title: AGHEt3
organism: Mycosarcoma maydis
description: Protocols: For RNAseq, strains were inoculated in YNB (pH 5.8) supplemented with 1% glucose and 0.2% ammonium sulfate (YNBG) overnight to an OD600 of 0.25 and shifted to YNB (pH 5.8) supplemented with 1% arabinose and 0.2% ammonium sulfate to induce Clp1 expression (Pcrg1:clp1). To induced the UPR, TM was added to a final concentration of 5 µg/ml and cells were further incubated for 4 hours, at 28°C. Cells were harvested and quick frozen in liquid nitrogen. RNA was prepared from cells during exponential growth using Trizol reagent (Invitrogen) according to the manufacturer's instructions (Scherer et al., 2006), followed by removal of residual DNA with TurboDNase (Ambion/Lifetechnologies). If RNA was used for RNAseq anaylsis samples were further column-purified with the RNeasy Kit (Qiagen). Integratity ofRNA was checked by ethidium bromide staining and by Bioanalyzer equipped with an RNA 6000 Nano LabChip kit (Agilent). NEB Next Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to reduce the amount of rRNA-derived sequences. For sequencing, the strand-specific cDNA libraries were constructed with a NEBNext Ultra directional RNA library preparation kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit® dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany)
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2019-04-04T04:03:49Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-12-03T09:59:33Z
attributes.tag: External Id
attributes.value: SAMEA5145523
attributes.tag: INSDC center name
attributes.value: Philipps University Institute for Molecular Biology and Tumor Research
attributes.tag: INSDC first public
attributes.value: 2019-04-04T04:03:49Z
attributes.tag: INSDC last update
attributes.value: 2018-12-03T09:59:33Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-7463:AGHEt3
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: growth condition
attributes.value: yeast nitrogen base media
attributes.tag: sample name
attributes.value: E-MTAB-7463:AGHEt3
attributes.tag: scientific_name
attributes.value: Ustilago maydis
attributes.tag: strain
attributes.value: JB1