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Ypt1 IPs

ABSTRACT: Yeast strains expressing either GST-tagged or untagged Ypt1 were grown in either normal media or in media treated with 10mM DTT, to induce UPR A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. GeneticModification: GST tagged/untagged YPT1 Media: DTT present/absent in media

ORGANISM(S): Methanocaldococcus jannaschii Saccharomyces cerevisiae

PROVIDER: GSE33749 | GEO | 2012/11/15

SECONDARY ACCESSION(S): PRJNA154355

REPOSITORIES: GEO

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Ypt1 IPs

Project description:Yeast strains expressing either GST-tagged or untagged Ypt1 were grown in either normal media or in media treated with 10mM DTT, to induce UPR A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. GeneticModification: GST tagged/untagged YPT1 Media: DTT present/absent in media replicate_design

2012-11-15 | E-GEOD-33749 | biostudies-arrayexpress

Adaptor candidates

Project description:IP of candidate adaptor Ada5/Gdi1, tagged with HA, versus Mock (untagged) replicates. IP associated RNA was assayed. A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. GeneticModification: HA-tagged candidate gene or control

2012-11-15 | GSE33747 | GEO

Adaptor candidates

2012-11-15 | E-GEOD-33747 | biostudies-arrayexpress

UV-crosslinking and high throughput sequencing of cDNAs (CRAC) of the RNA chaperone Hfq in enterohaemorhaggic E. coli

Project description:UV-crosslinking and high througput sequencing of cDNAs (CRAC) was used to map the binding sites Hfq in enterohaemorhaggic E. coli (EHEC). Hfq was tagged with a His-FLAG dual affintiy tag and UV crosslinked after growth in the MEM-HEPES media essentailly as per Granneman et al (2009) PNAS. We additionally crosslinked Hfq in non-pathogenic E. coli K12 str. MG1655 grown in LE media. Hfq-RNA complexes were purified and trimmed using RNase A/T1. RNA fragments were isolated and converted to cDNA, PCR amplified and sequenced using Illumina Solexa GAxII and HiSeq2000 platforms. His-FLAG tagged Hfq and untagged controls were cultured to an OD of 0.8 and crosslinked with UV-C. Five replicates of tagged EHEC Hfq and 2 replicates of untagged Hfq were crosslinked. We have additionally crosslinked 2 replicates each of E. coli K12 tagged and untagged Hfq.

2014-05-22 | E-GEOD-46118 | biostudies-arrayexpress

ChIP-seq of Ndt80 in a C. albicans, C. dubliniensis and C. tropicalis during biofilm formation in different media

Project description:The purpose of this experiment was to identify the genes bound by the regulator Ndt80 in C. albicans, C. dubliniensis and C. tropicalis during biofilm formation in different growth media. Ndt80 was tagged with a c-myc epitope in the three species and the immunoprecipitation of the tagged strain was compared to that of an untagged control strain in two different media for each species.

2021-04-14 | GSE161136 | GEO

Transcription profiling of T. brucei treated with dithiothreitol (DTT) or tunicamycin to invoke the unfolded protein response

Project description:Transcriptome responsiveness was further tested by attempts to invoke the unfolded protein repsonse (UPR), a classic ER-based pathway stimulated by the presence of increased levels of unfolded polypeptides. The UPR is mediated via transcriptional responses in both yeast and metazoan cells, and can be reliably activated by addition of dithiothreitol (DTT). Using DTT at concentrations that invoke a UPR in mammalian cells, Arabidopsis, yeast and other systems, we found that, in T. brucei, DTT exposure led to rapid cell death. We analysed the transcriptome at 1 mM DTT, under conditions where cells remained viable, as assessed by motility. part 1: 3 biological replicates of SMB cells grown under normal conditions, and 3 replicates of SMB cells treated with 1mM DTT for 1hr, as well as dye swaps were used. part 2: 3 biological replicates of SMB cells grown under normal conditions, and 3 replicates of SMB cells treated with 1mM DTT for 4hr, as well as dye swaps were used. The UPR can also be activated by addition of tunicamycin. Using tunicamycin at concentrations that invoke a UPR in mammalian cells, Arabidopsis, yeast and other systems, we found that, in T. brucei, tunicamycin exposure efficiently inhibits trypanosome N-glycosylation and that it resulted in growth arrest over a period of up to 24 hours. We analysed the transcriptome at 5 ?g/ml tunicamycin under conditions where cells remained viable, as assessed by motility. part 3: 3 biological replicates of SMB cells grown under normal conditions, and 3 replicates of SMB cells treated with 5 ?g/ml tunicamycin for 4hr, as well as dye swaps were used. part 4: 3 biological replicates of SMB cells grown under normal conditions, and 3 replicates of SMB cells treated with 5 ?g/ml tunicamycin for 24hr, as well as dye swaps were used.

2008-06-26 | E-MEXP-1533 | biostudies-arrayexpress

mRNA-seq of Arabidopsis mutants of UPR modulators responding to UPR inducers

Project description:The NGS-associated mRNA-seq analysis was conducted to survey transcriptome changes responding to three UPR inducers (tunicamycin, DTT, & Azetidine-2-cytosine) by four double mutant of three UPR-associated transcription factors (bZIP17, bZIP28, & bZIP60) and two activators (S1P & S2P).

2018-03-07 | GSE100371 | GEO

K. lactis Ste12-myc ChIP-Seq in pheromone-responding a cells

Project description:The purpose of this experiment was to determine the genes directly regulated by Ste12 in K. lactis. The experiment was performed in a cells to determine if the a-specific genes were bound by Ste12. Ste12 was tagged with c-myc and was immunoprecipitated with a c-myc antibody. Cells were starved in SD media lacking phosphate for 2 hours, then treated with 10µg/mL K. lactis alpha factor for 2 hours before harvesting. A control untagged strain was processed in parallel. The experiment was repeated 3 times, and sequenced on an Illumina HiSeq 2500. K. lactis Ste12-myc vs. untagged control under pheromone response condition with 3 technical replicates done on different days

2015-07-06 | E-GEOD-65792 | biostudies-arrayexpress

K. lactis Ste12-myc ChIP-Seq in pheromone-responding a cells

2015-07-06 | GSE65792 | GEO

Transcription profiling of S. cerevisiae unfolding response

Project description:The accumulation of unfolded proteins in the lumen of the endoplasmic reticulum (ER) causes stress and induces the unfolded protein response (UPR) which is characterised in part by the transcriptional induction of genes involved in assisting protein folding. Translational responses to ER stress have been less well described and here we report on a genome-wide analysis of translational regulation in the response to the ER stress-inducing agent dithiothreitol (DTT) in Saccharomyces cerevisiae. Although the observed polysome profiles were similar under control and ER stress conditions microarray analysis identified transcipt-specific translational regulation. Genes with functions in ribosomal biogenesis and assembly were translationally repressed under ER stress. In contrast mRNAs for known UPR genes, including the UPR transcription factor HAC1, the ER-oxidoreductase ERO1 and the ER-associated protein degradation (ERAD) gene DER1 were enriched in polysomal fractions under ER stress conditions. In addition, we show that splicing of HAC1 mRNA is required for efficient ribosomal loading and that Gcn2p is required for normal HAC1 splicing, so shedding light on the role of this protein kinase in the UPR pathway. Experiment Overall Design: Polyribosomes were extracted from S. cerevisiae cells treated with 2 mM DTT or water (control), and fractionated according to ribosome loading. Following RNA purification from these fractions, for each sub-polysomal and polysomal RNA sample, fractions from three independent extracts per treatment (DTT/control) were pooled.

2008-06-11 | E-GEOD-10091 | biostudies-arrayexpress

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