run_metadata: 68469
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 68469 | SRR17745597 | SRX13908015 | SRS11764615 | SRP356703 | PRJNA800448 | RNAseq analysis of the herbicide propyzamide on a pre clinical model of IBD on Danio rerio model | GSE194408 | Transcriptome Analysis | Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model Overall design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment 4 Propyzamide 20 uM and 4 Propyzamide 1 uM treatment. | parent bioproject:PRJNA800443 | pubmed:36266581 | Naive Control 0uM Lymph CGGAGCCT CTTAATAG | GSM5835358 | tissue:CGGAGCCT CTTAATAG|strain:AB|Sex:NA|age:NA | Naive Control 0uM Lymph CGGAGCCT CTTAATAG | The sample is aligned to GRCz38 transcriptome and quantified using Kallisto Genome build: GRCz38 Supplementary files format and content: gzipped abundance.tsv output from Kallisto | CGGAGCCT CTTAATAG | N/A | N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014. | N/A | strain:AB|Sex:NA|age:NA | GSM5835358 | GSM5835358: Naive Control 0uM Lymph CGGAGCCT CTTAATAG; Danio rerio; RNA Seq | GSM5835358 r1 | GSM5835358 | 1 | N/A Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described Trombetta et al 2014. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP356703 | CGGAGCCT_CTTAATAG.1.fastq.gz CGGAGCCT_CTTAATAG.2.fastq.gz | fastq fastq | 12008836.0 | 158011.0 | GSM5835358 r1 | 0:38 1:38 | A:1996134;C:3633783;G:4131965;T:2243758;N:3196 | 38 | 38 | 1996134 | 3633783 | 4131965 | 2243758 | 3196 | SRX13908015 | SRS11764615 | Brigham and Women's Hospital | 2 | 0.62464 | 0.65559 | 0.6019 | 0.63142 | 0.96566 | 0.96575 | 0.49372 | 0.50661 | 38 | 38 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2022-01-25 | Undetermined | Undetermined | Lymphatic System | Cardiovascular System |