RDF version of the data from Saarimaki et al. Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials (Version 1.0.0) [Zebodo Dataset] (2020)

Original Study Abstract

Toxicogenomics (TGx) approaches are increasingly applied to gain insight into the possible toxicity mechanisms of engineered nanomaterials (ENMs). Omics data can be valuable to elucidate the mechanism of action of chemicals and to develop predictive models in toxicology. While vast amounts of transcriptomics data from ENM exposures have already been accumulated, a unified, easily accessible and reusable collection of transcriptomics data for ENMs is currently lacking. In an attempt to improve the FAIRness of already existing transcriptomics data for ENMs, we curated a collection of homogenized transcriptomics data from human, mouse and rat ENM exposures in vitro and in vivo including the physicochemical characteristics of the ENMs used in each study. [Source:]

Data Sample

Experiment metadata sample

GSE GSM treatment group organism biological_system dose dose_unit time_point time_point_unit slide array dye platform filenames
GSE35193 GSM863285 Carbon black (Printex90) CB_Printex90_18ug_1d Mus musculus Lung 18 ug 1 d 251486818953_201002090953 1_2 Cy5 GPL4134 GSM863285_251486818953_201002090953_S01_GE2_107_Sep09_1_2.txt
GSE35193 GSM863286 Carbon black (Printex90) CB_Printex90_54ug_1d Mus musculus Lung 54 ug 1 d 251486818953_201002090953 1_3 Cy5 GPL4134 GSM863286_251486818953_201002090953_S01_GE2_107_Sep09_1_3.txt
GSE35193 GSM863287 Carbon black (Printex90) CB_Printex90_162ug_1d Mus musculus Lung 162 ug 1 d 251486818953_201002090953 1_4 Cy5 GPL4134 GSM863287_251486818953_201002090953_S01_GE2_107_Sep09_1_4.txt
GSE35193 GSM863288 control control_3d Mus musculus Lung 0 NA 3 d 251486818955_201002091001 1_1 Cy5 GPL4134 GSM863288_251486818955_201002091001_S01_GE2_107_Sep09_1_1.txt

Experiment differential gene expression data sample

logFC AveExpr t-statistic P.Value adj.P.Val B-statistic score ID
1,616980442 13,36264474 4,693059703 2,13306E-05 0,040153868 2,525330189 7,552910971 ENSMUSG00000020108
0,89837437 10,09100051 5,063483115 5,99402E-06 0,028874382 3,617696824 4,691564427 ENSMUSG00000027368
0,740675079 8,836615295 4,821705975 1,37695E-05 0,031680571 2,902082885 3,60048205 ENSMUSG00000054364
0,923918603 12,08307336 5,368712658 2,06751E-06 0,028874382 4,532413404 5,252064459 ENSMUSG00000019970

Data Summary

Group Count
# of Materials 153
# of Assays 35
# of Measurement groups 440
# of Endpoints 249350
# of Nanomaterial types 22
# of Assay types 35
# of Endpoint types 3
# of Units 21
# of Species 3
# of Unique genes 39947
# of Unique human genes (ENSG) 22841
# of Unique mouse genes (ENSMUSG) 16450
# of Unique rat genes (ENSRNOG) 609
# of not annotated genes 47