RNA-seq of mutant Mycobacterium neoaurum producing steroid intermediates compared with wild-type strain
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina Hiseq 2000, Illumina HiSeq 2000
ORGANISM(S): Mycobacterium neoaurum
SUBMITTER: Min Liu
PROVIDER: E-MTAB-6789 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2013-06-29 | E-GEOD-48416 | biostudies-arrayexpress
Project description:In this study, we undertook a comprehensive quantitative proteomic profiling of Arabidopsis roots from plants grown on Mn-deplete media, aiming at dissecting and cataloging the responses of Arabidopsis roots to Mn deficiency. We used LC-Q Exactive Orbitrap mass spectrometer to compile a near complete inventory of the Arabidopsis root proteome. We identified several novel components of cellular Mn homeostasis and show that many putatively important changes in response to Mn deficiency are only evident at one of the omics levels under investigation.
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Project description:Membranous nephropathy (MN) is an autoimmune kidney disease with the clinical hallmark of causing high level proteinuria. MN is caused by circulating antibodies binding to targeting antigens on the surface of podocytes – specialized endothelial cells contributing to the formation of the glomerular filtration barrier. Histomorphologically MN is characterized by a deposition of IgG along the glomerular basement membrane (GBM) – predominantly IgG4 in primary MN – as well as an accumulation of the respective target antigen, thickening of the GBM and effacement of podocyte foot processes. The predominant MN target antigen in 70-80% of MN patients is the phospholipase A2 receptor 1. Additional target antigens, which occur with lower frequencies, have recently been described. The aim of the study was the identification of a novel MN target antigen, which fulfills the typical criteria of MN target antigen: being a podocytic membrane protein, which is recognized by IgG4 subclass specific autoantibodies. Performing a mass spectrometry analysis based on a TMT-based relative quantification approach of immunoprecipitated samples resulted in the identification of Netrin G1 (NTNG1) as a novel MN target antigen. The results were validated using immunohistochemistry, Western Blot and ELISA. The molecular characterization of patients with MN will allow a better diagnosis and clinical management of these patients in the future.
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Project description:Amyotrophic Lateral Sclerosis is a fatal neurodegenerative disorder that affects motor neurons (MN). We used single cell RNA-seq of degenerating human MN derived from ALS patients to understand molecular drivers of MN degeneration. Patient-derived iPSC bearing a point mutation in the SOD1 gene (SOD1 E100G) were differentiated into MN. MN derived from CRISPR-Cas9 corrected isogenic control iPSC (SOD1 E100E) were used as control. Survival analysis indicated that at 44 days of in vitro differentiation, ALS MN dislpayed survival deficits. At this point, cells were harvested for single cell transcriptomics using the Fluidigm C1 system.
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Project description:During development, two cell-types born from closely related progenitor pools often express the identical transcriptional regulators despite their completely distinct characteristics. This phenomenon highlights the necessity of the mechanism that operates to segregate the identities of the two cell-types throughout differentiation after initial fate commitment. To understand this mechanism, we investigated the fate specification of spinal V2a interneurons, which share important developmental genes with motor neurons (MNs). Here we demonstrate that the paired homeodomain factor Chx10 functions as a critical determinant for V2a fate and is required to consolidate V2a identity in postmitotic neurons. Chx10 actively promotes V2a fate, downstream of the LIM-homeodomain factor Lhx3, while concomitantly suppressing MN developmental program by preventing the MN-specific transcription complex from binding and activating MN genes. This dual activity enables Chx10 to effectively separate V2a and MN pathways. Together, our study uncovers a widely applicable gene regulatory principle for segregating related cell fates. RNA samples from Chx10-ESC-derived MNs were prepared for sequencing according to the Illumina protocol, and sequenced on the Illumina HiSeq 2000. We will then compare the transcriptome changes between -Dox (no Chx10) and +Dox (Chx10) in order to identify genes rregulated by Chx10.
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Project description:During development, two cell-types born from closely related progenitor pools often express the identical transcriptional regulators despite their completely distinct characteristics. This phenomenon highlights the necessity of the mechanism that operates to segregate the identities of the two cell-types throughout differentiation after initial fate commitment. To understand this mechanism, we investigated the fate specification of spinal V2a interneurons, which share important developmental genes with motor neurons (MNs). Here we demonstrate that the paired homeodomain factor Chx10 functions as a critical determinant for V2a fate and is required to consolidate V2a identity in postmitotic neurons. Chx10 actively promotes V2a fate, downstream of the LIM-homeodomain factor Lhx3, while concomitantly suppressing MN developmental program by preventing the MN-specific transcription complex from binding and activating MN genes. This dual activity enables Chx10 to effectively separate V2a and MN pathways. Together, our study uncovers a widely applicable gene regulatory principle for segregating related cell fates. ChIP DNA samples from Chx10-ESC-derived MNs were prepared for sequencing according to the Illumina protocol, and sequenced on the Illumina HiSeq 2000. The peak calling was conducted with MACS software (Zhang et al., 2008). MEME-ChIP Suite (Bailey et al., 2009; Machanick and Bailey, 2011) and TOMTOM algorithm (Gupta et al., 2007) was used for motif analysis.
2016-07-28 | E-GEOD-83872 | biostudies-arrayexpress
Project description:In this study, we investigated Mn3+-cycling microbial populations enriched from Lake Matano, Indonesia using metagenomics and metaproteomics. Lake Matano contains an active Mn cycle that links the oxic-anoxic interface with anoxic deep waters that are enriched in iron and manganese, and depleted in sulfate, phosphate, and oxidized nitrogen (Crowe et al., 2008; Jones et al., 2011). Sediments were incubated with sequential transfers for ~1 year with Mn3+ as the sole electron acceptor and methane as organic carbon until achieving sediment-free conditions. Here we investigate this novel species of Dechloromonas (Betaproteobacteria), “Candidatus Dechloromonas occultata,” which was the dominant population in enrichment cultures with active Mn3+ reduction. “Ca. D. occultata” expressed electron conduits related to those involved in Fe2+ oxidation (Mto-like), as well as a novel cytochrome c-rich gene cluster putatively involved in extracellular electron transfer, and an atypical nitrous oxide reductase. According to ribosomal counts, Dechloromonas outnumber Geobacter. In terms of functional genes, Dechloromonas expresses a wider variety and number of genes. Dechloromonas therefore seems to have a (selective?) advantage over Geobacter. Previous experiments revealed that Dechloromonas express nitrogen regulators, reductases and scavenging genes, as well as many carbon central metabolic pathways, and aromatic carbon degradation pathways. Dechloromonas is a beta proteobacteria, and these are "experts" in nitrogen metabolism. Geobacter, on the other hand, is well known for carbon degradation. Our previous experiments lead to our hypothesis that Dechloromonas is more active because they are more successful at acquiring nitrogen, a limiting nutrient for Geobacter. This would further suggest that carbon is not the limiting nutrient. We will test 2 hypotheses with the next suite of experiments 1) pyrophosphate supports the community, by allowing carbon fixation , 2)Dechloromonas has a (selective?) advantage over Geobacter. To test this hypothesis, bioreactors will be used to grow biotriplicate cultures of (1)- CH4 vs. pyrophosphate and (2)-CH4 vs. Mn(III) pyrophosphate. Here we have analyzed whole cell pellets using gas phase fractionations on the Q Exactive. Are Dechloromonas capable of out-competing Geobacter when grown in media with methane as the only carbon source bioreactors because they are capable of acquiring more nitrogen? Source of inoculum. Lake Matano is a metal-rich, ancient ocean analog (Crowe et al. 2011, Jones et al. 2011). Organic carbon in Lake Matano is mostly mineralized via methanogenesis before reaching the iron-rich sediments, limiting organic matter bioavailability for metal-reducers (Kuntz et al. 2015). A 15-cm sediment core from 200 m water depth in Lake Matano, Sulawesi Island, Indonesia (02°26′27.1′′S, 121°15′12.3′′E; in situ sediment temperature ~27°C) was sampled in November 2014 and sub-sampled at 5 cm increments. Sediments were sealed in gas-tight Mylar bags with no headspace (Hansen et al. 2000) and stored at 4°C until incubations began in December 2015.
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2012-12-15 | E-GEOD-42919 | biostudies-arrayexpress
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