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rna-seq experiments and data analyses (Macrogen)

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Macrogen rna-seq experiments and data analyses
Rna Seq Experiments And Data Analyses, supplied by Macrogen, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/rna+seq+data+analyses/rna+seq/pm38175358-77-0-8
Average 90 stars, based on 1 article reviews

rna-seq experiments and data analyses - by Bioz Stars, 2026-10

90/100 stars

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RNA Sequencing:

Article Title: Aberrant multicellular interferon signaling underlies Adar1 mutation-driven Aicardi-Goutières syndrome-like encephalopathy.
Article Snippet: Total RNA was extracted from isolated brains using TRIzol reagent (Thermo Fisher Scientific) by following the manufacturer’s instructions as previously described.46 After measuring the RNA concentration using a NanoDrop One (Thermo Fisher Scientific), total RNA samples were stored at − 80◦C until use. .. Poly(A) RNA-seq analyses were performed at Macrogen (Tokyo, Japan), including the removal of ribosomal RNA for total RNA-seq and a library preparation. .. The library samples were subjected to deep sequencing using Illumina NovaSeq 6000 sequencing platforms with 101-bp paired-end reads as previously described.46 RNA sequencing reads were mapped to the mouse reference genome, GRCm39, using STAR 2.7.11a.78 The resulting alignments were then assembled into potential transcripts and quantified using StringTie 2.2.179, generating a sample-by-gene count table.

Article Title: ZSTK3744, a novel aryl hydrocarbon receptor agonist, exhibits efficacy against chemotherapy-resistant triple-negative breast cancer
Article Snippet: 231 232 Gene expression analysis 233 Total RNA was extracted from the breast cancer cells using the RNeasy Mini Kit (74104, Qiagen, 234 Hilden, Germany) according to the manufacturer’s instructions. .. RNA-seq analysis of MM468/AR 235 and MM468/PR cells was performed by Macrogen Japan Corp (Tokyo, Japan). .. DNA microarray of 236 MM468 cells treated with ZSTK3744 was conducted by Filgen, Inc. (Aichi, Japan).

Article Title: MAPK/PMK-1 innate immune signaling protects the nematode Caenorhabditis elegans from increased intestinal colonization in an animal host-pathogen model in space.
Article Snippet: Statistical Analysis AR TI CL E IN P RE SS Statistical analyses (as detailed in each figure legend) were performed using Microsoft Excel software (Microsoft, USA) and GraphPad Prism (Prism 10 for Windows 64-bit, GraphPad Software, LLC). .. RNA-seq data were processed by Macrogen NGS Service, and differential gene expression was analyzed using DESeq2 with a negative binomial Wald test. ..

Article Title: Fibroblast- and Macrophage-Derived Thrombospondin-1 Orchestrates the Fibroinflammatory Niche in Metabolic Dysfunction-Associated Steatohepatitis-Induced Fibrosis.
Article Snippet: Serum concentrations of THBS1 and FAP were quantified using ELISA kits (THBS1: ab051274; FAP: ab053429; IL-6: ab178013) from Abcam (Cambridge, UK) according to the manufacturer’s instructions. .. Single-cell RNA sequencing (scRNA-seq) was outsourced to Macrogen Inc. (Seoul, Korea). .. Liver tissues from control, CDAHFD, CDAHFD+nintedanib-treated mice and CDAHFD+resmetiromtreated mice (n=2 per group) were enzymatically dissociated into single-cell suspensions using the MACS Liver Dissociation Kit (Miltenyi Biotec).

Analysis:

Isolation:

Article Title: ER-phagy drives resistance to mitochondria-targeted therapy in breast cancer.
Article Snippet: .. In brief, 1 × 106 cells were plated in 10 cm dishes and treated with 3 μg/ml ISOXUS or DMSO for 24 h. Total RNA was isolated using the High Pure RNA Isolation Kit (Roche Diagnostics), and RNA-Seq libraries were prepared and sequenced by Macrogen (Seoul, South Korea). ..

RNA sequencing:

Next-Generation Sequencing:

Gene Expression:

Single Cell:

other:

Article Title: Newly isolated human-derived Lactobacillus fermentum strain stimulates IFN-γ-secreting CD8 + T cells for enhanced anti-cancer immunity
Article Snippet: RNA-seq and statistical analyses were conducted by Macrogen Inc. (Seoul, South Korea).

Article Title: CD32b defines distinct dendritic cell lineages generated from the culture of bone marrow with GM-CSF
Article Snippet: Cell sorting was performed on a BD FACSAria II cell sorter (BD Biosciences), and sorted cells were collected into FBS-coated tubes containing ice-cold DMC7 medium.

Article Title: Supernatants from DNase-deficient Prevotella intermedia strains enhance oral squamous cell carcinoma cell migration and invasion by activating inflammatory and epithelial-mesenchymal transition pathways.
Article Snippet: Introductions: Oral squamous cell carcinoma (OSCC) has been increasingly associated with dysbiosis of the oral microbiome.. Among oral pathogens, Prevotella intermedia (P. intermedia) is frequently enriched in patients with OSCC; however, the role of its virulence factors—particularly its deoxyribonuclease (DNase) activity—remains

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$Generating a humanized stroma PDX (HS-PDX). A Tumor growth curves (i–iii) and (iv) summary of relative final tumor volumes of HS-PDXs with the indicate EC (combination iHUVEC/iHDMEC or EPC sources. TC + CA-MSC in the absence or presence of human EC (TC + CA-MSC; n = 6) (iHDMEC + iHUVEC) and Pt. EC/EPC (TC + CA-MSC + EC/EPC; n = 7). Tumor volumes in A (iv) are normalized TC + CA-MSC alone at 100%. B Representative IF evaluation of human tumor vascular antigen CD31 (red) in PDXs with the indicated EC/EPC sources. 4′,6-diamidino-2-phenylindole (DAPI; blue) was used to label cell nuclei. C IF evaluation of a tumor-specific vascular marker EGFL6 (red). Cell nuclei were counterstained with DAPI (blue). D RNA-Seq-based relative mRNA expression for two patient PDXs without and with the addition of human endothelial cells. E Growth curves for standard PDX and HS-PDX, derived from a patient with platinum refractory ovarian cancer, treated with carboplatin (blue arrows indicate timing of carboplatin administration ( n = 4–7/treatment group). Tumor volumes are internally normalized to the initial measurement for each tumor (~ 100 mm 3 ). Abbreviations : CA-MSC, cancer-associated mesenchymal stem cells; EC, endothelial cells; EPC, endothelial progenitor cells; iHDMEC, immortalized human dermal microvascular endothelial cells; iHUVEC, immortalized human umbilical vein endothelial cells; PDX, patient-derived xenograft; P0 and P1, passage 0 and passage 1. The first generation of PDX is denoted P0, and P0 is subsequently passaged to second generation (P1); Pt., patient; TC, tumor cells. * p < 0.05, ** p < 0.01, *** p < 0.001. Scale bars in B and C are 20 µm$

Journal: Cancer Immunology, Immunotherapy : CII

Article Title: A novel humanized immune stroma PDX cancer model for therapeutic studies

doi: 10.1007/s00262-026-04349-4

Figure Lengend Snippet: Generating a humanized stroma PDX (HS-PDX). A Tumor growth curves (i–iii) and (iv) summary of relative final tumor volumes of HS-PDXs with the indicate EC (combination iHUVEC/iHDMEC or EPC sources. TC + CA-MSC in the absence or presence of human EC (TC + CA-MSC; n = 6) (iHDMEC + iHUVEC) and Pt. EC/EPC (TC + CA-MSC + EC/EPC; n = 7). Tumor volumes in A (iv) are normalized TC + CA-MSC alone at 100%. B Representative IF evaluation of human tumor vascular antigen CD31 (red) in PDXs with the indicated EC/EPC sources. 4′,6-diamidino-2-phenylindole (DAPI; blue) was used to label cell nuclei. C IF evaluation of a tumor-specific vascular marker EGFL6 (red). Cell nuclei were counterstained with DAPI (blue). D RNA-Seq-based relative mRNA expression for two patient PDXs without and with the addition of human endothelial cells. E Growth curves for standard PDX and HS-PDX, derived from a patient with platinum refractory ovarian cancer, treated with carboplatin (blue arrows indicate timing of carboplatin administration ( n = 4–7/treatment group). Tumor volumes are internally normalized to the initial measurement for each tumor (~ 100 mm 3 ). Abbreviations : CA-MSC, cancer-associated mesenchymal stem cells; EC, endothelial cells; EPC, endothelial progenitor cells; iHDMEC, immortalized human dermal microvascular endothelial cells; iHUVEC, immortalized human umbilical vein endothelial cells; PDX, patient-derived xenograft; P0 and P1, passage 0 and passage 1. The first generation of PDX is denoted P0, and P0 is subsequently passaged to second generation (P1); Pt., patient; TC, tumor cells. * p < 0.05, ** p < 0.01, *** p < 0.001. Scale bars in B and C are 20 µm

Article Snippet: RNA-seq data analyses were performed by Novogene and Dr. Hui Shen’s research group.

Techniques: Marker, RNA Sequencing, Expressing, Derivative Assay

Identifying the optimal humanized bone marrow mouse type for the humanized immune stroma PDX (HIS-PDX). PDX models established in immunodeficient NSG, humanized HuNSG-SGM3 and humanized BLT mice were named as NSG-PDX, HuSGM3-PDX and BLT-PDX models, respectively. A-C RNA-seq-based mRNA analysis of the indicated lymphocyte ( A ), myeloid cell ( B ) and NK cell ( C ) markers genes in NSG-PDX, HuSGM3-PDX and BLT-PDX tumors. Expression is normalized using the expression in matched primary patient-derived tumor. D IF for human CD3, CD8, CD14 and CD163 evaluating tumor immune infiltrates in the indicated PDX tumor models. Cell nuclei were counterstained with DAPI (blue). Scale bars, 20 µm

Journal: Cancer Immunology, Immunotherapy : CII

Article Title: A novel humanized immune stroma PDX cancer model for therapeutic studies

doi: 10.1007/s00262-026-04349-4

Figure Lengend Snippet: Identifying the optimal humanized bone marrow mouse type for the humanized immune stroma PDX (HIS-PDX). PDX models established in immunodeficient NSG, humanized HuNSG-SGM3 and humanized BLT mice were named as NSG-PDX, HuSGM3-PDX and BLT-PDX models, respectively. A-C RNA-seq-based mRNA analysis of the indicated lymphocyte ( A ), myeloid cell ( B ) and NK cell ( C ) markers genes in NSG-PDX, HuSGM3-PDX and BLT-PDX tumors. Expression is normalized using the expression in matched primary patient-derived tumor. D IF for human CD3, CD8, CD14 and CD163 evaluating tumor immune infiltrates in the indicated PDX tumor models. Cell nuclei were counterstained with DAPI (blue). Scale bars, 20 µm

Article Snippet: RNA-seq data analyses were performed by Novogene and Dr. Hui Shen’s research group.

Techniques: RNA Sequencing, Expressing, Derivative Assay

Analysis of complete humanized immune stroma PDX (HIS-PDX). HIS-PDX were created by co-engraftment of PDX TC, CA-MSC and EC (iHUVEC + iHDMEC). A IF for alpha smooth muscle actin (αSMA; red), and human-specific mitochondrial antigen (hMitoc; green) or pan-cytokeratin (PanCK; green) to label tumor cells in standard and HIS-PDX. Cell nuclei were counterstained with DAPI (blue) ( n = 3). B Hematoxylin and eosin (H&E) staining for a cell line-derived xenograft, standard PDX, humanized immune stroma PDX (HIS-PDX) and matched patient’s primary tumor ( n = 3). C RNA-seq derived heat map for stromal and immune gene expression in solid tumor-derived standard PDXs (StndPDX), HIS-PDX and patient primary tumor ( n = 3). D Total gene expression correlation between primary human tumor and primary tumor-derived HIS-PDX for patient 1 and patient 4. Scale bars in ( A ), 40 µm; scale bars in ( B ), 100 µm

Journal: Cancer Immunology, Immunotherapy : CII

Article Title: A novel humanized immune stroma PDX cancer model for therapeutic studies

doi: 10.1007/s00262-026-04349-4

Figure Lengend Snippet: Analysis of complete humanized immune stroma PDX (HIS-PDX). HIS-PDX were created by co-engraftment of PDX TC, CA-MSC and EC (iHUVEC + iHDMEC). A IF for alpha smooth muscle actin (αSMA; red), and human-specific mitochondrial antigen (hMitoc; green) or pan-cytokeratin (PanCK; green) to label tumor cells in standard and HIS-PDX. Cell nuclei were counterstained with DAPI (blue) ( n = 3). B Hematoxylin and eosin (H&E) staining for a cell line-derived xenograft, standard PDX, humanized immune stroma PDX (HIS-PDX) and matched patient’s primary tumor ( n = 3). C RNA-seq derived heat map for stromal and immune gene expression in solid tumor-derived standard PDXs (StndPDX), HIS-PDX and patient primary tumor ( n = 3). D Total gene expression correlation between primary human tumor and primary tumor-derived HIS-PDX for patient 1 and patient 4. Scale bars in ( A ), 40 µm; scale bars in ( B ), 100 µm

Article Snippet: RNA-seq data analyses were performed by Novogene and Dr. Hui Shen’s research group.

Techniques: Staining, Derivative Assay, RNA Sequencing, Gene Expression

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Related Articles

RNA Sequencing:

Analysis:

Isolation:

RNA sequencing:

Next-Generation Sequencing:

Gene Expression:

Single Cell:

other:

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