SPELL - Nematode

Citation	van Wijk MH, Riksen JAG, Elvin M, Poulin GB, Maulana MI, Kammenga JE, Snoek BL, Sterken MG. Cryptic genetic variation of eQTL architecture revealed by genetic perturbation in C. elegans. G3 (Bethesda), 2023.
PubMed ID	36861370
Short Description	Cryptic genetic variation of eQTL architecture revealed by genetic perturbation in C. elegans. GEO Record: N.A. Platform: N.A. Download gene-centric, log2 transformed data: WBPaper00065209.ce.mr.csv
# of Conditions	94
Full Description	Genetic perturbation in different genetic backgrounds can cause a range of phenotypes within a species. These phenotypic differences can be the result of the interaction between the genetic background and the perturbation. Previously we reported that perturbation of gld-1, an important player in developmental control of C. elegans, released cryptic genetic variation affecting fitness in different genetic backgrounds. Here we investigated the change in transcriptional architecture. We found 414 genes with a cis-eQTL and 991 genes with a trans-eQTL that were specifically found in the gld-1 RNAi treatment. In total, we detected 16 eQTL-hotspots, of which 7 were only found in the gld-1 RNAi treatment. Enrichment analysis of those 7 hotspots showed that the regulated genes were associated with neurons and the pharynx. Furthermore, we found evidence of accelerated transcriptional aging in the gld-1 RNAi treated nematodes. Overall, our results illustrate that studying CGV leads to the discovery of hidden polymorphic regulators. Experimental Details: WBPaper00065209:Sample_1_WN129_gld-1(RNAi) WBPaper00065209:Sample_2_WN134_gld-1(RNAi) WBPaper00065209:Sample_3_WN057_gld-1(RNAi) WBPaper00065209:Sample_4_WN135_gld-1(RNAi) WBPaper00065209:Sample_5_WN098_gld-1(RNAi) WBPaper00065209:Sample_6_WN185_gld-1(RNAi) WBPaper00065209:Sample_7_WN111_gld-1(RNAi) WBPaper00065209:Sample_8_WN067_gld-1(RNAi) WBPaper00065209:Sample_9_WN174_gld-1(RNAi) WBPaper00065209:Sample_10_WN076_gld-1(RNAi) WBPaper00065209:Sample_11_WN036_gld-1(RNAi) WBPaper00065209:Sample_12_WN054_gld-1(RNAi) WBPaper00065209:Sample_13_WN058_gld-1(RNAi) WBPaper00065209:Sample_14_WN146_gld-1(RNAi) WBPaper00065209:Sample_15_WN124_gld-1(RNAi) WBPaper00065209:Sample_16_WN049_gld-1(RNAi) WBPaper00065209:Sample_17_WN038_empty-vector WBPaper00065209:Sample_18_WN161_gld-1(RNAi) WBPaper00065209:Sample_19_WN190_empty-vector WBPaper00065209:Sample_20_WN071_empty-vector WBPaper00065209:Sample_21_WN109_gld-1(RNAi) WBPaper00065209:Sample_22_WN105_empty-vector WBPaper00065209:Sample_23_WN116_empty-vector WBPaper00065209:Sample_24_WN152_empty-vector WBPaper00065209:Sample_25_WN048_gld-1(RNAi) WBPaper00065209:Sample_26_WN176_gld-1(RNAi) WBPaper00065209:Sample_27_WN020_empty-vector WBPaper00065209:Sample_28_WN171_empty-vector WBPaper00065209:Sample_29_CB4856_empty-vector WBPaper00065209:Sample_30_WN158_empty-vector WBPaper00065209:Sample_31_WN196_gld-1(RNAi) WBPaper00065209:Sample_32_WN159_empty-vector WBPaper00065209:Sample_33_WN177_empty-vector WBPaper00065209:Sample_34_WN113_empty-vector WBPaper00065209:Sample_35_WN013_empty-vector WBPaper00065209:Sample_36_N2_gld-1(RNAi) WBPaper00065209:Sample_37_WN162_empty-vector WBPaper00065209:Sample_38_WN186_gld-1(RNAi) WBPaper00065209:Sample_39_CB4856_empty-vector WBPaper00065209:Sample_40_WN142_gld-1(RNAi) WBPaper00065209:Sample_41_WN140_empty-vector WBPaper00065209:Sample_42_WN106_empty-vector WBPaper00065209:Sample_43_WN128_empty-vector WBPaper00065209:Sample_44_CB4856_gld-1(RNAi) WBPaper00065209:Sample_45_WN153_empty-vector WBPaper00065209:Sample_46_WN034_gld-1(RNAi) WBPaper00065209:Sample_47_WN021_empty-vector WBPaper00065209:Sample_48_WN071_gld-1(RNAi) WBPaper00065209:Sample_49_WN080_gld-1(RNAi) WBPaper00065209:Sample_50_WN021_gld-1(RNAi) WBPaper00065209:Sample_51_WN020_gld-1(RNAi) WBPaper00065209:Sample_52_WN177_gld-1(RNAi) WBPaper00065209:Sample_53_WN158_gld-1(RNAi) WBPaper00065209:Sample_54_WN162_gld-1(RNAi) WBPaper00065209:Sample_55_WN105_gld-1(RNAi) WBPaper00065209:Sample_56_WN040_gld-1(RNAi) WBPaper00065209:Sample_57_WN072_empty-vector WBPaper00065209:Sample_58_WN031_gld-1(RNAi) WBPaper00065209:Sample_59_WN038_gld-1(RNAi) WBPaper00065209:Sample_60_WN113_gld-1(RNAi) WBPaper00065209:Sample_61_WN190_gld-1(RNAi) WBPaper00065209:Sample_62_WN041_gld-1(RNAi) WBPaper00065209:Sample_63_WN153_gld-1(RNAi) WBPaper00065209:Sample_64_WN054_empty-vector WBPaper00065209:Sample_65_WN171_gld-1(RNAi) WBPaper00065209:Sample_66_WN146_empty-vector WBPaper00065209:Sample_67_WN129_empty-vector WBPaper00065209:Sample_68_WN116_gld-1(RNAi) WBPaper00065209:Sample_69_WN067_empty-vector WBPaper00065209:Sample_70_WN109_empty-vector WBPaper00065209:Sample_71_WN196_empty-vector WBPaper00065209:Sample_72_WN013_empty-vector WBPaper00065209:Sample_73_WN159_gld-1(RNAi) WBPaper00065209:Sample_74_WN135_empty-vector WBPaper00065209:Sample_75_WN161_empty-vector WBPaper00065209:Sample_76_N2_empty-vector WBPaper00065209:Sample_77_WN185_empty-vector WBPaper00065209:Sample_78_WN152_gld-1(RNAi) WBPaper00065209:Sample_79_WN176_empty-vector WBPaper00065209:Sample_80_WN098_empty-vector WBPaper00065209:Sample_81_WN058_empty-vector WBPaper00065209:Sample_82_WN048_empty-vector WBPaper00065209:Sample_83_N2_empty-vector WBPaper00065209:Sample_84_WN111_empty-vector WBPaper00065209:Sample_85_WN140_gld-1(RNAi) WBPaper00065209:Sample_86_CB4856_gld-1(RNAi) WBPaper00065209:Sample_87_WN128_gld-1(RNAi) WBPaper00065209:Sample_88_WN186_empty-vector WBPaper00065209:Sample_89_WN034_empty-vector WBPaper00065209:Sample_90_WN142_empty-vector WBPaper00065209:Sample_91_N2_gld-1(RNAi) WBPaper00065209:Sample_92_WN049_empty-vector WBPaper00065209:Sample_93_WN106_gld-1(RNAi) WBPaper00065209:Sample_94_WN057_empty-vector.
Tags	Method: microarray, Species: Caenorhabditis elegans, Topic: natural variant, Topic: RNA interference