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.
Project description:We show that the non-specific lethal (NSL) complex in Drosophila binds to housekeeping genes. Individual ChIP-qPCR experiments of NSL target genes indicated a role of the NSL complex in RNA Polymerase II (Pol II) recruitment to promoters. Consequently, we obtained ChIP-Seq profiles of the Pol-II-subunit Rbp3 in S2 cells that were depleted of either NSL1 or NSL3. Rbp3-ChIP from S2 cells treated with siRNA targeted against GFP were used as a control. This experiment is related to experiment E-MTAB-214 and E-MTAB-1085.
Project description:The Nrd1-Nab3-Sen1 (NNS) complex plays a pivotal role in the control of pervasive transcription and the generation of sn- and snoRNAs in S. cerevisiae. The NNS-complex terminates transcription of non-coding RNA genes and promotes processing/degradation of transcripts by the nuclear exosome. To assess the role of the Nrd1p CTD-interacting domain (CID) in the function of the NNS-complex, we re-examined whether this domain is required for efficient transcription termination by the NNS pathway. We compared the RNA polymerase II distribution by ChIP and tiling arrays (ChIP-chip) in wild type and nrd1 deltaCID cells. Moreover, we compared the genome-wide chromatin distribution of Nrd1p in the presence and the absence of the CID by ChIP-chip analysis. ChIP of RNA polymerase II was performed using an anti-Rpb3 antibody (1Y26, Neoclone). ChIP of Nrd1 was performed using TAP-tagged S. cerevisiae strains. For details see protocols. To download the wild-type Pol II and Nrd1 data go to E-MTAB-1626 and E-MTAB-1060, respectively.
Project description:The major H4K16 acetylase MOF has been found in two complexes, the Male-Specific Lethal (MSL) and the Non-Specific Lethal (NSL) complex. The latter one consists of at least 7 members: NSL1, NSL2, NSL3, MBD-R2, MCRS2, WDS, and MOF. To investigate it's function, we performed genome-wide profiling of NSL3 and MBD-R2 in S2 cells. In addition, we obtained ChIP-Seq profiles for NSL1 and MCRS2 from 3rd instar larvae salivary glands that can be accessed via the accession number E-MTAB-214. This submission is also related to E-MTAB-1084.
Project description:Identifying N-linked and O-linked sites of glycosylation on PTP69D (Drosophila melanogaster) by sHCD and CID neutral loss-trigged MS3.
Project description:DNase-seq over 2 matching developmental time points in Drosophila melanogaster and Drosophila virilis embryos was performed. The aim is to assess conservation of hypersensitive regions between two distantly related species. Samples were sequenced using Illumina NextSeq. This Study is an extension to the previously published Study E-MTAB-3797.
