Widespread genetic epistasis among cancer genes.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Kevin White
PROVIDER: E-GEOD-58834 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:We performed NGS-based transcript profiling (RNA-seq) to profile transcripts that are expressed in MCF10A cells. 12,332 genes with FPKM>1 were considered as expressed in MCF10A cells.
2014-08-01 | GSE58834 | GEO
Project description:Histone 3 lysine 4 trimethylation (H3K4me3) is known to be associated with transcriptionally active or poised genes and required for postnatal neurogenesis within the subventricular zone (SVZ) in the rodent model. Previous comparisons have shown significant correlation between baboon (Papio anubis) and human brain. In this study, we demonstrate that chromatin activation mark H3K4me3 is present in undifferentiated progenitor cells within the SVZ of adult baboon brain. To identify the targets and regulatory role of H3K4me3 within the baboon SVZ, we developed a technique to purify undifferentiated SVZ cells while preserving the endogenous nature without introducing culture artifact to maintain the in vivo chromatin state for genome-wide studies (ChIP-Seq and RNA-Seq). We identified that H3K4me3 is significantly enriched for genes involved in cell cycle, cell signaling, nervous system development, metabolism, and ribosomal biogenesis. Among these genes, RNA-Seq identified that genes associated with cellular signaling/maintenance, DNA replication, metabolism, and protein synthesis are expressed. We found that 72% of H3K4me3-enriched genes in undifferentiated SVZ cells are expressed (1913 genes are detectable by RNA-Seq; 2663 genes enriched with H3K4me3 by ChIP-Seq). On the other hand, 750 out of total 2663 H3K4me3-enriched genes are not detectable by RNA-Seq, suggesting 28% of genes in SVZ are poised for activation. RNA-seq profiles were generated from adult baboon subventricular zone primary cells by paired-end deep sequencing with an Illumina HiSeq 2000. RNA-Seq Analysis: Total RNA was extracted from purified baboon SVZ cells using TRIzol reagent, and sequencing libraries were generated with the Illumina RNA-Seq library kit. Paired-end RNA-deepSeq (76 base pair; >300 million tag reads; 269,081,636 mapped reads) were aligned to hg19. DESeq was used to normalize raw read counts, and Cufflink reports read counts and estimated FPKM (fragments per kilobase of exon per million fragments mapped; http://cufflinks.cbcb.umd.edu/faq.html#fpkm). Genes with expression values >1 FPKM were considered for subsequent analyses.
2014-07-16 | E-GEOD-58527 | biostudies-arrayexpress
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2016-06-01 | E-GEOD-67894 | biostudies-arrayexpress
Project description:Our goal is to convert methane efficiently into liquid fuels that may be more readily transported. Since aerobic oxidation of methane is less efficient, we focused on anaerobic processes to capture methane, which are accomplished by anaerobic methanotrophic archaea (ANME) in consortia. However, no pure culture capable of oxidizing and growing on methane anaerobically has been isolated. In this study, Methanosarcina acetivorans, an archaeal methanogen, was metabolically engineered to take up methane, rather than to generate it. To capture methane, we cloned the DNA coding for the enzyme methyl-coenzyme M reductase (Mcr) from an unculturable archaeal organism from a Black Sea mat into M. acetivorans to effectively run methanogenesis in reverse. The engineered strain produces primarily acetate, and our results demonstrate that pure cultures can grow anaerobically on methane. Differential gene analysis of two growth conditions (three biological replicates each) was performed: (i) M. acetivorans/pES1-MATmcr3 grown on methane and (ii) M. acetivorans/pES1-MATmcr3 grown on methanol. All starter cultures (200 mL) were grown on methanol for 5 days, and harvested by centrifugation. Cell pellets were washed three times with HS medium, and resuspended using 5 mL HS medium, 2 µg/mL puromycin, and 0.1 mM FeCl3. For condition (i), methane was filled into the headspace of the cultures. For condition (ii), 150 mM methanol was added. All cultures were incubated at 37C for 5 days, followed by rapid centrifugation in the presence of 50 µL RNAlater solution (Ambion, Austin, TX) per mL of culture. Total RNA was isolated using RNeasy Mini kit (Qiagen, Valencia, CA) were then digested with terminator 5â-phosphate-dependent exonuclease (Epicentre, Madison, WI) to partially remove ribosomal RNA. Digested RNA were cleaned up using AgenCourt RNAClean XP beads (AgenCourt Bioscience, Beverly, MA) and used for cDNA library construction using the TruSeq Stranded mRNA Library kit (Illumina). Pooled and barcoded cDNA library was then sequenced on a HiSeq sequencing platform (Illumina). Obtained reads were mapped to the reference genome of M. acetivorans (Genbank accession NC_003552.1) using STAR. The mapped reads were assembled using Cufflink v2.2.1 to identify potential novel transcripts. Assembled, unannotated novel transcripts for all the strains were combined with the list of known genes. Differential expression of genes and potential novel transcripts were determined using Cuffdiff at a significance cutoff at q < 0.07 with a false discovery rate of 0.05. Expression levels of gene transcripts are expressed as fragments per kilobase of transcript per million mapped fragments (FPKM), and expression changes are determined by the ratio of FPKM of culture replicates grown on methane to FPKM of culture replicates grown on methanol.
2015-12-20 | E-GEOD-66445 | biostudies-arrayexpress
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Project description:Stem cells are highly abundant and proliferate rapidly during early development but become a rare population in most adult organs. The molecular mechanisms causing stem cells to exit proliferation at a specific time are not well understood. Here, we show that changes in energy metabolism induced by the steroid hormone Ecdysone initiate an irreversible cascade of events leading to cell cycle exit in Drosophila neural stem cells. We show that the timely induction of oxidative phosphorylation and the mitochondrial respiratory chain are required in neuroblasts to uncouple cell cycle progression from cell growth. This results in a progressive reduction in neuroblast cell size and ultimately in terminal differentiation. Neuroblasts isolated from brain tumors fail to undergo this shrinkage process and this may explain why they are immortalized. Our findings show that cell size control can be modified by systemic hormonal signaling and reveal a unique connection between metabolism and proliferation control in stem cells. Comparison of transcriptomes of Drosophila melanogaster central brain NBs from wild-type larval NBs, wild type pupal NBs and med27 RNAi pupal NBs.
2014-08-14 | E-GEOD-53265 | biostudies-arrayexpress
Project description:Our aim was to classify and quantify transcripts in primary duck hepatocytes cultured in medium with 5% FBS or 1.5% DMSO for 8 days. Methods: The transcriptome of PDHs under different conditions was analyzed by the pair-end sequencing on the Illumina Solexa platform. High-quality reads were mapped to the Anas platyrhynchos genome with TopHat v2.0.12 software. TopHat allows multiple alignments per read and default parameters were used. Cufflinks v2.2.1 software was later used for analyses that included transcript assembly and FPKM value calculations to quantify gene expression; this program was also run with default parameters. The transcriptome of PDHs under different culture conditions were analyzed by the paired-end sequencing on the Illumina Solexa platform.
2016-03-09 | E-GEOD-72868 | biostudies-arrayexpress
Project description:Drosophila neuroblasts have emerged as a model for stem cell biology that is ideal for genetic analysis but is limited by the lack of cell-type specific gene expression data. Here, we describe a methodology to isolate large numbers of pure neuroblasts and differentiating neurons that retain both cell cycle and lineage characteristics. We determine transcriptional profiles by mRNA sequencing and identify 28 predicted neuroblast specific transcription factors, which can be arranged in a network containing hubs for Notch signaling, growth control and chromatin regulation. Overexpression and RNAi for these factors identify Klumpfuss as a regulator of self-renewal. We show that loss of Klu function causes premature differentiation while overexpression results in the formation of transplantable brain tumors. Our data represent a valuable resource for Drosophila developmental neurobiology and we describes methodology that can be applied to other invertebrate stem cell lineages as well. comparison of transcriptomes of Drosophila melanogaster larval neuroblasts and their differentiated daughter cells (neurons)
2012-08-21 | E-GEOD-38764 | biostudies-arrayexpress
Project description:The development of affinity purification technologies together with mass spectrometric analyses of the purified protein mixtures (AP-MS) has been used both to identify new protein-protein interactions and to define the subunit composition of protein complexes. Transcription factor protein interactions, however, have not been systematically analyzed using these approaches. Here, we have investigated whether ectopic expression of an affinity tagged transcription factor as bait in AP-MS experiments perturbs gene expression in cells resulting in false positive identification of bait associated proteins when typical experimental controls are used. Using quantitative proteomics and RNA-Seq, we determined that the increase in the abundance of a set of proteins caused by overexpression of the transcription factor RelA is not sufficient for these proteins to then copurify non-specifically and be misidentified as bait associated proteins. Therefore typical controls should be sufficient and a number of different baits can be compared with a common set of controls. This is of practical interest when identifying bait interactors from a large number of different baits. As expected, we found several known RelA interactors enriched in our RelA purifications (NFêB1, NFêB2, Rel, RelB, IêBá, IêBâ and IêBå). We also found several proteins not previously described in association with RelA, including the small mitochondrial chaperone Tim13. Using a variety of biochemical approaches, we further investigated the nature of the association between Tim13 and NFêB family transcription factors. The work here therefore provides a conceptual and experimental framework for analyzing transcription faction protein interactions. Gene expression profiles were assayed in triplicate from HEK293 cells expressing either Halo-RelA, Halo-NFkB1, or Halo tag alone.
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