These datasets are referred to as the MicroArray Quality Control Phase II (MAQC-II) Project (GSE16716) that has been published. We extracted a part of the dataset which included HER2-negative patients treated with weekly paclitaxel (T) (80 mg/m2) for 12 treatments, followed by 5-fluorouracil (500 mg/m2), doxorubicin (50 mg/m2), and cyclophosphamide (500 mg/m2) for four treatments, given once every 21 days (FAC), with available clinical data. Samples were placed in RNAlater (Ambion, Austin, TX) storage reagent and stored at -80°C until gene expression analysis. As described by Hess et al., all gene expression data were generated using Affymetrix U133A gene chips (Affymetrix, Inc, Santa Clara, CA) 9 (link). Gene expression data were normalized with the MAS5 algorithm, mean centered to 600, and log 2 transformed before further analysis. Probe sets with the lowest 25% mean expression value were removed from all higher level analyses to reduce noise from low expressed probe sets. This left 16,712 probe sets for analysis. Tumors with normalized ESR1 mRNA expression (probe set 205225_at) >10.18 were considered ER-positive 10 (link). Tumors with normalized HER2 mRNA expression (probe set 216836_s_at) >12.54 were considered HER2-positive 10 (link). All statistical analysis was performed with BRB-ArrayTools version 3.8.1 α software and R software version 2.10.1.
U133a genechips
Manufactured by Thermo Fisher Scientific
Sourced in United States
The U133A GeneChips is a DNA microarray product from Thermo Fisher Scientific. It is designed to analyze the expression of over 22,000 human genes simultaneously. The GeneChip contains thousands of oligonucleotide probes that can hybridize to specific gene transcripts, allowing for the quantification of gene expression levels in a sample.
Automatically generated - may contain errors
Lab products found in correlation
Human genome 133 plus 2, by Thermo Fisher Scientific (2 mentions)
Rnalater, by Thermo Fisher Scientific (1 mentions)
Rnase free dnase 1, by Thermo Fisher Scientific (1 mentions)
Genechip expression analysis manual, by Thermo Fisher Scientific (1 mentions)
Bioanalyser 2100 system, by Agilent Technologies (1 mentions)
Trizol reagent, by Thermo Fisher Scientific (1 mentions)
Streptavidin phycoerythrin, by MoBiTec (1 mentions)
450 k chips, by Illumina (1 mentions)
Superscript double stranded cdna synthesis kit, by Thermo Fisher Scientific (1 mentions)
Genearray scanner, by Thermo Fisher Scientific (1 mentions)
Genechip software mas 5, by Thermo Fisher Scientific (1 mentions)
Humanht 12 v4.0 expression beadchip, by Thermo Fisher Scientific (1 mentions)
Hiseq 2000, by Illumina (1 mentions)
Rneasy column purification, by Qiagen (1 mentions)
Trizol, by Thermo Fisher Scientific (1 mentions)
11 protocols using u133a genechips
1
Gene Expression Analysis of HER2-Negative Breast Cancer
2
Comprehensive Profiling of CN-AML Patients
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Gene expression and methylation data have been previously published (accession number GSE1159 [27 (link)], GSE9476 [28 (link)], GSE6891 [53 (link)] and GSE12417 [54 (link)] for expression, The Cancer Genome Atlas (TCGA) [50 (link)] for methylation). Briefly, gene expression data were obtained using Affymetrix Human Genome 133 plus 2.0 and U133A Gene Chips. All the designs and quality control for microarray experiment were according to the standard Affymetrix protocols. Expression data for microRNA were from TCGA obtained using whole-genome high-throughput sequencing, which provided 79 CN-AML patients [50 (link)]. In addition, genome-wide methylation levels in these patients were determined using Illumina 450K chips [50 (link)]. Patients with RUNX1 expression values above the median of all patients were classified as having RUNX1high, and the others were considered to have RUNX1low. Levels of ERG, BAALC, LEF1, MN1, WT1, DNMT3B, TCF4, MIR155HG, ITPR2 and MAPKBP1 expression were also determined from the microarray data.
3
Transcriptomic and Proteomic Analysis of PEO1R
4
Affymetrix Gene Expression Analysis Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Sample preparation and processing was performed according to the Affymetrix GeneChip Expression Analysis Manual (http://www.Affymetrix.com ). Total RNA was isolated from HUVECs using Trizol-Reagent (Life Technologies, Inc., Rockville, MD, USA). DNase treatment was carried out, using RNase free DNase I (Ambion, Woodward, Austin, TX, USA). RNA concentration and quality were assessed by RNA 6000 nano assays on a Bioanalyser 2100 system (Agilent, Waldbronn, Germany). 5 µg of RNA was converted into cDNA using T7-(dT)24 primers and the SuperScript Choice system for cDNA synthesis (Life Technologies, Inc., Rockville, MD, USA). Biotin-labelled cDNA was prepared by in vitro transcription using the BioArray high yield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY, USA). The resulting cDNA was purified, fragmented and hybridized to U133A gene chips (Affymetrix, Santa Clara, CA, USA). After hybridization the chips were stained with streptavidin–phycoerythrin (MoBiTec, Goettingen, Germany) and analysed on a GeneArray scanner (Hewlett Packard Corporation, Palo Alto, CA, USA).
5
Integrated Genomic Profiling of CN-AML
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Gene/microRNA expression and methylation data were previously published (accession number GSE1159,GSE9476, GSE30029, GSE6891 and GSE12417 for gene expression). The Cancer Genome Atlas (TCGA) database was used for mRNA/microRNA expression and genome-wide promoter methylation. Briefly, gene expression data were obtained by Affymetrix Human Genome 133 plus 2.0 and U133A Gene Chips. All designs and quality control of the microarray experiment and data normalization were in line with the standard Affymetrix protocols. RNA-Seq data of mRNA/microRNA and genome-wide promoter methylation levels were derived from TCGA obtained by whole-genome high-throughput sequencing and Illumina 450 K chips, respectively, which provided 73 CN-AML patients with all data for mRNA, microRNA and methylation. Patients with MAP7 expression values (whether microarray in GEO or RNA-Seq in TCGA) above the median for all patients were classified as having MAP7high, and the others were considered to have MAP7low. ERG, BAALC, LEF1, WT1, DNMT3A, DNMT3B, MAPKBP1, ITPR2, and ATP1B1 expression levels were also determined from the microarray data.
6
Gene Expression Profiling of Quiescent Cells
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Gene expression profiles of patient- and passage-matched OMFs and SFs were assessed using Affymetrix™ GeneChip® Microarray technology, as previously described [9 (link),14 (link)]. Briefly, total RNA was isolated from quiescent OMFs and SFs, and RNA extraction was performed according to standard phenol/chloroform extraction protocol. Briefly, first strand cDNA was synthesized from 5 mg total RNA using a T7-(dT)24 primer (Genset Corporation, La Jolla, CA, USA) and reverse-transcribed using a Superscript Double-Stranded cDNA Synthesis Kit (ThermoFisher Scientific). cDNA was purified, and the subsequent in vitro transcription reaction was performed using a Bioarray Kit (Enzo Life Sciences, Exeter, UK) to generate biotinylated cRNA in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix for cRNA amplification and biotin labeling. cRNA was subsequently fragmented and hybridized to Affymetrix™ U133A GeneChips, containing B23 500 sequences derived from the GenBank™ database. Following hybridization and GeneArray® scanning, the resultant image files (.CEL) were analyzed in R, using the Bioconductor RMA package and algorithm to generate expression intensity values for each probe set generated.
7
Affymetrix GeneChip cRNA Hybridization
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Double-strained cDNA from RNA was used as a template for isolation and preparation of cRNA. Isolation and hybridization of cRNA and scanning of the arrays were performed according to protocols specified by the manufacturer. Hybridization was done using three sets of human U133A GeneChips (Affymetrix, CA, USA). The arrays were scanned using the GeneArray scanner (Affymetrix). Image analysis was performed with GeneChip software (MAS 5.0; Affymetrix).
8
Comprehensive Cancer Transcriptome Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
All clinical and gene expression data were collected previously and are available from public databases. Gene expression data of The Cancer Genome Atlas (TCGA cohort, n = 513) was downloaded from the UCSC Cancer Genomics Browser (Available online: https://genome-cancer.ucsc.edu/ ). The data from the Institute for Medical Informatics, Statistics and Epidemiology (Leipzig cohort, GSE65858, n = 270) and AHEPA Hospital in Thessaloniki (Greece cohort, GSE27020, n = 109) were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database (Available online: http://www.ncbi.nlm.nih.gov/geo ) and used as the test sets [25 (link),26 (link)]. Gene expression data of the TCGA cohort were generated by Illumina HiSeq2000, the Leipzig cohort by Illumina HumanHT-12 V4.0 Expression Beadchip, and the Greece cohort by Affymetrix U133A Genechips. All gene expression data were standardized because of different platforms.
9
Microarray Analysis of Barrett's Esophagus
10
Gene Expression Profiling of Follicular Lymphoma
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Affymetrix U133A gene chips were used for gene expression profiling of 72 FL samples. The transcriptome analyses were performed using RMA system software packages (version 2.8.0) including Bioconductor (version 2.0). Raw gene expression data from Affymetrix CEL files were analyzed using the affy R library from Bioconductor to generate probe level intensity. Gene-centric expression values were generated using a CDF file based on remapping of probes to the human genome 36.1. The raw data for 72 FL patient samples (CEL file) and the normalized matrix have been deposited in GEO (GSE37088 ).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!