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Effect of Cell Free Nucleic Acids (CFNA) extracted from blood products (red blood cells, plasma, platelets) on macrophage/dendritic cells gene regulation

ABSTRACT: Effect of Cell Free Nucleic Acids (CFNA) extracted from blood products (red blood cells, plasma, platelets) on macrophage/dendritic cells gene regulation

PROVIDER: PRJNA408251 | ENA |

REPOSITORIES: ENA

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Effect of Cell Free Nucleic Acids (CFNA) extracted from blood products (red blood cells, plasma, platelets) on macrophage/dendritic cells gene regulation

Project description:Macrophages were exposed to CFNA from different blood products prior to gene expression array: Red Blood Cells units (RBC), Fresh Frozen Plasma Units (FFP) and Platelet Concentrates (PC). Extracts from PBS were used as controls. Biological triplicates were included with three different macrophage cell lines (M1, M2, M3).

2017-09-22 | GSE104108 | GEO

Effect of cell free nucleic acids extracted from blood products on human leukocytes gene regulation: mononuclear cells and macrophages

Project description:Effect of cell free nucleic acids extracted from blood products on human leukocytes gene regulation: mononuclear cells and macrophages

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Effect of blood product - derived Cell Free Nucleic Acids (CFNA) on peripheral mononuclear cells gene regulation

Project description:PBMC were exposed to Cell Free Nucleic Acids (CFNA) extracted from blood products eligible for transfusion: Red Blood Cell units (RBC), Fresh Frozen Plasma units (FFP). PBMC alone exposed to the same extract from PBS were used as a control (PBMC+control). PBMC alone were also used as control. The used positive control was PBMC exposed to Lipopolysaccharide (LPS)

2017-09-22 | GSE104107 | GEO

Effect of cell free nucleic acids extracted from blood products on human leukocytes gene regulation: mononuclear cells and macrophages

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-09-22 | GSE104109 | GEO

Human Sweat EV nucleic acids

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5mC oxidation products in the nucleic acids of the Basidiomycete fungi Laccaria bicolor and Coprinopsis cinerea

Project description:We analyzed oxidized 5-methylcytosine derivatives 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in nucleic acids of multicellular fungi Laccaria bicolor and Coprinopsis cinerea which have been used as models to study DNA methylation, developmental processes and symbiotic interactions. All three cytosine derivatives were detected in the genomes of both fungi, and importantly, we discovered 5carC in the RNA fractions, potentially including large non-coding, messenger RNAs and small RNA molecules, indicating gene regulatory functions of 5carC.

2022-01-16 | GSE185550 | GEO

The effect of AML on platelets

Project description:Early diagnosis of acute myeloid leukemia (AML) in the pre-leukemic stage remains a clinical challenge, as pre-leukemic patients show no symptoms, lacking any known morphological or numerical abnormalities in blood cells. Here, we demonstrate that platelets with structurally abnormal mitochondria emerge at the pre-leukemic phase of AML, preceding detectable changes in blood cell counts or detection of leukemic blasts in blood. We visualized frozen-hydrated platelets from mice at different time points during AML development in situ using electron cryo-tomography (cryo-ET) and identified intracellular organelles through an unbiased semi-automatic process followed by quantitative measurement. A large proportion of platelets exhibited changes in the overall shape and depletion of organelles in AML. Notably, 23% of platelets in pre-leukemic cells exhibit abnormal, round mitochondria with unfolded cristae, accompanied by a significant drop in ATP levels and altered expression of metabolism-related gene signatures. Our study demonstrates that detectable structural changes in pre-leukemic platelets may serve as a biomarker for the early diagnosis of AML.

2022-02-08 | GSE189844 | GEO

Identification of nucleic acids that supports protein renaturation

Project description:Many proteins require RNA to remain soluble in cell and tissue lysate. Here we used RNA- and DNA- immunoprecipitation to identify what types of nucleic acids are associated with these proteins after in vitro renaturation.

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Direct chemical reprogramming of human cord blood erythroblasts to induced megakaryocytes that produce platelets

Project description:The shortage of platelets is becoming increasingly prominent owing to their short shelf life, limited supply, and increasing demand in response to public health incidents. It is an attractive idea to obtain large numbers of transfusible megakaryocytes (MKs) and platelets from somatic cells via cell lineage reprogramming. However, generating human MKs from somatic cells using a pharmacological reprogramming approach has not been widely explored. Here, we report the successful generation of human induced MKs (iMKs) from cord blood erythroblasts (EBs) using a chemical reprogramming strategy with a combination of four small molecules (4M): Bix01294, RG108, VPA, and PD0325901. The iMKs exhibited the ability to produce proplatelets and release vital functional platelets in vitro, demonstrating their similarity to natural MKs. Importantly, after injection into mice, iMKs were able to mature and give rise to functional platelets that were incorporated into newly formed thrombi. The reprogramming process was carefully examined using single-cell RNA sequencing, which revealed an efficient, rapid, and successful cell fate conversion of EBs to iMKs by 4M via the intermediate state of bipotent precursors. Assay for transposase-accessible chromatin sequencing results indicated that 4M induced genome-wide chromatin remodeling during MK reprogramming from EBs. 4M drove the transition of the transcription factor gene network by downregulating the key erythroid transcription factor genes KLF1 and MYB and subsequently upregulating MK development-associated transcription factor genes, including FLI1 and MEIS1. This process eventually led human cord blood EBs to acquire the MK fate. Thus, our chemical reprogramming of cord blood EBs to iMKs provides a simple and efficient approach to generating clinically transfusible MKs and platelets.

2022-08-28 | GSE207654 | GEO

RNA-seq of tumor-educated platelets enables blood-based pan-cancer, multiclass and molecular pathway cancer diagnostics

Project description:We report RNA-sequencing data of 283 blood platelet samples, including 228 tumor-educated platelet (TEP) samples collected from patients with six different malignant tumors (non-small cell lung cancer, colorectal cancer, pancreatic cancer, glioblastoma, breast cancer and hepatobiliary carcinomas). In addition, we report RNA-sequencing data of blood platelets isolated from 55 healthy individuals. This dataset highlights the ability of TEP RNA-based 'liquid biopsies' in patients with several types with cancer, including the ability for pan-cancer, multiclass cancer and companion diagnostics. Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing EDTA anti-coagulant by standard centrifugation. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the Truseq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina Hiseq 2500 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the human reference genome using STAR, and intron-spanning reads were summarized using HTseq. The processed data includes 285 samples (columns) and 57736 ensemble gene ids (rows). The supplementary data file (TEP_data_matrix.txt) contains the intron-spanning read counts, after data summarization by HTseq.

2015-10-30 | E-GEOD-68086 | biostudies-arrayexpress

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