run_metadata: 71601
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 71601 | SRR21780862 | SRX17775675 | SRS15301942 | SRP400655 | PRJNA885906 | Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish | PRJNA885906 | Other | The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota. | CV2 | CV2 HWLY5BBXX | strain:Tgnkx2.2a; eGFP|dev stage:6dpf|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal | conventional 6dpf whole larvae | HWLY5BBXX CV2 | HWLY5BBXX CV2 | data is culmination of two HiSeq4000 runs. One run CV/GF samples were both run on the same line and in the second run CV/GF samples were run on individual lanes. Data was demultiplexed and treatment groups combined for total number of reads per group to be above spec. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP400655 | CV2_S1_L006_R1_001.fastq.gz CV2_S1_L006_R2_001.fastq.gz | fastq fastq | 42260060400.0 | 140866868.0 | CV2 S1 L006 R1 001.fastq.gz | 0:150 1:150 | A:10306378433;C:7083604228;G:7794391616;T:17070639212;N:5046911 | 150 | 150 | 10306378433 | 7083604228 | 7794391616 | 17070639212 | 5046911 | SRX17775675 | SRS15301942 | SRA1511285 | University of Oregon|Institute of Molecular Biology | University of Oregon | 2 | 0.0311 | 0.89818 | 0.0069 | 0.11191 | 0.99257 | 0.78642 | 0.52164 | 0.50459 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | random_priming | unknown | sc | unknown | unknown | United States | 2022-10-02 | Larval | Larval | Whole Organism | All anatomical structures |