run_metadata: 65778
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 65778 | SRR15606832 | SRX11904306 | SRS9915513 | SRP334037 | PRJNA757618 | RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites. | GSE182725 | Transcriptome Analysis | Here we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long pec stage 2 dpf and sequenced at a depth of 80 100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA Seq analysis. Of these 42 were rescued with the treatment of zebrafish gut derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA seq analysis of conventionally raised zebrafish larvae compared to germ free zebrafish larvae and germ free larvae treated with zebrafish metabolites. | pubmed:35996200 | Germ free GF Rep1 | GSM5535700 | tissue:Zebrafish larvae|strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Germ free | Germ free GF Rep1 | Demultiplexed read quality was checked for each sample using FastQC v0.11.8. Reads were aligned to GRCz11 using HISAT2 2.1.0 Expression estimates were calclulated using StringTie v1.3.4d and htseq count v0.11.0 Differential expression analysis was conducted using DESeq2 1.29.13 Genome build: GRCz11 Supplementary files format and content: abundance measurements in FPKM for all samples | Zebrafish larvae | Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina | strain:Tubingen|tissue type:head|developmental stage:long pec|protocol:Germ free | GSM5535700 | GSM5535700: Germ free GF Rep1; Danio rerio; RNA Seq | GSM5535700 | 1 | Heads were surgically removed from the body at the base of the hindbrain. RNA was extracted from a pool of five heads for each treatment using the GENEzol™ TriRNA Pure Kit Froggabio. RNA samples were DNase treated using the Invitrogen™ DNA free™ DNA Removal Kit PolyA mRNA was prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina | GEO Accession:GSM5535700 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP334037 | loader:fastq load.py | GF1_R1.fastq.gz GF1_R2.fastq.gz | fastq fastq | 15494890731.0 | 51452768.0 | GSM5535700 r1 | 0:150.51 1:150.64 | A:4204554108;C:3538500955;G:3719345305;T:4032206656;N:283707 | 150 | 150 | 4204554108 | 3538500955 | 3719345305 | 4032206656 | 283707 | SRX11904306 | SRS9915513 | SRA1283476 | GEO | Van Raay Lab, Molecular and Cellular Biology, University of Guelph | 2 | 0.96626 | 0.97207 | 0.0762 | 0.07568 | 0.69357 | 0.69388 | 0.45129 | 0.45751 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | nebnext | bulk | unknown | unknown | Canada | 2021-08-25 | Hatching | Embryo | Multi-tissue | Multi-system |