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Gene expression profile at single cell level of two TDT patients' PBMCs after gene editing treatment.

ABSTRACT: Gene expression profile at single cell level of two TDT patients' PBMCs after gene editing treatment.

PROVIDER: PRJNA842851 | ENA |

REPOSITORIES: ENA

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Gene expression profile at single cell level of two TDT patients' PBMCs after gene editing treatment.

Project description:BCL11A encodes for a zinc-finger transcription factor that plays an important role in B-cell and pDC development. Although the +58 BCL11A enhancer we disrupted was reported as a erythroid specific enhancer, we needed to further evaluate the potential down regulation of BCL11A in other subpopulations of edited PBMCs. To study the transcriptional impact of BCL11A enhancer gene editing, we performed single-cell RNA sequencing (scRNA-seq) on PBMCs.

2022-05-29 | GSE204688 | GEO

Transcription profiling of Arabidopsis mutant tdt-1 and wild type

Project description:The object of this study was to explore whether the loss of mRNA decapping in the Arabidopsis mutant tdt-1 resulted in global dfferences of RNA profiles, as compared to wild type. Experiment Overall Design: In this experiment we compared expression in tdt-1 and wild type 3 day whole seedlings. We performed three biological replicates, in which one experiment was dye-swapped.

2008-06-15 | E-GEOD-7359 | biostudies-arrayexpress

Oligonucleotide library synthesis using TdT

Project description:Oligonucleotide library synthesis using TdT

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Comparing the transcriptome expression differences between breast cancer cells EO771-tdT-Parental and EO771-tdT-LM2 using high-throughput sequencing.

Project description:The molecular mechanisms that regulate breast cancer cell (BCC) metastasis and proliferation within the leptomeninges (LM) are poorly understood, limiting development of effective therapies. Here we show that BCCs in mice can invade the LM by abluminal migration along blood vessels that connect vertebral/calvarial bone marrow and meninges, bypassing the blood-brain barrier. To screen for signaling pathways in EO-LM2 cells that could support their survival or proliferation in the meningeal niche, we performed RNA-seq analysis of EO771-tdT-Parental and EO771-tdT-LM2 to compare their transcriptome expression differences.

2025-04-03 | GSE263184 | GEO

Characterizing gene expression changes that accompany succinate dehydrogenase subunit B (SDHB) RNA editing in monocyte-enriched peripheral blood mononuclear cell cultures

Project description:The goal of this study is to identify global changes in gene expression that accompany induction of site-specific RNA editing that targets the SDHB gene in monocyte-enriched peripheral blood mononuclear cell cultures. The results provide important information to understand the function of this programmed SDHB RNA mutation within the context of global gene expression changes that occur in cultured immune cells when the editing is induced. The study also specifically tests whether expression changes occur in SDH subunit genes, cytidine deaminase family of genes and hypoxia-inducible pathways. Overall design includes pairwise comparison of total gene expression profiles from uncultured cold-aggregated PBMCs (day 0), low-editing (culture day 3) and high-editing (culture days 5-8) samples, each from 4 donors. Submitted manuscript reported summary results from comparison of cultured low- and high-editing samples.

2013-04-10 | E-GEOD-45900 | biostudies-arrayexpress

A-to-I mRNA editing enables bacteria to produce two protein versions from a single gene and affects bacterial growth

Project description:Adenosine-to-inosine (A-to-I) mRNA editing can affect the sequence and function of translated proteins because the ribosome reads inosine (I) as guanosine (G). Previously, we discovered that A-to-I mRNA editing occurs in Escherichia coli. However, the prevalence of A-to-I mRNA editing across bacteria and its biological significance are still unknown. Here, we show that A-to-I mRNA editing occurs in hundreds of genes across dozens of bacterial species. We find that editing events occur within and require a conserved sequence motif. Notably, most editing events (80%) are predicted to recode protein sequences. Indeed, by mass spectrometry, we show for the first time that A-to-I mRNA editing enables bacteria to produce two versions of a protein from a single gene. Finally, we find that perturbing mRNA editing in Acinetobacter baylyi affects bacterial growth, especially at high temperatures. Overall, our work reveals that A-to-I mRNA editing is widespread and can impact bacterial physiology, likely by modulating protein function

2025-07-21 | PXD051887 | Pride

Next Generation Sequencing of T regulatory cells (GFP+, dTomato+) and ex-T regulatory cells (GFP-, dTomato+) harvested from lymph nodes of bone marrow chimeras (50% Foxp3GFP-tdT or Foxp3GFP-Fth/-tdT and 50% C57BL/6 bone marrow into Rag2-/- recipients)

Project description:Purpose: To address whether FTH regulates gene expression in TREG cells, irrespective of bystander inflammation. For this, we compared the gene expression profile of TREG and Ex-TREG cells sorted from the lymph nodes of mixed BM chimeras Results: Using an optimized data analysis workflow, we mapped an average 30.14 million sequence reads per sample to the mouse genome (build mm39) and identified 34,321 transcripts in the mRNA of Treg and Ex-Treg cells from mixed bone marrow chimeras. Differential gene expression was performed using the DESeq2 R package (v.1.32) and gene expression was modeled by genotype and condition. Differentially expressed genes were considered for genes with an adjusted p-value<0.05 and an absolute log2 fold change>0. Conclusions: Analysis of RNAseq data showed that Fth deletion in TREG cells (CD45.2+GFP+tdT+) developing from the BM of Foxp3GFP-Fth∆/∆-tdT mice, up-regulated 149 genes and down-regulation of 96 genes, compared to TREG cells from control Foxp3GFP-tdT mice. Ex-TREG cells (CD45.2+GFP-tdT+) up-regulated 90 genes and down-regulated 36 genes. The genes regulated in TREG and ex-TREG cells originating from the BM of Foxp3GFP-Fth∆/∆-tdT vs. Foxp3GFP-tdT mice were associated with the oxidative stress response regulated by NRF2 . This suggests that FTH exerts cell-autonomous control of TREG cell redox homeostasis, irrespective of bystander inflammation.

2024-01-29 | GSE226032 | GEO

Comparison of expression in Arabidopsis mutant tdt-1 and wild type

2007-07-31 | GSE7359 | GEO

Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee and macaque brains

Project description:we used RNA-Seq to quantify the RNA editing level at more than 8,000 previously annotated exonic A-to-I RNA editing sites in two brain regions - prefrontal cortex and cerebellum - of humans, chimpanzees and rhesus macaques. We observed substantial conservation of RNA editing levels between the brain regions, as well as among the three primate species. Evolutionary changes in RNA editing were nonetheless evident among the species. Across lifespan, we observed an increase of the RNA editing level with advanced age in both brain regions of all three primate species. poly(A) enriched RNAs extracted from pooled samples of two brain regions: CBC and PFC of chimpanzee and macaque, fragmented, revers transcribed to double-stranded cDNA using random hexamers. Sequencing libraries were prepared according to the paired-end non-strand-specific sample preparation protocol of Illumina. Each sample was sequenced in a separate lane in the Illumina Genome Analyzer II system, using the 75-bp paired-end sequencing protocol. human data was downloaded from SRA [SRP005169]

2014-01-07 | E-GEOD-45244 | biostudies-arrayexpress

Global gene expression analysis in PBMCs of individuals from normal and high level natural radiation areas of Kerala Coast, India

Project description:Gene expression changes in human populations exposed to chronic low level radiation have important implications. There are few areas around the world where human population is exposed to elevated levels of natural background radiation. The high level natural radiation areas (HLNRAs) of Kerala coast in south west India is unique for its wide variation in the background radiation dose (<1.0mGy to 45mGy/year). The areas with a background radiation dose of ≤ 1.5mGy/year are considered as normal level natural radiation areas (NLNRA), whereas areas with > 1.5mGy/year are considered as HLNRA. We used microarray analysis to find out global changes in gene expression in peripheral blood mononuclear cells (PBMCs) of individuals belonging to different HLNRA groups as compared to individuals from normal level natural radiation areas (NLNRA).

2017-10-26 | GSE95279 | GEO

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