E-MTAB-5856 - Transcriptome profiling by microarray of Caenorhabditis elegans MT2124 x CB4856 RILs used for eQTL mapping

Status
Last updated on 21 July 2017, released on 21 July 2017
Organism
Caenorhabditis elegans
Samples (48)
Array (1)
Protocols (5)
Description
We crossed the MT2124 strain carrying the let-60 (n1046) gain of function mutation with the wild-type strain CB4856. From this cross a panel of mutation introgression recombinant inbred lines (miRILs) was generated. Using this population, the influence of genetic variation on the the let-60 (gf) mutation can be investigated. This analysis can pinpoint genetic loci A panel of 33 miRILs, the parental strains (4x), and transgenic lines amx-2(lf);Si[amx-2(Bristol)];let-60(gf) and amx-2(lf);Si[amx-2(Hawaii)];let-60(gf) containing the N2- or CB4856-allele of amx-2 in a amx-2(lf);let-60(gf) background were sampled. All the strains were grown on nematode growth medium dishes seeded with E. coli OP50. The temperature at which the strains were kept was 20 degrees Celsius and the strains were grown for 72 hours after synchronization by bleaching. Thereafter RNA was isolated, labelled, and hybridized on microarray. The gene expression profiles of the miRILs were used for eQTL mapping. The gene expression profiles of the transgenic strains were used for trans-band confirmation.
Experiment types
transcription profiling by array, strain or line design
Contact
Citation
Ras/MAPK Modifier Loci Revealed by eQTL in Caenorhabditis elegans. Sterken MG, van Bemmelen van der Plaat L, Riksen JAG, Rodriguez M, Schmid T, Hajnal A, Kammenga JE, Snoek BL. 7(9):3185-3193 (2017), PMID:28751501
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MTAB-5856.idf.txt
Sample and data relationshipE-MTAB-5856.sdrf.txt
Raw data (2)E-MTAB-5856.raw.1.zip, E-MTAB-5856.raw.2.zip
Array designA-MEXP-2316.adf.txt