genechip human transcriptome array 2 0  (Thermo Fisher)


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    Name:
    GeneChip Human Transcriptome Assay 2 0
    Description:
    Designed to empower next generation expression profiling studies the GeneChip Human Transcriptome Assay 2 0 provides the ability to go beyond gene level expression profiling by providing the coverage and accuracy required to accurately detect all known transcript isoforms produced by a gene View the data sheet for details on HTA 2 0 content and coverage Comprehensive exploration of the transcriptome Research has shown that the tens of thousands of human genes contain hundreds of thousands of exons which produce hundreds of thousands of different transcript isoforms These transcript isoforms are produced when the exons of a gene may be included within or excluded from the final processed messenger RNA produced from that gene Until now measuring and analyzing these transcript isoforms has been nearly impossible due to technology limitations sample input requirements and lack of analysis capabilities tools Comprehensive transcriptome analysis requires combining transcript diversity from multiple data sources Most genes produce multiple transcript isoforms and measuring changes in the relative abundance of each isoform provides new insights into disease and biology HTA 2 0 has combined multiple data sources to ensure you are able to independently analyze the broadest collection of transcript isoforms available Data sources used to design and annotate the assay RefSeq Vertebrate Genome Annotation Vega database Ensembl MGC Mammalian Gene Collection v10 UCSC Known Genes www noncode org UCSC lincRNA transcripts lncRNA db Broad Institute Human Body Map lincRNAs and TUCP transcripts of uncertain coding potential catalog Better data than 2 full lanes of sequencing See the HTA 2 0 Flyer in the Documents Section below for additional information HTA 2 0 provides superior accuracy and precision coupled with the most comprehensive view of the transcriptome Bioinformatics built into the array design no assembly required HTA 2 0 maximizes the amount of unique and valuable information possible by minimizing the conserved sequence synthesized on the array This high resolution array design contains an unprecedented 6 0 million probes covering coding transcripts and non coding transcripts 70 of the probes on this array cover exons for coding transcripts and the remaining 30 of probes on the array cover exon exon splice junctions and non coding transcripts The unparalleled coverage of this array provides the deepest insight into all coding and non coding transcripts available Simple fast and free analysis solution For the first time ever HTA 2 0 coupled with Expression Console Software and TAC Software offers researchers a complete solution from data to decision making in minutes This complete analysis solution is provided to all researchers using our expression arrays at no additional cost In addition HTA 2 0 data analysis is supported by the same analysis solutions and service providers being used for other expression array data Related LinksGeneChip Hybridization Wash and Stain Kit
    Catalog Number:
    902309
    Price:
    None
    Applications:
    DNA & RNA Microarray Analysis|Microarray Analysis
    Category:
    Microarrays PCR Arrays
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    Structured Review

    Thermo Fisher genechip human transcriptome array 2 0
    Comparison of toll-like receptors’ (TLRs) mRNA expressions by <t>GeneChip</t> ® human <t>transcriptome</t> array 2.0 between acute-stage Kawasaki disease patients and KD patients after receiving IVIG treatment Asterisks denote significance ( p
    Designed to empower next generation expression profiling studies the GeneChip Human Transcriptome Assay 2 0 provides the ability to go beyond gene level expression profiling by providing the coverage and accuracy required to accurately detect all known transcript isoforms produced by a gene View the data sheet for details on HTA 2 0 content and coverage Comprehensive exploration of the transcriptome Research has shown that the tens of thousands of human genes contain hundreds of thousands of exons which produce hundreds of thousands of different transcript isoforms These transcript isoforms are produced when the exons of a gene may be included within or excluded from the final processed messenger RNA produced from that gene Until now measuring and analyzing these transcript isoforms has been nearly impossible due to technology limitations sample input requirements and lack of analysis capabilities tools Comprehensive transcriptome analysis requires combining transcript diversity from multiple data sources Most genes produce multiple transcript isoforms and measuring changes in the relative abundance of each isoform provides new insights into disease and biology HTA 2 0 has combined multiple data sources to ensure you are able to independently analyze the broadest collection of transcript isoforms available Data sources used to design and annotate the assay RefSeq Vertebrate Genome Annotation Vega database Ensembl MGC Mammalian Gene Collection v10 UCSC Known Genes www noncode org UCSC lincRNA transcripts lncRNA db Broad Institute Human Body Map lincRNAs and TUCP transcripts of uncertain coding potential catalog Better data than 2 full lanes of sequencing See the HTA 2 0 Flyer in the Documents Section below for additional information HTA 2 0 provides superior accuracy and precision coupled with the most comprehensive view of the transcriptome Bioinformatics built into the array design no assembly required HTA 2 0 maximizes the amount of unique and valuable information possible by minimizing the conserved sequence synthesized on the array This high resolution array design contains an unprecedented 6 0 million probes covering coding transcripts and non coding transcripts 70 of the probes on this array cover exons for coding transcripts and the remaining 30 of probes on the array cover exon exon splice junctions and non coding transcripts The unparalleled coverage of this array provides the deepest insight into all coding and non coding transcripts available Simple fast and free analysis solution For the first time ever HTA 2 0 coupled with Expression Console Software and TAC Software offers researchers a complete solution from data to decision making in minutes This complete analysis solution is provided to all researchers using our expression arrays at no additional cost In addition HTA 2 0 data analysis is supported by the same analysis solutions and service providers being used for other expression array data Related LinksGeneChip Hybridization Wash and Stain Kit
    https://www.bioz.com/result/genechip human transcriptome array 2 0/product/Thermo Fisher
    Average 99 stars, based on 21 article reviews
    Price from $9.99 to $1999.99
    genechip human transcriptome array 2 0 - by Bioz Stars, 2020-09
    99/100 stars

    Images

    1) Product Images from "Identifying genetic hypomethylation and upregulation of toll-like receptors in Kawasaki disease"

    Article Title: Identifying genetic hypomethylation and upregulation of toll-like receptors in Kawasaki disease

    Journal: Oncotarget

    doi: 10.18632/oncotarget.14497

    Comparison of toll-like receptors’ (TLRs) mRNA expressions by GeneChip ® human transcriptome array 2.0 between acute-stage Kawasaki disease patients and KD patients after receiving IVIG treatment Asterisks denote significance ( p
    Figure Legend Snippet: Comparison of toll-like receptors’ (TLRs) mRNA expressions by GeneChip ® human transcriptome array 2.0 between acute-stage Kawasaki disease patients and KD patients after receiving IVIG treatment Asterisks denote significance ( p

    Techniques Used:

    Comparison of toll-like receptors’ (TLRs) mRNA expressions by GeneChip ® human transcriptome array 2.0 between Kawasaki disease patients after IVIG treatment and control subjects Asterisks denote significance ( p
    Figure Legend Snippet: Comparison of toll-like receptors’ (TLRs) mRNA expressions by GeneChip ® human transcriptome array 2.0 between Kawasaki disease patients after IVIG treatment and control subjects Asterisks denote significance ( p

    Techniques Used:

    Comparison of toll-like receptors’ (TLRs) mRNA expressions by geneChip ® human transcriptome array 2.0 between acute-stage Kawasaki disease patients and control subjects Asterisks denote significance ( p
    Figure Legend Snippet: Comparison of toll-like receptors’ (TLRs) mRNA expressions by geneChip ® human transcriptome array 2.0 between acute-stage Kawasaki disease patients and control subjects Asterisks denote significance ( p

    Techniques Used:

    2) Product Images from "Decreased Steroid Hormone Receptor NR4A2 Expression in Kawasaki Disease Before IVIG Treatment"

    Article Title: Decreased Steroid Hormone Receptor NR4A2 Expression in Kawasaki Disease Before IVIG Treatment

    Journal: Frontiers in Pediatrics

    doi: 10.3389/fped.2019.00007

    mRNA expressions of steroid hormone receptors by GeneChip® Human Transcriptome Array 2.0 between patients of Kawasaki disease (KD) and control subjects. Data are expressed as mean ± standard error for the three replications. * Significance ( p
    Figure Legend Snippet: mRNA expressions of steroid hormone receptors by GeneChip® Human Transcriptome Array 2.0 between patients of Kawasaki disease (KD) and control subjects. Data are expressed as mean ± standard error for the three replications. * Significance ( p

    Techniques Used:

    3) Product Images from "Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2"

    Article Title: Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2

    Journal: Frontiers in Oncology

    doi: 10.3389/fonc.2018.00104

    Nuclear factor κB (NF-κB) regulates hexokinase (HK) 2 in sarcoma cells. (A) Gene set enrichment analysis plot of MSigDB Mootha_Glycolysis gene signature in vector and IκBα SR expressing RH30 cells. Gene expression profile data were obtained by Affymetrix GeneChip Human Transcriptome Array 2.0. Nominal p -value
    Figure Legend Snippet: Nuclear factor κB (NF-κB) regulates hexokinase (HK) 2 in sarcoma cells. (A) Gene set enrichment analysis plot of MSigDB Mootha_Glycolysis gene signature in vector and IκBα SR expressing RH30 cells. Gene expression profile data were obtained by Affymetrix GeneChip Human Transcriptome Array 2.0. Nominal p -value

    Techniques Used: Plasmid Preparation, Expressing

    4) Product Images from "Identifying genetic hypomethylation and upregulation of toll-like receptors in Kawasaki disease"

    Article Title: Identifying genetic hypomethylation and upregulation of toll-like receptors in Kawasaki disease

    Journal: Oncotarget

    doi: 10.18632/oncotarget.14497

    Comparison of toll-like receptors’ (TLRs) mRNA expressions by GeneChip ® human transcriptome array 2.0 between acute-stage Kawasaki disease patients and KD patients after receiving IVIG treatment Asterisks denote significance ( p
    Figure Legend Snippet: Comparison of toll-like receptors’ (TLRs) mRNA expressions by GeneChip ® human transcriptome array 2.0 between acute-stage Kawasaki disease patients and KD patients after receiving IVIG treatment Asterisks denote significance ( p

    Techniques Used:

    Comparison of toll-like receptors’ (TLRs) mRNA expressions by GeneChip ® human transcriptome array 2.0 between Kawasaki disease patients after IVIG treatment and control subjects Asterisks denote significance ( p
    Figure Legend Snippet: Comparison of toll-like receptors’ (TLRs) mRNA expressions by GeneChip ® human transcriptome array 2.0 between Kawasaki disease patients after IVIG treatment and control subjects Asterisks denote significance ( p

    Techniques Used:

    Comparison of toll-like receptors’ (TLRs) mRNA expressions by geneChip ® human transcriptome array 2.0 between acute-stage Kawasaki disease patients and control subjects Asterisks denote significance ( p
    Figure Legend Snippet: Comparison of toll-like receptors’ (TLRs) mRNA expressions by geneChip ® human transcriptome array 2.0 between acute-stage Kawasaki disease patients and control subjects Asterisks denote significance ( p

    Techniques Used:

    5) Product Images from "Epigenetic hypomethylation and upregulation of matrix metalloproteinase 9 in Kawasaki disease"

    Article Title: Epigenetic hypomethylation and upregulation of matrix metalloproteinase 9 in Kawasaki disease

    Journal: Oncotarget

    doi: 10.18632/oncotarget.19650

    Comparison of matrix metalloproteinase (MMP) -8, -9, and -25 mRNA expressions by GeneChip ® Human Transcriptome Array 2.0 between acute-stage Kawasaki disease patients and control subjects * indicates significance ( p
    Figure Legend Snippet: Comparison of matrix metalloproteinase (MMP) -8, -9, and -25 mRNA expressions by GeneChip ® Human Transcriptome Array 2.0 between acute-stage Kawasaki disease patients and control subjects * indicates significance ( p

    Techniques Used:

    6) Product Images from "Decreased Steroid Hormone Receptor NR4A2 Expression in Kawasaki Disease Before IVIG Treatment"

    Article Title: Decreased Steroid Hormone Receptor NR4A2 Expression in Kawasaki Disease Before IVIG Treatment

    Journal: Frontiers in Pediatrics

    doi: 10.3389/fped.2019.00007

    mRNA expressions of steroid hormone receptors by GeneChip® Human Transcriptome Array 2.0 between patients of Kawasaki disease (KD) and control subjects. Data are expressed as mean ± standard error for the three replications. * Significance ( p
    Figure Legend Snippet: mRNA expressions of steroid hormone receptors by GeneChip® Human Transcriptome Array 2.0 between patients of Kawasaki disease (KD) and control subjects. Data are expressed as mean ± standard error for the three replications. * Significance ( p

    Techniques Used:

    7) Product Images from "NK cells produce high levels of IL‐10 early after allogeneic stem cell transplantation and suppress development of acute GVHD"

    Article Title: NK cells produce high levels of IL‐10 early after allogeneic stem cell transplantation and suppress development of acute GVHD

    Journal: European Journal of Immunology

    doi: 10.1002/eji.201747134

    The transcriptional profile of NK cells at day 14 following allo‐SCT compared to healthy donor NK cells. (A) The NK cells were enriched, total RNA was extracted, labelled and hybridized to GeneChip® Human Transcriptome array 2.0 (Affymetrix, USA). Volcano plot demonstrating overall transcript profile of D14‐NK ( n = 4) compared to NK cells from healthy donors ( n = 5). The expression of genes shown to the left is reduced in NK‐14 and those to the right are increased. (B) Heatmap displaying the differentially expressed genes between D14‐NK and NK cells from healthy donors (absolute log 2 FC > 1 and adjusted p ‐value of
    Figure Legend Snippet: The transcriptional profile of NK cells at day 14 following allo‐SCT compared to healthy donor NK cells. (A) The NK cells were enriched, total RNA was extracted, labelled and hybridized to GeneChip® Human Transcriptome array 2.0 (Affymetrix, USA). Volcano plot demonstrating overall transcript profile of D14‐NK ( n = 4) compared to NK cells from healthy donors ( n = 5). The expression of genes shown to the left is reduced in NK‐14 and those to the right are increased. (B) Heatmap displaying the differentially expressed genes between D14‐NK and NK cells from healthy donors (absolute log 2 FC > 1 and adjusted p ‐value of

    Techniques Used: Expressing

    8) Product Images from "Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2"

    Article Title: Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2

    Journal: Frontiers in Oncology

    doi: 10.3389/fonc.2018.00104

    Nuclear factor κB (NF-κB) regulates hexokinase (HK) 2 in sarcoma cells. (A) Gene set enrichment analysis plot of MSigDB Mootha_Glycolysis gene signature in vector and IκBα SR expressing RH30 cells. Gene expression profile data were obtained by Affymetrix GeneChip Human Transcriptome Array 2.0. Nominal p -value
    Figure Legend Snippet: Nuclear factor κB (NF-κB) regulates hexokinase (HK) 2 in sarcoma cells. (A) Gene set enrichment analysis plot of MSigDB Mootha_Glycolysis gene signature in vector and IκBα SR expressing RH30 cells. Gene expression profile data were obtained by Affymetrix GeneChip Human Transcriptome Array 2.0. Nominal p -value

    Techniques Used: Plasmid Preparation, Expressing

    9) Product Images from "Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2"

    Article Title: Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2

    Journal: Frontiers in Oncology

    doi: 10.3389/fonc.2018.00104

    Nuclear factor κB (NF-κB) regulates hexokinase (HK) 2 in sarcoma cells. (A) Gene set enrichment analysis plot of MSigDB Mootha_Glycolysis gene signature in vector and IκBα SR expressing RH30 cells. Gene expression profile data were obtained by Affymetrix GeneChip Human Transcriptome Array 2.0. Nominal p -value
    Figure Legend Snippet: Nuclear factor κB (NF-κB) regulates hexokinase (HK) 2 in sarcoma cells. (A) Gene set enrichment analysis plot of MSigDB Mootha_Glycolysis gene signature in vector and IκBα SR expressing RH30 cells. Gene expression profile data were obtained by Affymetrix GeneChip Human Transcriptome Array 2.0. Nominal p -value

    Techniques Used: Plasmid Preparation, Expressing

    10) Product Images from "Inhibition of miR-328–3p Impairs Cancer Stem Cell Function and Prevents Metastasis in Ovarian Cancer"

    Article Title: Inhibition of miR-328–3p Impairs Cancer Stem Cell Function and Prevents Metastasis in Ovarian Cancer

    Journal: Cancer research

    doi: 10.1158/0008-5472.CAN-18-3668

    DDB2 is a direct target of miR-328 and mediates the function of miR-328 in the regulation of CSC properties. A, Gene expression heatmap from microarray analysis of miR-328–overexpressing ovarian cancer cells. OV2008 cells were transfected with miR-328 mimics or NC miR for 2 days. Total RNA was isolated, and the differentially expressed genes were screened using GeneChip Human Transcriptome Array 2.0. B, Predicted binding of miR-328 to the 3′-UTR of DDB2 . C and D, Dual luciferase reporter assay shows the interaction of miR-328 and its targeting sequence in the DDB2 3′-UTR. OV2008 cells were transfected with psiCHECK-2 containing the wild-type (WT) or mutated (Mut) target site of the DDB2 3′-UTR ( C ) plus miR-328-M or NC miR for 48 hours. The luciferase activity was determined and normalized to the Firefly activity and presented as relative activity to the corresponding NC miR ( D ). N = 3; bar, SD; **, P
    Figure Legend Snippet: DDB2 is a direct target of miR-328 and mediates the function of miR-328 in the regulation of CSC properties. A, Gene expression heatmap from microarray analysis of miR-328–overexpressing ovarian cancer cells. OV2008 cells were transfected with miR-328 mimics or NC miR for 2 days. Total RNA was isolated, and the differentially expressed genes were screened using GeneChip Human Transcriptome Array 2.0. B, Predicted binding of miR-328 to the 3′-UTR of DDB2 . C and D, Dual luciferase reporter assay shows the interaction of miR-328 and its targeting sequence in the DDB2 3′-UTR. OV2008 cells were transfected with psiCHECK-2 containing the wild-type (WT) or mutated (Mut) target site of the DDB2 3′-UTR ( C ) plus miR-328-M or NC miR for 48 hours. The luciferase activity was determined and normalized to the Firefly activity and presented as relative activity to the corresponding NC miR ( D ). N = 3; bar, SD; **, P

    Techniques Used: Expressing, Microarray, Transfection, Isolation, Binding Assay, Luciferase, Reporter Assay, Sequencing, Activity Assay

    11) Product Images from "Circulating CD1c+ myeloid dendritic cells are potential precursors to LCH lesion CD1a+CD207+ cells"

    Article Title: Circulating CD1c+ myeloid dendritic cells are potential precursors to LCH lesion CD1a+CD207+ cells

    Journal: Blood Advances

    doi: 10.1182/bloodadvances.2019000488

    HLA-DQB2 is specifically expressed in LCH CD1c + mDCs, CD1a + CD207 − , CD1a + CD207 low , and CD1a + CD207 high subpopulations. (A) Scatter plots illustrate expression of 6 genes ( CD1a , CD1c , CD207 , TNFα , HLADQA2 , and HLADQB2 ) among the top 50 most overexpressed genes in LCH CD1a + CD207 + DCs relative to healthy donor blood CD1c + mDCs. Gene-expression profiles were obtained from FACS-sorted LCH lesion CD1a + CD207 + DCs (n = 11) and blood CD1c + mDCs (n = 3) from healthy donors. Affymetrix Human Transcriptome Array 2.0 Platform was used for this study. All samples used in the study are listed in supplemental Table 3a. (B) Control skin specimens (n = 4), peripheral blood samples (n = 4) from healthy donors, and lesion from LCH patients (n = 6) were FACS-purified. RNA was extracted, cDNA was amplified and then the HLA-DQB2 expression was determined by qPCR (normalized to GAPDH messenger RNA [mRNA] expression). HLA-DQB2 expression was detected in lesion CD1a + populations as well as CD1c + mDCs, but not in other lineages, consistent with BRAF V600E distribution. Epidermal LCs were used as a positive control. Technical duplicates were used. LCH samples used in the study are listed in supplemental Table 3b. (C) Overlay histograms of HLA-DQB2 surface expression in 6 LCH lesion subpopulations (colored) compared with control (gray) demonstrates increasing surface expression of HLA-DQB2 from lesion CD1c + mDCs through CD1a + CD207 + populations.
    Figure Legend Snippet: HLA-DQB2 is specifically expressed in LCH CD1c + mDCs, CD1a + CD207 − , CD1a + CD207 low , and CD1a + CD207 high subpopulations. (A) Scatter plots illustrate expression of 6 genes ( CD1a , CD1c , CD207 , TNFα , HLADQA2 , and HLADQB2 ) among the top 50 most overexpressed genes in LCH CD1a + CD207 + DCs relative to healthy donor blood CD1c + mDCs. Gene-expression profiles were obtained from FACS-sorted LCH lesion CD1a + CD207 + DCs (n = 11) and blood CD1c + mDCs (n = 3) from healthy donors. Affymetrix Human Transcriptome Array 2.0 Platform was used for this study. All samples used in the study are listed in supplemental Table 3a. (B) Control skin specimens (n = 4), peripheral blood samples (n = 4) from healthy donors, and lesion from LCH patients (n = 6) were FACS-purified. RNA was extracted, cDNA was amplified and then the HLA-DQB2 expression was determined by qPCR (normalized to GAPDH messenger RNA [mRNA] expression). HLA-DQB2 expression was detected in lesion CD1a + populations as well as CD1c + mDCs, but not in other lineages, consistent with BRAF V600E distribution. Epidermal LCs were used as a positive control. Technical duplicates were used. LCH samples used in the study are listed in supplemental Table 3b. (C) Overlay histograms of HLA-DQB2 surface expression in 6 LCH lesion subpopulations (colored) compared with control (gray) demonstrates increasing surface expression of HLA-DQB2 from lesion CD1c + mDCs through CD1a + CD207 + populations.

    Techniques Used: Expressing, FACS, Purification, Amplification, Real-time Polymerase Chain Reaction, Positive Control

    12) Product Images from "Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2"

    Article Title: Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2

    Journal: Frontiers in Oncology

    doi: 10.3389/fonc.2018.00104

    Nuclear factor κB (NF-κB) regulates hexokinase (HK) 2 in sarcoma cells. (A) Gene set enrichment analysis plot of MSigDB Mootha_Glycolysis gene signature in vector and IκBα SR expressing RH30 cells. Gene expression profile data were obtained by Affymetrix GeneChip Human Transcriptome Array 2.0. Nominal p -value
    Figure Legend Snippet: Nuclear factor κB (NF-κB) regulates hexokinase (HK) 2 in sarcoma cells. (A) Gene set enrichment analysis plot of MSigDB Mootha_Glycolysis gene signature in vector and IκBα SR expressing RH30 cells. Gene expression profile data were obtained by Affymetrix GeneChip Human Transcriptome Array 2.0. Nominal p -value

    Techniques Used: Plasmid Preparation, Expressing

    13) Product Images from "Epigenetic hypomethylation and upregulation of matrix metalloproteinase 9 in Kawasaki disease"

    Article Title: Epigenetic hypomethylation and upregulation of matrix metalloproteinase 9 in Kawasaki disease

    Journal: Oncotarget

    doi: 10.18632/oncotarget.19650

    Comparison of matrix metalloproteinase (MMP) -8, -9, and -25 mRNA expressions by GeneChip ® Human Transcriptome Array 2.0 between acute-stage Kawasaki disease patients and control subjects * indicates significance ( p
    Figure Legend Snippet: Comparison of matrix metalloproteinase (MMP) -8, -9, and -25 mRNA expressions by GeneChip ® Human Transcriptome Array 2.0 between acute-stage Kawasaki disease patients and control subjects * indicates significance ( p

    Techniques Used:

    14) Product Images from "Epigenetic hypomethylation and upregulation of matrix metalloproteinase 9 in Kawasaki disease"

    Article Title: Epigenetic hypomethylation and upregulation of matrix metalloproteinase 9 in Kawasaki disease

    Journal: Oncotarget

    doi: 10.18632/oncotarget.19650

    Comparison of matrix metalloproteinase (MMP) -8, -9, and -25 mRNA expressions by GeneChip ® Human Transcriptome Array 2.0 between acute-stage Kawasaki disease patients and control subjects * indicates significance ( p
    Figure Legend Snippet: Comparison of matrix metalloproteinase (MMP) -8, -9, and -25 mRNA expressions by GeneChip ® Human Transcriptome Array 2.0 between acute-stage Kawasaki disease patients and control subjects * indicates significance ( p

    Techniques Used:

    15) Product Images from "Environmental Enteric Dysfunction Includes a Broad Spectrum of Inflammatory Responses and Epithelial Repair Processes"

    Article Title: Environmental Enteric Dysfunction Includes a Broad Spectrum of Inflammatory Responses and Epithelial Repair Processes

    Journal: Cellular and Molecular Gastroenterology and Hepatology

    doi: 10.1016/j.jcmgh.2015.12.002

    Schematic flow chart of human fecal transcriptome analysis. Fecal samples were collected fresh from subjects, immediately flash-frozen in liquid nitrogen, and transported to the laboratory. In the laboratory the cells were suspended in buffer with inert beads and centrifuged at 500 g . The resulting pellet was kept, resuspended in lysis buffer, and used for total nucleic acids extraction. DNase was added to the nucleic acids mixture, and RNA was separated from the suspension using a bead-based affinity method. The RNA then was amplified and hybridized to a chip containing 25mers covering the entire human genome. The signals corresponding to luminescence for each 25mer were aggregated into genes, and normalized using 3 standard methods. Those transcripts that showed significant correlation with %L, a marker of EED, and differential expression with subsets of increased and normal %L were identified. All transcripts then were used to determine pathway expression for all canonical and KEGG pathways. Transcripts that were correlated with %L, differentially expressed between children with no EED and severe EED, and present in pathways also associated with EED were considered to be of biological significance for EED. HTA, Human Transcriptome Array 2.0 (Affymetrix).
    Figure Legend Snippet: Schematic flow chart of human fecal transcriptome analysis. Fecal samples were collected fresh from subjects, immediately flash-frozen in liquid nitrogen, and transported to the laboratory. In the laboratory the cells were suspended in buffer with inert beads and centrifuged at 500 g . The resulting pellet was kept, resuspended in lysis buffer, and used for total nucleic acids extraction. DNase was added to the nucleic acids mixture, and RNA was separated from the suspension using a bead-based affinity method. The RNA then was amplified and hybridized to a chip containing 25mers covering the entire human genome. The signals corresponding to luminescence for each 25mer were aggregated into genes, and normalized using 3 standard methods. Those transcripts that showed significant correlation with %L, a marker of EED, and differential expression with subsets of increased and normal %L were identified. All transcripts then were used to determine pathway expression for all canonical and KEGG pathways. Transcripts that were correlated with %L, differentially expressed between children with no EED and severe EED, and present in pathways also associated with EED were considered to be of biological significance for EED. HTA, Human Transcriptome Array 2.0 (Affymetrix).

    Techniques Used: Flow Cytometry, Lysis, Amplification, Chromatin Immunoprecipitation, Marker, Expressing

    Related Articles

    Microarray:

    Article Title: Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2
    Article Snippet: .. Affymetrix GeneChip Human Transcriptome Array 2.0 (Affymetrix) arrays were used for microarray. .. Probe intensity (CEL) files were obtained, and Affymetrix Transcriptome Analysis Console software was used for array analysis.

    Article Title: Decreased Steroid Hormone Receptor NR4A2 Expression in Kawasaki Disease Before IVIG Treatment
    Article Snippet: .. We executed a microarray assay study to establish gene expression profiles with GeneChip® Human Transcriptome Array 2.0 (HTA 2.0, Affymetrix, Santa Clara). .. Following the Affymetrix instruction manual, the HTA 2.0 chips' raw data were subjected to quality control, as previously described ( ).

    Purification:

    Article Title: Inhibition of miR-328–3p Impairs Cancer Stem Cell Function and Prevents Metastasis in Ovarian Cancer
    Article Snippet: .. Total RNA were extracted using Norgen Total RNA Purification Kit (Norgen Biotek), and processed for Affymetrix transcriptsome assay using GeneChip Human transcriptome array 2.0 (Affymetrix). .. Data were analyzed by using Affymetrix transcriptsome console software as we previously conducted , and deposited in GEO repository ( ).

    Expressing:

    Article Title: Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2
    Article Snippet: .. Global gene expression analysis was performed using Affymetrix GeneChip Human Transcriptome Array 2.0, and data were interpreted using gene set enrichment analysis. .. Seahorse Bioscience XFe 24 was used to analyze oxygen consumption rate as a measure of aerobic respiration.

    Article Title: Identifying genetic hypomethylation and upregulation of toll-like receptors in Kawasaki disease
    Article Snippet: .. For TLR genes and their cytosine-phosphate-guanine (CpG) markers, we used Affymetrix GeneChip® Human Transcriptome Array 2.0 and Illumina HumanMethylation450 BeadChip to evaluate gene expression levels and methylation patterns, respectively. .. KD patients demonstrated a significantly differential expression of TLR mRNA levels compared to both the healthy and febrile controls, with only TLR 3 and 7 not differing between the KD patients and the controls.

    Article Title: Decreased Steroid Hormone Receptor NR4A2 Expression in Kawasaki Disease Before IVIG Treatment
    Article Snippet: .. We executed a microarray assay study to establish gene expression profiles with GeneChip® Human Transcriptome Array 2.0 (HTA 2.0, Affymetrix, Santa Clara). .. Following the Affymetrix instruction manual, the HTA 2.0 chips' raw data were subjected to quality control, as previously described ( ).

    Methylation:

    Article Title: Identifying genetic hypomethylation and upregulation of toll-like receptors in Kawasaki disease
    Article Snippet: .. For TLR genes and their cytosine-phosphate-guanine (CpG) markers, we used Affymetrix GeneChip® Human Transcriptome Array 2.0 and Illumina HumanMethylation450 BeadChip to evaluate gene expression levels and methylation patterns, respectively. .. KD patients demonstrated a significantly differential expression of TLR mRNA levels compared to both the healthy and febrile controls, with only TLR 3 and 7 not differing between the KD patients and the controls.

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    Thermo Fisher genechip human transcriptome array 2 0
    Genechip Human Transcriptome Array 2 0, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/genechip human transcriptome array 2 0/product/Thermo Fisher
    Average 99 stars, based on 21 article reviews
    Price from $9.99 to $1999.99
    genechip human transcriptome array 2 0 - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    Thermo Fisher human transcriptome array 2 0
    Human Transcriptome Array 2 0, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 75 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human transcriptome array 2 0/product/Thermo Fisher
    Average 99 stars, based on 75 article reviews
    Price from $9.99 to $1999.99
    human transcriptome array 2 0 - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

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