Affymetrix gene 1.1 st arrays

Manufactured by Thermo Fisher Scientific

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The Affymetrix Gene 1.1 ST arrays are high-density oligonucleotide microarrays designed for whole-transcriptome expression profiling. The arrays feature probes targeting the entire length of each transcript, providing a comprehensive view of the transcriptome.

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Lab products found in correlation

Trizol chloroform extraction, by Thermo Fisher Scientific (3 mentions) Genetitan instrument, by Thermo Fisher Scientific (1 mentions) Rneasy micro kit, by Qiagen (1 mentions) Trizol reagent, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

Gene 1.1 ST array (12 citations) 1.1 ST Arrays (2 citations) Affymetrix GeneChip Mouse Gene 1.1 ST arrays (2 citations)

5 protocols using affymetrix gene 1.1 st arrays

Whole Transcriptome Profiling of Mouse Samples

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Total RNA (100 ng) was labelled by a Whole Transcript Sense Target Assay and hybridized to mouse whole-genome Affymetrix Gene 1.1 ST arrays targeting 21,115 unique genes (Affymetrix, Santa Clara, CA). Hybridization, washing, and scanning of all Affymetrix Genechips was performed according to standard Affymetrix protocols. Scans of the Affymetrix arrays were processed using the Affymetrix GeneTitan Instrument.
Quality control was performed on raw data by assessing the signal distribution by using scatter plot, MA-plot and a normal probability plot. Positive (landmark) and negative (blank) spots were used in the quality control and not used in further analyses. Normalized data were visualized by Principal Component Analysis (PCA) for additional quality assessment. The gene expression data have been deposited in NCBI's Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE102016.

Shi Q., Fijten R.R., Spina D., Riffo Vasquez Y., Arlt V.M., Godschalk R.W, & Van Schooten F.J. (2017). Altered gene expression profiles in the lungs of benzo[a]pyrene-exposed mice in the presence of lipopolysaccharide-induced pulmonary inflammation. Toxicology and Applied Pharmacology, 336, 8-19.

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Whole-Genome Microarray Analysis of Lipolysis Genes

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RNA was extracted from frozen AT (∼500 mg) using Trizol chloroform extraction (Invitrogen, Cergy Pontoise, France). Next, total RNA (100 ng per sample) was labeled by Whole-Transcript Sense Target Assay and hybridized to human whole-genome Affymetrix Gene 1.1 ST arrays targeting 19793 unique genes (Affymetrix, Santa Clara, CA, USA). Quality control and data analysis have been described in detail previously [22]. Relevant lipolysis related genes were selected from the total microarray as published in the clinical trail where the current study is part of (GEO GSE76003) [23].

Jocken J.W., Reijnders D., Canfora E.E., Boekschoten M.V., Plat J., Goossens G.H, & Blaak E.E. (2018). Effects of gut microbiota manipulation on ex vivo lipolysis in human abdominal subcutaneous adipocytes. Adipocyte, 7(2), 106-112.

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Adipose Tissue Gene Expression Analysis

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RNA was extracted from frozen adipose tissue (~150 mg) using Trizol chloroform extraction (Invitrogen, Breda, The Netherlands). Next, total RNA (100 ng per sample) was labeled by Whole‐Transcript Sense Target Assay and hybridized to human whole‐genome Affymetrix Gene 1.1 ST arrays targeting 19,654 unique genes (Affymetrix, Santa Clara, CA). Quality control and data analysis have been described in detail previously (Vink et al. 2017a). We performed a supervised gene expression analysis focusing on 22 genes important for uptake, storage, and release of FA by adipose tissue (Table S1) and analyzed gene expression before and after DI‐period. Changes in mRNA levels were defined as significantly different when the q‐value was <0.05 in a paired t‐test with Bayesian correction (Limma). Array data have been submitted to the Gene Expression Omnibus (number GSE77962).

van der Kolk B.W., Vink R.G., Jocken J.W., Roumans N.J., Goossens G.H., Mariman E.C., van Baak M.A, & Blaak E.E. (2018). Effect of diet‐induced weight loss on angiopoietin‐like protein 4 and adipose tissue lipid metabolism in overweight and obese humans. Physiological Reports, 6(13), e13735.

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Gene Expression Profiling of Intestinal Mucosa

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Total RNA was extracted from frozen mucosal samples obtained from the duodenum or the jejunum using TRIzol reagent (Invitrogen), and purified on columns using the Qiagen RNeasy Micro Kit (Qiagen). Total RNA (35 ng/ml) was labelled by using Whole-Transcript Sense Target Assay and hybridised to human whole-genome Affymetrix Gene 1.1 ST arrays targeting 19 682 unique genes (Affymetrix). Individual genes were defined as 'changed' when comparison of the normalised signal intensities showed a P value ,0•05 in a two-tailed paired intensity-based moderated t statistic. Further functional data analysis was performed on the filtered dataset with gene set enrichment analysis, and on the differentially expressed genes with Ingenuity Pathway Analysis software.

De Smet E., Mensink R.P., Boekschoten M.V., de Ridder R., Germeraad W.T., Wolfs T.G, & Plat J. (2015). An acute intake of plant stanol esters alters immune-related pathways in the jejunum of healthy volunteers. The British journal of nutrition, 113(5).

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Adipocyte Morphometry and Transcriptomics

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Abdominal subcutaneous AT biopsies were taken under local anesthesia under fasted conditions. One portion was embedded in paraffin. Sections were cut for staining, digital imaging, and computerized morphometric measurement of individual adipocytes (Goossens et al., 2011) . One portion ($500 mg) was snapfrozen in liquid nitrogen, from which RNA was extracted (Trizol chloroform extraction, Invitrogen) and used for microarray analysis. 100 ng total RNA was labeled by Whole-Transcript Sense Target Assay and hybridized to human whole-genome Affymetrix Gene 1.1 ST arrays, targeting 19,793 unique genes (Affymetrix). Quality control and data analysis pipeline have been described in detail previously (Lin et al., 2011) . Individual genes on the array were defined as changed when comparison of the normalized signal intensities showed a FDRq < 0.05 in a two-tailed paired t test with Bayesan correction (Limma) (Smyth, 2004) . Further functional data analysis was performed on the filtered dataset with Gene Set Enrichment Analysis (GSEA, http://www.broad.mit.edu/gsea). Gene sets were selected based upon FDRq < 0.2.

Reijnders D., Goossens G.H., Hermes G.D., Neis E.P., van der Beek C.M., Most J., Holst J.J., Lenaerts K., Kootte R.S., Nieuwdorp M., Groen A.K., Olde Damink S.W., Boekschoten M.V., Smidt H., Zoetendal E.G., Dejong C.H, & Blaak E.E. (2016). Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial. Cell metabolism, 24(1).

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