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tag: Namespace:Chengdu research base of giant panda breeding

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text: feces

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text: feces

text: panda

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text: The stool of giant panda


text: CDR St Atnoine

text: public

characteristic: SRA accession

tag: Namespace:CDR St Atnoine

characteristic: Submitter Id

characteristic: age

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text: Homo sapiens

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text: public

tag: Namespace:Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, South Africa

text: ArrayExpress

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text: Protocols: Soil preservation in RNAlater solution Natural conditions No treatment CTAB lysis buffer (5% CTAB, 0.7 M NaCl, 240 mM KH2PO4, pH 8), TRIzol extraction ScriptSeq v2 Complete Gold Kit (Epidemiology)(Epicentre), ScriptSeq Index PCR primers (Set 1) (Epicentre)

characteristic: description

text: desert soil (hyperarid)

characteristic: environmental material

text: dessication

characteristic: environmental stress

text: soil metagenome

text: soil metagenome

text: -23.56, 15.04 (Gobabeb, Namibia)

characteristic: sampling site

text: soil metagenome


characteristic: ENA-CHECKLIST

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text: Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, South Africa

characteristic: INSDC center name

text: public

text: ArrayExpress

text: desert soil (hyperarid)

text: dessication

text: soil metagenome

text: soil metagenome

text: -23.56, 15.04 (Gobabeb, Namibia)

text: soil metagenome


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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: desert soil (hyperarid)

text: dessication, solar radiation

text: soil metagenome

text: soil metagenome

text: -23.56, 15.04 (Gobabeb, Namibia)

text: soil metagenome


text: public

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text: ArrayExpress

text: Protocols: Throughout the triple-phase process, six sequential biomass samples were harvested in a fast sampling procedure at various growth rates and oxygen availabilities. For this purpose, approximately 2 ∙ 109 cells of cell suspension were filled into precooled ( 21 °C) 2 mL reaction tubes. Pellets were then harvested in an immediate centrifugation (≥ 13,000 rcf, 30 s; centrifuge MiniSpin®, rotor F 45 12 11 (pre-cooled to -21 °C), Eppendorf AG, Hamburg, Germany). Then, the supernatant was discarded, the cell pellets frozen in liquid N2 and stored at 70 °C. Triple-phase bioprocess. To investigate the adaptation of C. glutamicum to a transition from aerobiosis via microaerobiosis to anaerobiosis a bioprocess in a 30 L stainless steel bioreactor (Bioengineering AG, Wald, Switzerland) was conceptualized. The seed train was established as follows (cultivation condition / inoculum / incubation time): 2x TY agar plate / streaked from glycerol stock / 2 3 days; o/n1 in 5 mL 2x TY / single colony / 15-16 h; o/d in 50 mL 2x YT / complete o/n1 / 7 8 h; o/n2 in 200 mL CGXII + 40 g glucose L 1 in 2 L flasks with baffles / o/d (starting biomass ~ 0.2 g CDW L 1) / 11-12 h; main culture in 10 L CGXII* + 60 g glucose L 1 in the 30 L bioreactor / o/n2 (starting biomass ~ 0.4 g CDW L 1). The online pH and dissolved oxygen concentration (DO) were measured using standard probes (Mettler-Toledo GmbH, Gießen, Germany). Calibration was achieved ex situ at 30 °C for the DO electrode at 0 % (dH2O + sodium sulfite) and 100 % (dH2O + air gassing) and pH electrodes in buffer solutions at pH 4.0 and pH 7.0. To maintain a pH of 7.4 throughout the cultivation, 25 % ammonia solution was added automatically. Excessive foaming was avoided by adding anti-foam solution manually on demand (Struktol™ J 647, Schill+Seilacher GmbH, Hamburg, Germany). Over the entire cultivation period the agitation was set to 445 rpm using a single six blade Rushton turbine and four baffles at the reactor wall. Low aeration rates of 0.1 vvm (1 L min 1; mass flow controller 0 2 L min 1, Analyt-MTC GmbH, Müllheim, Germany) were realized by gassing through a needle inside the cultivation broth. The exhaust gas was analyzed for O2 and CO2 content (BlueSens gas sensor GmbH, Herten, Germany) and the reactor overpressure kept at 0.5 bar. After 11 h of cultivation anaerobic conditions were initiated by a stop of aeration and flushing the headspace with 10 L nitrogen gas min 1 for 15 min. 2.3.4 RNA isolation was performed on sequential biomass samples (approximately 2 ∙ 10^9 cells), harvested in a fast sampling procedure, basically using the RNeasy Mini Kit (Qiagen) including a double DNA digestion step. RNA quality and quantity was checked by using NanoDrop (Peqlab) and by Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies). PCR was performed to assure no DNA remained in the samples. 4 µg of total RNA with RNA integrity number (RIN) > 8.0 were used for cDNA lbrary preparation. Stable RNAs were depleted with the Ribo-Zero rRNA Removal Kit (Bacteria) according to manufacturer’s instructions (Epicentre). Afterwards the remaining mRNA was purified using RNA MinElute columns (Qiagen) and checked for quality and successful rRNA depletion with the Agilent RNA Pico 6000 kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). The TruSeq Stranded mRNA Library Prep Kit from Illumina was applied to prepare the cDNA libraries.

text: aerobic

characteristic: growth condition

text: Corynebacterium glutamicum ATCC 13032

characteristic: organism

text: Corynebacterium glutamicum ATCC 13032

text: Corynebacterium glutamicum ATCC 13032


text: 1st Center for Biotechnology, Bielefeld University, Universitatsstraße 27, 33615 Bielefeld, Germany 2nd Institute for Biology-Microbiology, Freie Universitat Berlin, Konigin-Luise-Str. 12-16, 14195 Berlin, Germany

text: public

text: ArrayExpress

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text: Corynebacterium glutamicum ATCC 13032

text: Corynebacterium glutamicum ATCC 13032

text: Corynebacterium glutamicum ATCC 13032

characteristic: title


text: public

text: ArrayExpress

characteristic: description

text: initiation of anaerobic conditions

text: Corynebacterium glutamicum ATCC 13032

text: Corynebacterium glutamicum ATCC 13032

text: Corynebacterium glutamicum ATCC 13032


text: public

text: ArrayExpress

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text: Corynebacterium glutamicum ATCC 13032

text: Corynebacterium glutamicum ATCC 13032

text: Corynebacterium glutamicum ATCC 13032


text: Anopheles gambiae

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tag: Namespace:FISABIO- Public Health Research

characteristic: collection date

text: human oral metagenome

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text: Human-oral

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text: Spain

characteristic: geographic location (country and/or sea)

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text: Illumina

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text: Amplicon (V3-V4) of 16S rRNA gene


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