Mononuclear cells were sorted phenotypically: HSC, Lin-CD34+CD38–CD904+ CD45RA–; MEP, Lin–CD34+CD38+CD123-CD45RA–. Colony assays were performed using complete methylcellulose with 12-14 days incubation. For microarray, RNA samples were quantified, subjected to reverse transcription, underwent two rounds of linear amplification, and biotinylated. 15 µg of RNA per sample was assayed using Affymetrix HG U133 Plus 2.0 microarrays. Data were analyzed using the gene expression commons platform.
Hgu133 plus 2.0 microarrays
Manufactured by Thermo Fisher Scientific
Sourced in United States
The HGU133 Plus 2.0 microarrays are a type of gene expression analysis platform developed by Thermo Fisher Scientific. The arrays are designed to measure the expression levels of thousands of human genes simultaneously. They are used for various applications in genomics research, including gene expression profiling, biomarker discovery, and transcriptome analysis.
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Lab products found in correlation
Mirneasy mini kit, by Qiagen (1 mentions)
Expression analysis technical manual, by Thermo Fisher Scientific (1 mentions)
Hg u133 plus 2.0 array, by Thermo Fisher Scientific (1 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)
Microarray suite version 5, by Thermo Fisher Scientific (1 mentions)
Prism 5, by GraphPad (1 mentions)
Prism v5.0b, by GraphPad (1 mentions)
Ez pcr core reagents, by Thermo Fisher Scientific (1 mentions)
Axioplan 2, by Zeiss (1 mentions)
21 protocols using hgu133 plus 2.0 microarrays
1
Phenotypic Sorting of Hematopoietic Cells
2
Glioblastoma Transcriptomic Profiling
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All research performed was approved by IRB boards at University of California, San Diego Human Research Protections Program and were in accordance with the principles expressed at the declaration of Helsinki. Each patient was consented by a dedicated clinical research specialist prior to collection. Written consent was obtained for each patient. The consent process was approved by the ethics committee, and all records were documented in our electronic record system. The written consent from patients was also scanned into our electronic filing system. The specimens were collected at the University of California San Diego Medical Center under IRB 120345X.
In total, 25 consecutive glioblastomas were collected as fresh-frozen specimens. The specimens were secured from newly diagnosed glioblastoma patients who had not undergone temozolomide or radiation treatment. Total RNA was extracted from the specimens. Whole genome gene expression profiling was performed using Affymetrix HGU133 Plus 2.0 microarrays. Microarray data were GC Robust Multiarray Average normalized using R and thebioconductor.org package gcrma. G-CIMP status was determined using PAM as described above. The genomic data generated for this study has been made available on the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/ ) under accession number GSE60184.
In total, 25 consecutive glioblastomas were collected as fresh-frozen specimens. The specimens were secured from newly diagnosed glioblastoma patients who had not undergone temozolomide or radiation treatment. Total RNA was extracted from the specimens. Whole genome gene expression profiling was performed using Affymetrix HGU133 Plus 2.0 microarrays. Microarray data were GC Robust Multiarray Average normalized using R and the
3
Comparative Gene Expression Analysis of UC Dysplasia
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Validation series consisted of gene expression data from 96 samples from Hungary accessed from the Gene Expression Omnibus databank (dataset ID: GSE47908 (29 (link))). According to the Gene Expression Omnibus entries, total RNA was extracted from colonic biopsy samples of UC patients (n = 54) and of patients with colonic dysplasia in UC (n = 6) and were hybridized on Affymetrix HGU133 Plus 2.0 microarrays. Our selected gene panel was tested on the downloaded dataset, and comparison between dysplasia vs non-dysplasia was done using non-parametric Mann-Whitney U test adjusted for multiple comparison (P-value < 0.001).
4
Microarray-based Gene Expression Analysis Protocol
5
Transcriptomic Profiling of Diabetic Nephropathy
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Human renal biopsies from patients with diabetic nephropathy (DN) (n = 7) and livinv donor (LD) controls (n = 18) were collected within the framework of the European Renal cDNA Bank—Kröner-Fresenius Biopsy Bank (24 (link)). Biopsies were obtained from patients after informed consent and with approval of the local ethics committees. Following renal biopsy, the tissue was transferred to RNase inhibitor and microdissected into glomerular and tubular fragments. Total RNA was isolated from both micro-dissected compartments, linearly amplified and hybridized to Affymetrix HG-U133 Plus 2.0 microarrays as reported previously (25 (link)). Fragmentation, hybridization, staining, and imaging were performed according to the Affymetrix Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA). The raw data was normalized using Robust Multichip Algorithm (RMA) and annotated by Human Entrez Gene custom CDF annotation version 18 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp ). To identify differentially expressed genes the SAM (Significance analysis of Microarrays) method was applied using TiGR (MeV, Version 4.8.1) (26 (link)). A q-value below 5% was considered to be statistically significant.
6
Affymetrix HG-U133 Plus 2.0 Microarray Protocol
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The cell line samples were subjected to nucleic acid extraction, verification, amplification, and hybridization per the protocol regarding the use of the Affymetrix HG-U133 plus 2.0 arrays (54,675 probesets, Affymetrix, Santa Clara, CA). Affymetrix HG-U133 Plus 2.0 microarrays were normalized (background adjustment, interquartile normalization, and median polish) using robust multichip averaging [17 (link)] in R.
7
Transcriptional Profiling of Doxycycline-Inducible Cells
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Integrity of total RNA was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies). Copy RNA synthesis, hybridization to HG U133 plus 2.0 microarrays (Affymetrix), and subsequent steps were performed according to the manufacturers’ protocol. Data analysis was performed in R version 3.6.3. The Affy package (93 (link)), version 1.64.0, was used for Robust Multichip Average (RMA) normalization. All +dox samples (n = 9) were compared with the –dox samples (n = 9), using the Limma package (94 (link)), version 3.42.2. Upregulated (log2 fold change > 0.6, P < 0.05, and q < 0.1) and downregulated (log2 fold change < –0.6, P < 0.05, and q < 0.1) probe sets were collapsed to genes. The gene names were used for GO term analysis in the web version of PANTHER (released 20200407, ref. 95 (link)), using the human data set with default settings. Heatmaps were created using Pheatmap package in R.
8
TNBC Cell Line Expression Analysis
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We obtained the TNBC microarray gene expression data from the Cancer Cell Line Encyclopedia (GSE36133). These cell lines were profiled using Affymetrix HG-U133 Plus 2.0 microarrays. Raw CEL files for these cell lines were normalized using Robust Multiarray Average (RMA) approach in Affymetrix Power Tools (APT).
9
Colorectal Cancer Expression Profiling
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CRC expression profiling studies including relevant clinical information were identified by searching the public datasets. Dataset GDS2947 included 32 prospectively collected adenomas with those of normal mucosa from the same individuals.24 And the comparison between 40 paired colorectal adenoma and adjacent normal tissue samples were performed by dataset GSE31737.25 Datasets with gene expression profile comparing CRC or colorectal adenoma to paired adjacent normal tissue were obtained from Dataset GSE32323 which contained 17 paired samples.26 GSE41328 contained five colorectal adenocarcinomas and matched normal colonic tissues were analysed with Affymetrix HG‐U133‐Plus‐2.0 microarrays.27 GSE38832 includes survival information of 122 patients with CRC.28 GSE17537 includes expression and clinical data for 55 patients with CRC.29 CRC expression and copy number profiling study from TCGA dataset were used to analysis association and survival.
10
Bone Gene Expression and Hip Geometry Association
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