Genechip human gene 1.0 st array

Manufactured by Thermo Fisher Scientific

Sourced in United States, Belgium, United Kingdom

The GeneChip Human Gene 1.0 ST Array is a gene expression microarray platform designed by Thermo Fisher Scientific. It provides comprehensive coverage of the human genome, allowing for the analysis of over 28,000 well-annotated genes. The array utilizes probe sets that target the entire length of each gene, enabling the detection and quantification of all known and predicted transcripts.

Automatically generated - may contain errors

Lab products found in correlation

220 protocols using genechip human gene 1.0 st array

Affymetrix GeneChip Human Gene 1.0-ST Array Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

The Affymetrix GeneChip Human Gene 1.0-ST array (Affymetrix, Santa
Clara, CA, USA) was used to define gene expression profiles from the samples.
Synthesis and labeling of cDNA targets, hybridization, and scanning of GeneChips
were carried out by the Integrative Genomics Core Facility at City of Hope.
Briefly, cRNA was generated according to the manufacturer’s protocol
using Affymetrix’s GeneChip Whole Transcript Sense Target Labeling Assay
Hybridization cocktails containing 5.5 μg of fragmented, end-labeled cDNA
were prepared and applied to GeneChip Human Gene 1.0 ST arrays. Hybridization
was performed for 16 h, and the arrays were washed and stained with a GeneChip
Fluidics Station 450 using FS450_0007 script. Arrays were scanned at 5 μm
resolution using Affymetrix GCS 3000 7G.
Raw intensity measurements of all probe sets were background-corrected,
normalized, and converted into expression measurements using Affymetrix’s
Expression Console v1.1.1. The Bioconductor “ArrayTools” package
was then used to identify the genes differentially expressed between the treated
and untreated samples. Significant genes were selected with a cutoff of adjusted
P < 0.05 and fold change of 2. The DAVID functional
annotation tool https://david.ncifcrf.gov/content.jsp?file=citation.htm) was
then used to identify modulated KEGG signaling pathways.

Zhang X.H., Chen C., Li H., Hsiang J., Wu X., Hu W., Horne D., Nam S., Shively J, & Rosen S.T. (2021). Targeting the non‐ATP‐binding pocket of the MAP kinase p38γ mediates a novel mechanism of cytotoxicity in cutaneous T‐cell lymphoma (CTCL). Febs Letters, 595(20), 2570-2592.

+ Open protocol

+ Expand

Affymetrix Gene Expression Profiling of CBX7 in Thyroid Cancer

Check if the same lab product or an alternative is used in the 5 most similar protocols

GeneChip Human Gene 1.0 ST Arrays (Affymetrix, Santa Clara, CA), consisting of 764,885 probe sets covering over 28,869 genes, was used to evaluate genes differentially expressed. The whole hybridization procedure was performed following the Affymetrix instructions. The amplification and labeling processes were verified using a GeneChip Eukaryotic Poly-A RNA Control Kit (Affymetrix) with exogenous positive controls. 15 µg of each biotinylated cRNA preparation was fragmented and placed in hybridization mixture containing biotinylated hybridization controls (GeneChip Expression Hybridization Controls, Affymetrix). Samples were then hybridized onto a GeneChip Human Gene 1.0 ST Array at 45 °C for 16 hours at constant rotation (60 rpm) in a Hybridization Oven (Affymetrix). Microarray scanned images were obtained with a GeneChip Scanner (Affymetrix) using the default settings. Images were analyzed with Affymetrix Gene Expression Analysis Software (Affymetrix). Comparisons were made between FRO-EV-1 and FRO-CBX7-1 samples, considering FRO-EV-1 as baseline. The fold change values, indicating the relative change in the expression levels between FRO-EV-1 and FRO-CBX7-1, were used to identify genes differentially expressed.
Microarray data are available in the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-2420.

Pallante P., Sepe R., Federico A., Forzati F., Bianco M, & Fusco A. (2014). CBX7 Modulates the Expression of Genes Critical for Cancer Progression. PLoS ONE, 9(5), e98295.

+ Open protocol

+ Expand

Affymetrix GeneChip Gene Expression Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

The Affymetrix GeneChip Human Gene 1.0‐ST array (Affymetrix, Santa Clara, CA, USA) was used to define gene expression profiles from the samples. Synthesis and labeling of cDNA targets, hybridization, and scanning of GeneChips were carried out by the Integrative Genomics Core Facility at City of Hope. Briefly, cRNA was generated according to the manufacturer's protocol using Affymetrix's GeneChip Whole Transcript Sense Target Labeling Assay Hybridization cocktails containing 5.5 µg of fragmented, end‐labeled cDNA were prepared and applied to GeneChip Human Gene 1.0 ST arrays. Hybridization was performed for 16 h, and the arrays were washed and stained with a GeneChip Fluidics Station 450 using FS450_0007 script. Arrays were scanned at 5 μm resolution using Affymetrix GCS 3000 7G.
Raw intensity measurements of all probe sets were background‐corrected, normalized, and converted into expression measurements using Affymetrix’s Expression Console v1.1.1. The Bioconductor “ArrayTools” package was then used to identify the genes differentially expressed between the treated and untreated samples. Significant genes were selected with a cutoff of adjusted P < 0.05 and fold change of 2. The DAVID functional annotation tool https://david.ncifcrf.gov/content.jsp?file=citation.htm) was then used to identify modulated KEGG signaling pathways.

+ Open protocol

+ Expand

Comprehensive Gene Expression and Methylation Analysis

Cited 3 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Total RNA was extracted from 25 mg tumor tissue using TRIzol reagent (Invitrogen), according to the manufacturer's procedure. cRNA was generated, labeled and hybridized to the Affymetrix (Santa Clara, CA) GeneChip® Human GENE 1.0 ST arrays by the Center for Medical Genomics at the Indiana University School of Medicine (Indianapolis, IN, http://cmg.iupui.edu/), as we have described previously [10 (link)]. The hybridized GeneChip® Human GENE 1.0 ST arrays were scanned using a Affymetrix GeneChip Scanner 3000 and analyzed using the Affymetrix Microarray Analysis Suite (MAS) version 5.0. The average density of hybridization signals from independent slides (4 slides per biopsy) was used for data analysis and genes with signal density less than 300 pixels were omitted from the data analysis. Genome-wide DNA methylation analysis using the Infinium HumanMethylation27 BeadChips (Illumina, San Diego, CA) was performed as previously published [12 (link), 13 (link)]. The gene expression analysis results are available for download at Gene Expression Omnibus data repository at the National Center for Biotechnology Information (NCBI) under the accession number GSE55410.

Fang F., Zuo Q., Pilrose J., Wang Y., Shen C., Li M., Wulfridge P., Matei D, & Nephew K.P. (2014). Decitabine reactivated pathways in platinum resistant ovarian cancer. Oncotarget, 5(11), 3579-3589.

+ Open protocol

+ Expand

Genome-wide Expression Profiling by Microarray

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Genome-wide expression profiles of NI, LI, and HI were determined using the GeneChip Human Gene 1.0ST Arrays (Affymetrix), as described^{49 (link)}. Briefly, total RNA was extracted using QIAGEN RNeasy Mini Kit (Qiagen), processed using the Affymetrix WT Expression kit before being hybridized on Affymetrix GeneChip Human Gene 1.0 ST arrays, according to the manufacturer’s instructions (protocol P/N 702808 Rev.6). Upon hybridization, microarrays were washed, stained and scanned according to manufacturer’s standard procedures. Microarray data are available in the Gene Expression Omnibus (GEO) repository under accession number GSE134470.

Schuster A., Klein E., Neirinckx V., Knudsen A.M., Fabian C., Hau A.C., Dieterle M., Oudin A., Nazarov P.V., Golebiewska A., Muller A., Perez-Hernandez D., Rodius S., Dittmar G., Bjerkvig R., Herold-Mende C., Klink B., Kristensen B.W, & Niclou S.P. (2020). AN1-type zinc finger protein 3 (ZFAND3) is a transcriptional regulator that drives Glioblastoma invasion. Nature Communications, 11, 6366.

+ Open protocol

+ Expand

Transcriptome Analysis of Gene Expression

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Total RNA was isolated using an RNeasy Kit (QIAGEN, CA, USA) according to the manufacturer’s instructions. Preparation of terminal-labeled complementary DNA (cDNA), hybridization to the whole-transcript GeneChip Human Gene 1.0 ST Array (Affymetrix, USA) and scanning of the arrays were performed according to the manufacturer’s protocols. Raw data were preprocessed with the robust multichip average (RMA) algorithm. Genes were considered differentially expressed if log₂ fold change values were >1 or <−1, with P < 0.05. All these steps were conducted using R packages affy and limma hosted on the Bioconductor website.^{20 (link),21 (link)}

Comi M., Avancini D., Santoni de Sio F., Villa M., Uyeda M.J., Floris M., Tomasoni D., Bulfone A., Roncarolo M.G, & Gregori S. (2019). Coexpression of CD163 and CD141 identifies human circulating IL-10-producing dendritic cells (DC-10). Cellular and Molecular Immunology, 17(1), 95-107.

+ Open protocol

+ Expand

Differential Gene Expression in LPA-Treated HCT-116 Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols

Total RNA from FBS-depleted HCT-116 cells that were either treated or not with LPA for 12h were obtained using an RNeasy Mini Kit (QIAGEN, USA) according to the manufacturer's instructions. One hundred nanograms of total RNA was used to synthesize the biotinylated cRNA according to the GeneChip whole transcription (WT) sense target-labeling assay (Affymetrix, USA). After, the biotinylated cRNA was hybridized to the GeneChip human gene 1.0 ST array (Affymetrix, USA), washed and stained according to the manufacturer’s protocols. The GeneChip arrays were scanned using a GeneChip® Scanner 3000. The Affymetrix Expression Console Software Version 1.0 was used to create summarized expression values (CHP-files), and the Robust Multichip Analysis (RMA) algorithm was applied. The data were analyzed using Partek^® software (http://www.partek.com) [24 ]; differentially expressed genes with ≥ 2-fold-change were used as the criteria to define overexpression or down regulation. The pathway analysis and related processes were obtained using MetaCore^TM software (http://thomsonreuters.com/metacore) and Ingenuity^® Pathway analysis software (http://www.ingenuity.com).

Leve F., Peres-Moreira R.J., Binato R., Abdelhay E, & Morgado-Díaz J.A. (2015). LPA Induces Colon Cancer Cell Proliferation through a Cooperation between the ROCK and STAT-3 Pathways. PLoS ONE, 10(9), e0139094.

+ Open protocol

+ Expand

Transcriptomic Profiling of CEP-37440 Treatment

Check if the same lab product or an alternative is used in the 5 most similar protocols

FC-IBC02 cells were treated with 1000 nM CEP-37440 for 48 h and RNA was isolated. Affymetrix Genechip® Human Gene 1.0 ST array (Affymetrix Inc., Santa Clara, CA, USA) were used for gene expression studies (Additional file 12). Data analyses were performed using GeneSpring software 13.1 (Agilent Technologies, Inc., Santa Clara, CA, USA). The criteria for differentially expressed genes were set at ≥ 2.0-fold changes. Statistical analysis was performed to compare two groups using t test unpaired with a p value less than or equal to 0.05. A heat map was generated from the differentially expressed gene list. The list of differentially expressed genes was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (http://www.ingenuity.com) to perform biological network and functional analyses.

Salem I., Alsalahi M., Chervoneva I., Aburto L.D., Addya S., Ott G.R., Ruggeri B.A., Cristofanilli M, & Fernandez S.V. (2016). The effects of CEP-37440, an inhibitor of focal adhesion kinase, in vitro and in vivo on inflammatory breast cancer cells. Breast Cancer Research : BCR, 18, 37.

+ Open protocol

+ Expand

Profiling 12q13-q14 Amplified Tumors

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Twelve tumors (n=6 with 12q13-q14 amplification; n=6 without 12q13-q14 amplification) were selected from 57 cases reported in a previous study (9 (link)). Criteria for selection included PAX3-FOXO1 expression, prior analysis by copy number arrays (9 (link)), and availability of RNA. Oligonucleotide microarray expression analysis was performed on the 12 selected cases using the Affymetrix GeneChip Human Gene 1.0 ST Array at the University of Pennsylvania Microarray Facility. We defined a gene as overexpressed in a sample if its expression level was >1 standard deviation (SD) from the mean expression level of that gene across all samples. More stringent analysis was also performed by defining overexpression as >2 SD from the mean. The total number of overexpressed genes in each sample was used as a relative measure of E2F pathway activation. Additional details are described in Supplemental methods.

Olanich M.E., Sun W., Hewitt S.M., Abdullaev Z., Pack S.D, & Barr F.G. (2015). CDK4 amplification reduces sensitivity to CDK4/6 inhibition in fusion-positive rhabdomyosarcoma. Clinical cancer research : an official journal of the American Association for Cancer Research, 21(21), 4947-4959.

+ Open protocol

+ Expand

Microarray-based mRNA Profiling Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

mRNA profiling was performed using GeneChip Human Gene 1.0ST Array (Affymetrix, Santa Clara, CA, USA). This array comprises>750,000 unique 25-mer oligonucleotide features constituting over 28,000 gene-level probe sets.
Microarray experiments were conducted according to the manufacturer's instructions. Briefly, 200 ng total RNA was labeled using WT Expression Kit (Ambion). The labeling reaction was hybridized on the Human Gene Array in Hybridization Oven 640 (Affymetrix) at 45°C for 18hours. The eight arrays for each group were stained with Fluidics Station 450 using fluidics script FS450_0007 (Affymetrix) then scanned on GeneChip Scanner 3000 7G (Affymetrix). GeneChip® Command Console®software supplied by Affymetrix was used to perform gene expression analysis. All raw data regarding mRNA expression has been deposited in ArrayExpress, a publicly accessible database.

Borras C., M. Abdelaziz K., Gambini J., Serna E., Inglés M., de la Fuente M., Garcia I., Matheu A., Sanchís P., Belenguer A., Errigo A., Avellana J.A., Barettino A., Lloret-Fernández C., Flames N., Pes G., Rodriguez-Mañas L, & Viña J. (2016). Human exceptional longevity: transcriptome from centenarians is distinct from septuagenarians and reveals a role of Bcl-xL in successful aging. Aging (Albany NY), 8(12), 3185-3201.

+ Open protocol

+ Expand

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?

Revolutionizing how scientists
search and build protocols!