gut total RNA st95 mut1; Danio rerio; RNA Seq | GSM4848258 | 1 | Toal RNA extracted by using the RNAqueous Micro Total RNA Isolation Kit Ambion. Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA seq kit. Magnetic oligo dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity low bias PCR. | GEO Accession:GSM4848258 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP288161 | ZEB_003-gut-mut1_Organ_TTAGGC_L007_R1_001.fastq.gz ZEB_003-gut-mut1_Organ_TTAGGC_L007_R2_001.fastq.gz | fastq fastq | 3161333750.0 | 12645335.0 | GSM4848258 r1 | 0:125 1:125 | A:866363507;C:708829199;G:732878242;T:852858127;N:404675 | 125 | 125 | 866363507 | 708829199 | 732878242 | 852858127 | 404675 | SRX9343285 | SRS7566337 | SRA1146317 | GEO | UNC Chapel Hill | 2 | 0.94869 | 0.95379 | 0.07608 | 0.07624 | 0.79551 | 0.78871 | 0.6497 | 0.63595 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | unknown | bulk | bulk | bulk | United States | 2020-10-22 | Adult | Adult | Gut | Digestive System |