Ontology highlight
ABSTRACT:
PROVIDER: PRJNA782791 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Expression analysis of Alpha-gliadin Genes in Bread Wheat
| PRJNA683747 | ENA
Project description:The alpha gliadins are a complex group of proteins with very similar sequences that comprise about 15-20% of the total flour protein and contribute to the functional properties of wheat flour dough. Some alpha gliadins also contain immunodominant epitopes relevant to celiac disease, a chronic autoimmune disease that affects nearly 1.4% of the worldwide population. In an attempt to reduce the immunogenic potential of wheat flour in the U.S. spring wheat cultivar Butte 86, RNA interference was used to silence a subset of alpha gliadin genes encoding proteins containing celiac disease epitopes. Two of the resulting transgenic lines were analyzed in detail by quantitative two-dimensional gel electrophoresis combined with tandem mass spectrometry. Although only some genes were targeted by the RNA interference construct, all alpha gliadins were effectively silenced in the transgenic plants. Some off-target silencing of high molecular weight glutenin subunits also was detected in both transgenic lines even though there was no homology with the target sequence. Reactivities of IgG and IgA serum antibodies from a cohort of patients with confirmed cases of celiac disease were decreased in flour from the two transgenic lines relative to the non-transgenic line. However, functional properties of the flour were also altered in the transgenic lines as evidenced by decreases in both mixing times and SDS sedimentation values. Although it may be possible to reduce the immunogenic potential of the flour and retain the viscoelastic properties essential for the utilization of wheat by eliminating only the most immunogenic alpha gliadins, the data suggest that it will be very difficult to selectively silence specific genes within families as complex as the wheat alpha gliadins.
2020-02-28 | PXD016930 | Pride
Project description:Genome editing was conducted on a t(3;8) K562 model to investigate the effects of deleting different modules or CTCF binding sites within the MYC super-enhancer. To check mutations after targeting with CRISPR-Cas9 we performed amplicon sequencing using the Illumina PCR-based custom amplicon sequencing method using the TruSeq Custom Amplicon index kit (Illumina). The first PCR was performed using Q5 polymerase (NEB), the second nested PCR with KAPA HiFi HotStart Ready mix (Roche). Samples were sequenced paired-end (2x 250bp) on a MiSeq (Illumina).
2021-07-26 | E-MTAB-9937 | biostudies-arrayexpress
Project description:Following a CRISPR enhancer scan covering the GATA2 super-enhancer region, the top sgRNAs were selected for further inspection. MUTZ3 cells were thus treated with the selected sgRNAs and the region of interested was subjected to amplicons sequencing (amplicon-seq). To that end, we used the Illumina PCR-based custom amplicon sequencing method using the TruSeq Custom Amplicon index kit (Illumina). The same experiment was conducted in K562 cells, which do not harbor an inv(3)/t(3;3), to investigate the role of MYB in this enhancer in other leukemia settings
2021-07-26 | E-MTAB-9945 | biostudies-arrayexpress
Project description:This submission contains raw data obtained from RNA sequencing of mouse spleen cells. Spleen cells were derived from adult female HLA-DQ8, huCD4 transgenic Ab0 NOD mice, treated intravenously either with tolerogenic, immune-modifying nanoparticles containing gliadin (TIMP-GLIA), particles containing irrelevant control ovalbumin (TIMP-OVA), or not receiving treatment. Mice were then immunized with gliadin (except for negative controls), and spleens were collected after 28-30 days. Spleen cells were stimulated with gliadin (or controls) in culture for 72h, and RNA was obtained from cells for transcriptomic studies.
2019-11-21 | GSE140736 | GEO
Project description:Gluten proteins are responsible for the unique viscoelastic properties of wheat dough, but they also trigger the immune response in celiac disease patients. RNA interference (RNAi) wheat lines with strongly silenced gliadins were obtained to reduce the immunogenic response of wheat. The E82 line presents the highest reductions of gluten, but other grain proteins increased, maintaining a total nitrogen content comparable to that of the wild type. To better understand the regulatory mechanisms in response to gliadin silencing, we carried out a transcriptomic analysis of grain and leaf tissues of the E82 line during grain filling. A network of candidate transcription factors (TFs) that regulates the synthesis of the seed storage proteins (SSPs), α-amylase/trypsin inhibitors, lipid transfer proteins, serpins, and starch in the grain was obtained. Moreover, there were a high number of differentially expressed genes in the leaf of E82, where processes such as nutrient availability and transport were enriched. The source-sink communication between leaf and grain showed that many down-regulated genes were related to protease activity, amino acid and sugar metabolism, and their transport. In the leaf, specific proline transporters and lysine-histidine transporters were down- and up-regulated respectively. Overall, the silencing of gliadins in the RNAi line is compensated mainly with lysine-rich globulins, which are not related to the proposed candidate network of TFs, suggesting that these proteins are independently regulated to the other SSPs. Results reported here can explain the protein compensation mechanisms and contribute to decipher the complex TF network operating during grain filling.
2022-07-26 | GSE199525 | GEO
Project description:Gliadin triggers T-cell mediated immunity in celiac disease, and has cytotoxic effects on enterocytes mediated through obscure mechanisms. In addition, gliadin transport mechanisms, potential cell surface receptors and gliadin-activated downstream signaling pathways are not completely understood. In order to screen for novel downstream gliadin target genes we performed a systematic whole genome expression study on intestinal epithelial cells. Undifferentiated Caco-2 cells were exposed to pepsin- and trypsin- digested gliadin (PT-G), a blank pepsin-trypsin control (PT) and to a synthetic peptide corresponding to gliadin p31-43 peptide for six hours. RNA from four different experiments was used for hybridization on Agilent one color human whole genome DNA microarray chips. The microarray data were analyzed using the Bioconductor package LIMMA. Genes with nominal p < 0.01 were considered statistically significant. Compared to the untreated cells 1705, 1755 and 211 probes were affected by PT-G, PT and p31-43 respectively. 46 probes were significantly different between PT and PT-G treated cells. Among the p31-43 peptide affected probes, 10 and 21 probes were affected by PT-G and PT respectively. Only PT-G affected genes could be validated by quantitative real-time polymerase chain reaction. All the genes were, nonetheless, also affected to a comparable level by PT treated negative controls. In conclusion, we could not replicate previously reported direct effects of gliadin peptides on enterocytes. The PT-G affected genes in the microarray analysis were validated by qRT-PCR, however these genes were also affected by PT treated negative controls suggesting that certain epitopes derived from pepsin and trypsin may also affect epithelial cell gene transcription. Our study demonstrates novel non-enzymatic effects of pepsin and trypsin on cells and calls for proper controls in pepsin and trypsin digested gliadin experiments. It is conceivable that gliadin effects on enterocytes are secondary mediated through oxidative stress, NFkB activation and IL-15 up-regulation. In total, 16 samples were analyzed of which 4 were control (MED) samples, 4 samples of p31-43 treatment, 4 samples of PT treatmetn and 4 samples of PT-G treatment
2013-03-21 | E-GEOD-45357 | biostudies-arrayexpress
Project description:Amplicon-based sequencing of Pentavalent specific T-cells (unedited pathogen-specific T-cells targeting CMV, EBV, BKV, adenovirus and Aspergillus fumigatus) and Cerberus T-cells (CRISPR/Cas9 edited Glucocorticoid-resistant T-cells targeting CMV, EBV, BKV, adenovirus and Aspergillus fumigatus) for off-target sites prediction.
2021-01-14 | E-MTAB-9968 | biostudies-arrayexpress
Project description:It is well documented that biostimulants could play an important role in agriculture. Additionally, increased fertilizer use efficiency is essential for maintaining both yield and grain quality, especially for bread wheat, which is a major global crop. In the present study, we explored the effects of mixing urea-ammonium-nitrate fertilizer with Glutacetine® on the physiological responses, agronomic traits and grain quality of winter wheat. Grain proteome analysis revealed that Glutacetine strongly reduced 11 proteins including storage proteins. Indeed, 2 alpha-gliadins and 2 avenin-like proteins decreased after Glutacetine application, which were good for celiac disease patients. Moreover, 2 glutenin HMW subunit were reduced, changing the gliadin/glutenin ratio and the HMW/LMW ratio, thus modifying the wheat flour dough quality. Our investigation reveals the important role of these formulations in achieving significant increases in seed yield and grain quality.
2021-09-09 | PXD021512 | Pride