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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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    Related Articles

    RNA Sequencing:

    Article Title: Immune gene expression profiling reveals heterogeneity in luminal breast tumors
    Article Snippet: RNA sequencing (RNA-Seq) data was generated in 139 tumors and 92 histologically normal breast tissue paired samples that passed standard QC metrics at Macrogen Corporation on Illumina HiSeq4000 using TruSeq stranded RNA kit with Ribo-Zero for rRNA depletion and 100-bp paired-end method.

    Article Title: Immune gene expression profiling reveals heterogeneity in luminal breast tumors
    Article Snippet: RNA sequencing (RNA-Seq) data were generated in 139 tumors and 92 histologically normal breast tissue samples that passed on all quality control metrics at Macrogen Corporation on Illumina HiSeq4000 using TruSeq stranded RNA kit with Ribo-Zero for rRNA depletion and 100-bp paired-end method.

    Generated:

    Article Title: Immune gene expression profiling reveals heterogeneity in luminal breast tumors
    Article Snippet: RNA sequencing (RNA-Seq) data was generated in 139 tumors and 92 histologically normal breast tissue paired samples that passed standard QC metrics at Macrogen Corporation on Illumina HiSeq4000 using TruSeq stranded RNA kit with Ribo-Zero for rRNA depletion and 100-bp paired-end method.

    Article Title: Immune gene expression profiling reveals heterogeneity in luminal breast tumors
    Article Snippet: RNA sequencing (RNA-Seq) data were generated in 139 tumors and 92 histologically normal breast tissue samples that passed on all quality control metrics at Macrogen Corporation on Illumina HiSeq4000 using TruSeq stranded RNA kit with Ribo-Zero for rRNA depletion and 100-bp paired-end method.

    Control:

    Article Title: Immune gene expression profiling reveals heterogeneity in luminal breast tumors
    Article Snippet: RNA sequencing (RNA-Seq) data was generated in 139 tumors and 92 histologically normal breast tissue paired samples that passed standard QC metrics at Macrogen Corporation on Illumina HiSeq4000 using TruSeq stranded RNA kit with Ribo-Zero for rRNA depletion and 100-bp paired-end method.

    Article Title: Immune gene expression profiling reveals heterogeneity in luminal breast tumors
    Article Snippet: RNA sequencing (RNA-Seq) data were generated in 139 tumors and 92 histologically normal breast tissue samples that passed on all quality control metrics at Macrogen Corporation on Illumina HiSeq4000 using TruSeq stranded RNA kit with Ribo-Zero for rRNA depletion and 100-bp paired-end method.



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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 <t>RNA-Seq-based</t> 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
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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 <t>RNA-Seq-based</t> 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
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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 <t>RNA-Seq-based</t> 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
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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 <t>RNA-Seq-based</t> 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
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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 <t>RNA-Seq-based</t> 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
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    rna sequencing (rna-seq) data analyses  (Novogene)
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    Novogene rna sequencing (rna-seq) data analyses
    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 <t>RNA-Seq-based</t> 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
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    Image Search Results


    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