Project description:We performed RNAi knockdown experiments on 15 different signal transduction components in Drosophila S2 cells and prepared RNA libraries from the poly-adenylated fraction of the RNA. SOLiD sequencing of strand-specific, barcoded transcriptome libraries yielded expression profiles allowing us to extract common pathway signatures and indicated that Cka may function as novel regulator in Ras/MAPK signaling
Project description:RNAi of signal transduction components in Drosophila S2 cells We performed RNAi knockdown experiments on 15 different signal transduction components in Drosophila S2 cells and prepared RNA libraries from the poly-adenylated fraction of the RNA. SOLiD sequencing of strand-specific, barcoded transcriptome libraries yielded expression profiles allowing us to extract common pathway signatures and indicated that Cka may function as novel regulator in Ras/MAPK signaling. ArrayExpress Release Date: 2011-07-08 Person Roles: investigator Person Last Name: Boutros Person First Name: Michael Person Email: m.boutros@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ Person Roles: investigator Person Last Name: Sandmann Person First Name: Thomas Person Email: t.sandmann@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ Person Roles: investigator Person Last Name: Horn Person First Name: Thomas Person Email: t.horn@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ Person Roles: submitter Person Last Name: Kerr Person First Name: Grainne Person Email: g.kerr@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ
Project description:Transcription profiling by RNA-seq of Drosophila S2 cells after knock down of strongest cell cycle regulators to map their genome-wide transcriptional targets (155 assays). RNA samples used for this experiment are a subset of the 200 samples used in Affymetrix microarray experiment E-MTAB-453. E-MTAB-1648, E-MTAB-1364 and E-MTAB-453 are all data from: Bonke M, et al. (2013) Transcriptional networks controlling the cell cycle. G3 (Bethesda) 3, 75-90, PMID: 23316440.
Project description:ChIP-seq for the strongest cell cycle regulator transcription factors in Drosophila Melanogaster S2 cells. These assays have been used to validate the direct transcriptional targets of the same transcription factors investigated in RNA-seq (E-MTAB-1364) and Affymetrix microarray experiments (E-MTAB-453). ChIP-seq assays have been done with tagged fusion proteins (for example, since we dont have functional E2f antibodies against endogenous E2f , we are transfecting v5-tagged-E2f-ORF to S2 cells and then use antibodies against v5 to detect the signal from E2f binding). If the ChIP-seq has been done with tagged fusion proteins (such as v5-tagged-E2f-ORF), the protein expression has been induced with CuSO4 treatment 48h prior to cell crosslinking & lysis. Our fusion protein constructs are driven by metallothionein promoter, which is induced by CuSO4. E-MTAB-1648, E-MTAB-1364 and E-MTAB-453 are all data from: Bonke M, et al. (2013) Transcriptional networks controlling the cell cycle. G3 (Bethesda) 3, 75-90, PMID: 23316440.
