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Biotechnology Information microarray raw data files
Microarray Raw Data Files, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Microarray:

Article Title: Expression profiling of heat stress effects on mice fed ergot alkaloids.
Article Snippet: Gene ontology (GO) was obtained using DAVID (Dennis et al., 2003) and Entrez-Gene (http:// www.ncbi.nih.gov/entrez/query.fcgi?db1⁄4gene) from the National Center for Biotechnology Information. .. The microarray data files on which this paper is based have been deposited with National Center for Biotechnology Information Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) with series number GSE5642. ..

Article Title: Advancing a clinically relevant perspective of the clonal nature of cancer
Article Snippet: .. Data deposition: The microarray files reported in this paper have been deposited at the National Center for Biotechnology Information Gene Expression Omnibus (accession no. {"type":"entrez-geo","attrs":{"text":"GSE21660","term_id":"21660","extlink":"1"}} GSE21660 ). ..

Article Title: Gene signatures in wound tissue as evidenced by molecular profiling in the chick embryo model
Article Snippet: .. The microarray data files have be submitted to the US National Center for Biotechnology Information, Gene Expression Omnibus (GEO), and released in May 6 th , 2010 (GEO accession number: GSE21679). .. Real-time PCR was carried out in an Mx3000P thermocycler (Stratagene, La Jolla, CA) by using SYBR Green dye (ABgene, Courtaboeuf, France).

Article Title: The influence of orexin B on the transcriptome profile of porcine myometrial explants during early implantation.
Article Snippet: This study aimed to determine the effect of orexin B (OXB) on the global expression pattern and the relationships among differentially expressed genes (DE-genes) in the transcriptome of myometrial explants during the early implantation period in the pig (day 15 of pregnancy).. The changes in the transcriptome profile of the porcine myometrium were investigated using the Porcine (V2) Two-colour Gene Expression Microarray, 4 44.. An analysis of the data from the microarray experiment revealed that 1540 DE-genes were affected by OXB, of which 1135 exhibited fold changes (FC) greater than 1.2 (P < 0.05).

Article Title: Excessive Cytolytic Responses Predict Tuberculosis Relapse After Apparently Successful Treatment
Article Snippet: .. Microarray data files are deposited in the National Center for Biotechnology Information Gene Expression Omnibus Database under accession numbers GSE45386 (healthy BCG-vaccinated donors) and GSE67589 (patients with tuberculosis). .. Data were analyzed using GeneSpring GX 11.5 Software (Agilent Technologies).

Article Title: Nonsense mutations of the bHLH transcription factor TWIST2 found in Setleis Syndrome patients cause dysregulation of periostin
Article Snippet: .. The complete set of microarray data files can be found at the Gene Expression Omnibus website at the National Center for Biotechnology Information (NCBI GEO #GES16524). ..

Article Title: Nonsense mutations of the bHLH transcription factor TWIST2 found in Setleis Syndrome patients cause dysregulation of periostin
Article Snippet: Hence, POSTN was chosen as a potential target gene for the study of TWIST2 transactivation due to its key role in dermal tissue deposition and development and the prominent dermal phenotypes seen in Setleis Syndrome patients. table ft1 table-wrap mode=article t1 caption a4 Selected differentially regulated genes between Setleis syndrome patient fibroblasts and normal control Fibroblasts using human Affymetrix 3′IVT expression arrays. .. Microarray data files can be found at the National Center for Biotechnology Information ... ..

Article Title: Correlating Global Gene Regulation to Angiogenesis in the Developing Chick Extra-Embryonic Vascular System
Article Snippet: Annotation of genes was performed using NetAffx ( http://www.affymetrix.com ; March 2009). .. The 12 microarray data files have been submitted to the US National Center for Biotechnology Information, Gene Expression Omnibus (GEO), and will be released upon publication (approved accession number: GSE11636; sample numbers: GSM294982, GSM294983, GSM294984, GSM294985, GSM294986, GSM294987, GSM294988, GSM294989, GSM294990, GSM294991, GSM294992, GSM294993). ..

Gene Expression:

Article Title: Expression profiling of heat stress effects on mice fed ergot alkaloids.
Article Snippet: Gene ontology (GO) was obtained using DAVID (Dennis et al., 2003) and Entrez-Gene (http:// www.ncbi.nih.gov/entrez/query.fcgi?db1⁄4gene) from the National Center for Biotechnology Information. .. The microarray data files on which this paper is based have been deposited with National Center for Biotechnology Information Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) with series number GSE5642. ..

Article Title: Advancing a clinically relevant perspective of the clonal nature of cancer
Article Snippet: .. Data deposition: The microarray files reported in this paper have been deposited at the National Center for Biotechnology Information Gene Expression Omnibus (accession no. {"type":"entrez-geo","attrs":{"text":"GSE21660","term_id":"21660","extlink":"1"}} GSE21660 ). ..

Article Title: Gene signatures in wound tissue as evidenced by molecular profiling in the chick embryo model
Article Snippet: .. The microarray data files have be submitted to the US National Center for Biotechnology Information, Gene Expression Omnibus (GEO), and released in May 6 th , 2010 (GEO accession number: GSE21679). .. Real-time PCR was carried out in an Mx3000P thermocycler (Stratagene, La Jolla, CA) by using SYBR Green dye (ABgene, Courtaboeuf, France).

Article Title: The influence of orexin B on the transcriptome profile of porcine myometrial explants during early implantation.
Article Snippet: This study aimed to determine the effect of orexin B (OXB) on the global expression pattern and the relationships among differentially expressed genes (DE-genes) in the transcriptome of myometrial explants during the early implantation period in the pig (day 15 of pregnancy).. The changes in the transcriptome profile of the porcine myometrium were investigated using the Porcine (V2) Two-colour Gene Expression Microarray, 4 44.. An analysis of the data from the microarray experiment revealed that 1540 DE-genes were affected by OXB, of which 1135 exhibited fold changes (FC) greater than 1.2 (P < 0.05).

Article Title: Excessive Cytolytic Responses Predict Tuberculosis Relapse After Apparently Successful Treatment
Article Snippet: .. Microarray data files are deposited in the National Center for Biotechnology Information Gene Expression Omnibus Database under accession numbers GSE45386 (healthy BCG-vaccinated donors) and GSE67589 (patients with tuberculosis). .. Data were analyzed using GeneSpring GX 11.5 Software (Agilent Technologies).

Article Title: Nonsense mutations of the bHLH transcription factor TWIST2 found in Setleis Syndrome patients cause dysregulation of periostin
Article Snippet: .. The complete set of microarray data files can be found at the Gene Expression Omnibus website at the National Center for Biotechnology Information (NCBI GEO #GES16524). ..

Article Title: Correlating Global Gene Regulation to Angiogenesis in the Developing Chick Extra-Embryonic Vascular System
Article Snippet: Annotation of genes was performed using NetAffx ( http://www.affymetrix.com ; March 2009). .. The 12 microarray data files have been submitted to the US National Center for Biotechnology Information, Gene Expression Omnibus (GEO), and will be released upon publication (approved accession number: GSE11636; sample numbers: GSM294982, GSM294983, GSM294984, GSM294985, GSM294986, GSM294987, GSM294988, GSM294989, GSM294990, GSM294991, GSM294992, GSM294993). ..



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Gene expression dataset . A) The gene expression dataset analyzed comprises cell samples from different levels of myeloid differentiation process (stem/progenitor cells, precursors and terminally differentiated cells). The graph describes relationships between the cellular contexts analyzed within myeloid differentiation tree. For each cell type, the number of samples examined with independent <t>microarray</t> experiments is indicated in brackets. B) Dendrogram obtained by unsupervised hierarchical clustering on gene expression data matrix. Pearson correlation and average were used as similarity measure and linking method, respectively.
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Gene expression dataset . A) The gene expression dataset analyzed comprises cell samples from different levels of myeloid differentiation process (stem/progenitor cells, precursors and terminally differentiated cells). The graph describes relationships between the cellular contexts analyzed within myeloid differentiation tree. For each cell type, the number of samples examined with independent <t>microarray</t> experiments is indicated in brackets. B) Dendrogram obtained by unsupervised hierarchical clustering on gene expression data matrix. Pearson correlation and average were used as similarity measure and linking method, respectively.
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Gene expression dataset . A) The gene expression dataset analyzed comprises cell samples from different levels of myeloid differentiation process (stem/progenitor cells, precursors and terminally differentiated cells). The graph describes relationships between the cellular contexts analyzed within myeloid differentiation tree. For each cell type, the number of samples examined with independent <t>microarray</t> experiments is indicated in brackets. B) Dendrogram obtained by unsupervised hierarchical clustering on gene expression data matrix. Pearson correlation and average were used as similarity measure and linking method, respectively.
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Genetic deletion of SphK1 reduced CLDN2 in HER2/neu-induced mice breast tumors. (A) Whole genome expression profile evaluated by <t>microarray</t> analysis assessed the expression of 39000 gene transcripts. Gene expression microarray heatmap (n = 2 per group) of dysregulated genes. (B) Twenty molecules with the most significant expression changes (10 up-regulation and 20 down-regulation) between SphK1+/+ and SphK1−/− tumors are shown. (C) CLDN2 mRNA expression in tumors from SphK1+/+ and SphK1−/− mice was confirmed by qRT-PCR analysis and analyzed by unpaired t-test. ****P ≤ 0.0001 vs. SphK1+/+. (D) Representative paraffin-tumor sections immunostained for CLDN2 in tumors from SphK1+/+ and SphK1−/− mice (P = 0.1339).
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Genetic deletion of SphK1 reduced CLDN2 in HER2/neu-induced mice breast tumors. (A) Whole genome expression profile evaluated by <t>microarray</t> analysis assessed the expression of 39000 gene transcripts. Gene expression microarray heatmap (n = 2 per group) of dysregulated genes. (B) Twenty molecules with the most significant expression changes (10 up-regulation and 20 down-regulation) between SphK1+/+ and SphK1−/− tumors are shown. (C) CLDN2 mRNA expression in tumors from SphK1+/+ and SphK1−/− mice was confirmed by qRT-PCR analysis and analyzed by unpaired t-test. ****P ≤ 0.0001 vs. SphK1+/+. (D) Representative paraffin-tumor sections immunostained for CLDN2 in tumors from SphK1+/+ and SphK1−/− mice (P = 0.1339).
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Gene expression dataset . A) The gene expression dataset analyzed comprises cell samples from different levels of myeloid differentiation process (stem/progenitor cells, precursors and terminally differentiated cells). The graph describes relationships between the cellular contexts analyzed within myeloid differentiation tree. For each cell type, the number of samples examined with independent microarray experiments is indicated in brackets. B) Dendrogram obtained by unsupervised hierarchical clustering on gene expression data matrix. Pearson correlation and average were used as similarity measure and linking method, respectively.

Journal: BMC Genomics

Article Title: Genomic expression during human myelopoiesis

doi: 10.1186/1471-2164-8-264

Figure Lengend Snippet: Gene expression dataset . A) The gene expression dataset analyzed comprises cell samples from different levels of myeloid differentiation process (stem/progenitor cells, precursors and terminally differentiated cells). The graph describes relationships between the cellular contexts analyzed within myeloid differentiation tree. For each cell type, the number of samples examined with independent microarray experiments is indicated in brackets. B) Dendrogram obtained by unsupervised hierarchical clustering on gene expression data matrix. Pearson correlation and average were used as similarity measure and linking method, respectively.

Article Snippet: In particular, raw microarray data (Affymetrix .CEL files) were obtained for a total of 24 samples from 8 different cell types of all myelopoietic lineages, representing a reference dataset for a comprehensive analysis of genomic expression during cell differentiation.

Techniques: Expressing, Microarray

Genetic deletion of SphK1 reduced CLDN2 in HER2/neu-induced mice breast tumors. (A) Whole genome expression profile evaluated by microarray analysis assessed the expression of 39000 gene transcripts. Gene expression microarray heatmap (n = 2 per group) of dysregulated genes. (B) Twenty molecules with the most significant expression changes (10 up-regulation and 20 down-regulation) between SphK1+/+ and SphK1−/− tumors are shown. (C) CLDN2 mRNA expression in tumors from SphK1+/+ and SphK1−/− mice was confirmed by qRT-PCR analysis and analyzed by unpaired t-test. ****P ≤ 0.0001 vs. SphK1+/+. (D) Representative paraffin-tumor sections immunostained for CLDN2 in tumors from SphK1+/+ and SphK1−/− mice (P = 0.1339).

Journal: Carcinogenesis

Article Title: Genetic deletion of sphingosine kinase 1 suppresses mouse breast tumor development in an HER2 transgenic model

doi: 10.1093/carcin/bgx097

Figure Lengend Snippet: Genetic deletion of SphK1 reduced CLDN2 in HER2/neu-induced mice breast tumors. (A) Whole genome expression profile evaluated by microarray analysis assessed the expression of 39000 gene transcripts. Gene expression microarray heatmap (n = 2 per group) of dysregulated genes. (B) Twenty molecules with the most significant expression changes (10 up-regulation and 20 down-regulation) between SphK1+/+ and SphK1−/− tumors are shown. (C) CLDN2 mRNA expression in tumors from SphK1+/+ and SphK1−/− mice was confirmed by qRT-PCR analysis and analyzed by unpaired t-test. ****P ≤ 0.0001 vs. SphK1+/+. (D) Representative paraffin-tumor sections immunostained for CLDN2 in tumors from SphK1+/+ and SphK1−/− mice (P = 0.1339).

Article Snippet: Partek pre-processes raw intensity files from microarray experiment using GCRMA’s background subtraction and uses quantile normalization as the normalization technique.

Techniques: Expressing, Microarray, Gene Expression, Quantitative RT-PCR

SphK1 and CLDN2 levels are increased in HER2-positive breast cancers in humans. Tissue microarray containing breast cancer samples from 92 HER2-positive breast cancer patients and matched adjacent normal breast tissues (n = 34) are stained for SphK1 and CLDN2. Staining were scored based on the intensity (0–3) and proportion (0–3), and the total scores were used for the analysis. [(A) and (B)] SphK1 and CLDN2 expressions were compared with pathological features including grade, stage and hormone receptor status. [(C) and (D)] Representative image of high, moderate and low SphK1 and CLDN2 expressing tumors.

Journal: Carcinogenesis

Article Title: Genetic deletion of sphingosine kinase 1 suppresses mouse breast tumor development in an HER2 transgenic model

doi: 10.1093/carcin/bgx097

Figure Lengend Snippet: SphK1 and CLDN2 levels are increased in HER2-positive breast cancers in humans. Tissue microarray containing breast cancer samples from 92 HER2-positive breast cancer patients and matched adjacent normal breast tissues (n = 34) are stained for SphK1 and CLDN2. Staining were scored based on the intensity (0–3) and proportion (0–3), and the total scores were used for the analysis. [(A) and (B)] SphK1 and CLDN2 expressions were compared with pathological features including grade, stage and hormone receptor status. [(C) and (D)] Representative image of high, moderate and low SphK1 and CLDN2 expressing tumors.

Article Snippet: Partek pre-processes raw intensity files from microarray experiment using GCRMA’s background subtraction and uses quantile normalization as the normalization technique.

Techniques: Microarray, Staining, Expressing