B941c907-e0b5-412a-a67d-f844e48a98e6 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001010004 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Treg and Tfh cells (8 Samples)from the same donors was subject to RNA-seq (TruSeq Stranded Total RNA) processing. Single end fastq-files are supplied.
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Project description:Treg and Tfh cells (8 Samples)from the same donors was subject to ATAC-seq processing. Paired end fastq-files are supplied.
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Project description:The aim of this study was to investigate the transcriptome of 35 primary samples of pediatric patients diagnosed with T-cell acute lymphoblastic leukemia and 6 samples of healthy T-cell precursor subsets from pediatric donors (3 samples of CD34+ and 3 samples of CD4+ CD8+ thymic subsets). Samples were collected before treatment. Sequencing libraries were obtained with Illumina TruSeq Stranded mRNA protocol, with modified conditions of RNA fragmentation (90°C for 2 minutes). All libraries were sequenced on Illumina NovaSeq6000 platform, in 2x150PE mode (paired end sequencing with 150 nt reads), with a coverage of 150M reads/sample.
2025-12-31 | E-MTAB-14919 | biostudies-arrayexpress
Project description:SLAM-seq (thiol(SH)-linked alkylation for the metabolic sequencing of RNA) was applied to human primary CD8⁺ T cells subjected to in vitro activation with αCD3/αCD28 beads. To quantify mRNA half-lives and their dynamic changes during CD8⁺ T cell activation, we implemented a pulse-chase design with 24 hours of labelling using 100 µM 4-thiouridine (4SU), replenished every 4 hours with fresh RPMI medium containing 100 µM 4SU. This was followed by uridine washout for 0, 0.5, 1, 3, 6, and 16 hours. Samples were collected from non-activated, Day1-activated, and Day5-activated CD8⁺ T cells at each washout step (2 donors per time point). These datasets provide transcriptome-wide measurements of mRNA half-lives and reveal how mRNA turnover alters upon T cell activation.
2025-10-15 | E-MTAB-15648 | biostudies-arrayexpress
Project description:Comparison of mRNA expression showed widespread changes in the circulating CD8+ but not CD4+ T-cells from patients with severe asthma. No changes were observed in the CD4+ and CD8+ T-cells in non-severe asthmatics versus healthy controls. Bioinformatics analysis showed that the changes in CD8+ T-cell mRNA expression were associated with multiple pathways involved in T-cell activation. As with mRNAs, we also observed widespread changes in expression of non-coding RNA species including natural antisense, pseudogenes, intronic long ncRNAs and long intergenic long ncRNAs in CD8+ T-cells from severe asthmatics. Measurement of the miRNA expression profile showed selective down-regulation of miR-28-5p in CD8+ T-cells and reduction of miR-146a and miR-146b in both CD4+ and CD8+ T-cells. mRNA samples were collected from circulating CD4+ and CD8+ T-cells from healthy donors as well as donors with severe and non-severe asthma.
2011-08-31 | E-GEOD-31773 | biostudies-arrayexpress
Project description:Plants aquire nitrogen from the soil, most commonly in the form of either nitrate or ammonium. Unlike ammonium, nitrate must be reduced (with NADH and ferredoxin as electron donors) prior to assimilation. Thus, nitrate nutrition imposes a substantially greater energetic cost than ammonium nutrition. Our goal was to compare the transcriptomes of nitrate-supplied and ammonium-supplied plants, with a particular interest in characterizing the differences in redox metabolism elicited by different forms of inorganic nitrogen. We used microarrays to compare the short-term transcriptional response to either nitrogen supply or ammonium supply in Arabidopsis roots. Genes upregulated or downregulated by nitrate only, ammonium only, or both ammonium and nitrate were identified and analyzed.
2011-05-28 | GSE29589 | GEO
Project description:mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites such as splice sites and polyadenylation sites when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA processing. However, the regulatory role of RNA structure in mRNA processing remains unclear. Here, we performed in vivo SHAPE chemical profiling on Arabidopsis nuclear RNAs and generated the in vivo nuclear RNA structure landscape. We found that nuclear mRNAs fold differently from cytosolic mRNAs. Notably, we discovered a two-nucleotide single-stranded RNA structure feature upstream of 5’ splice site that regulates splicing and is responsible for the selection of alternative 5’ splice sites. Moreover, we found branch point single-strandedness is associated with 3’ splice site recognition. We also identified an RNA structure feature comprising two close-by single-stranded regions that is specifically associated with both polyadenylation and alternative polyadenylation events. Our work demonstrates an RNA structure regulatory mechanism for mRNA processing.
2020-12-10 | GSE135711 | GEO
Project description:In the present study, RNA sequencing of 6 human keratinocytes cell samples was performed. They are 3 samples of Poly (I:C)-treated cells, and 3 samples from un-treated control cells, from 3 different human donors. Total RNA was isolated from the cell samples and one RNA sequencing library was prepared from the 6 RNA samples with the Illumina TruSeq Stranded mRNA HT technolog. This approach uses fragmentation, a poly-T oligo pulldown and sequencing adaptor ligation. RNA sequencing was performed on the Illumina NextSeq500 next generation sequencing system and its high output mode with 1x75 bp single-end red chemistry.
2021-08-29 | GSE129346 | GEO
Project description:We used antibodies coupled to magnetic beads (MACS) to purify cell types out of whole blood from healthy donors (CD4+ T cells, CD8+ T cells, and B cells). We also profiled whole blood (collected in Pax tubes) and Peripheral Blood Mononuclear cells obtained by Ficoll-Paque based separation. RNA was extracted using Trizol, amplified linearly twice, labeled with Cy5 and co-hybridized with amplified Stratagene human reference (labeled with Cy3). A reference experiement design type is where all samples are compared to a common reference. Keywords: reference_design
2006-05-23 | GSE4889 | GEO
Project description:Interferon (IFN)-α is the earliest cytokine signature observed in individuals at risk for type 1 diabetes (T1D), but its effect on the repertoire of HLA Class I (HLA-I)-bound peptides presented by pancreatic β-cells is unknown. Using immunopeptidomics, we characterized the peptide/HLA-I presentation in in-vitro resting and IFN-α-exposed β-cells. IFN-α increased HLA-I expression and peptide presentation, including neo-sequences derived from alternative mRNA splicing, post-translational modifications - notably glutathionylation - and protein cis-splicing. This antigenic landscape relied on processing by both the constitutive and immune proteasome. The resting β-cell immunopeptidome was dominated by HLA-A-restricted ligands. However, IFN-α only marginally upregulated HLA-A and largely favored HLA-B, translating into a major increase in HLA-B-restricted peptides and into an increased activation of HLA-B-restricted vs. HLA-A-restricted CD8+ T-cells. A preferential HLA-B hyper-expression was also observed in the islets of T1D vs. non-diabetic donors, and islet-infiltrating CD8+ T-cells from T1D donors were reactive to some HLA-B-restricted granule peptides. Thus, the inflammatory milieu of insulitis may skew the autoimmune response toward epitopes presented by HLA-B, hence recruiting a distinct T-cell repertoire that may be relevant to T1D pathogenesis.
2025-01-08 | PXD045265 | Pride