100 ng of total RNA from PBMC from 4 controls and 5 PE at week 22–24 was subjected to GeneChip HT One-Cycle cDNA Synthesis Kit and GeneChip HT IVT Labeling Kit, following the manufacturer’s protocol for whole genome gene expression analysis (Affymetrix, Santa Clara, CA). Labeled and fragmented single stranded cDNAs were hybridized to the GeneChip Human Gene 1.0 ST Arrays (28,869 transcripts) (Affymetrix). The arrays were washed and stained using FS-450 fluidics station (Affymetrix). Signal intensities were detected by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA). The scanned images were processed using Affymetrix GeneChip Command Console (AGCC). The CEL files were imported into Partek Genomics Suite software (Partek, Inc. MO). Robust microarray analysis (RMA) was applied for normalization. Differentially expressed genes between groups were identified using one-way ANOVA analysis. Cluster analysis were generated in Partek Genomics Suite. Further bioinformatics analysis was conducted on the significant genes to identify functional significance by means of Ingenuity Pathways Analysis (Ingenuity Systems, Redwood City, CA).
Genearray scanner 3000 7g
Manufactured by Hewlett-Packard
Sourced in United States
The GeneArray Scanner 3000 7G is a high-performance scanning device designed for use in genetic research and analysis. It is capable of scanning DNA and RNA microarrays with a high resolution and accuracy. The scanner utilizes advanced optical technology to capture detailed images of gene expression data.
Automatically generated - may contain errors
Lab products found in correlation
Fs 450 fluidics station, by Thermo Fisher Scientific (3 mentions)
Ambion wt expression kit, by Thermo Fisher Scientific (3 mentions)
Genechip human gene 1.0 st array, by Thermo Fisher Scientific (2 mentions)
Fluidics station 450, by Hewlett-Packard (2 mentions)
Ingenuity pathways analysis, by Qiagen (1 mentions)
Genechip command console, by Thermo Fisher Scientific (1 mentions)
Genechip ht ivt labeling kit, by Thermo Fisher Scientific (1 mentions)
Genechip command console software agcc, by Thermo Fisher Scientific (1 mentions)
Genechip wt terminal labeling kit, by Thermo Fisher Scientific (1 mentions)
Genespring gx 12, by Agilent Technologies (1 mentions)
Genechip wt terminal labeling and controls kit, by Thermo Fisher Scientific (1 mentions)
Genechip human gene 2.0 st array, by Thermo Fisher Scientific (1 mentions)
Transcriptome analysis console 4, by Thermo Fisher Scientific (1 mentions)
Encore biotin module, by Tecan (1 mentions)
Ovation pico wta system v2 kit, by Tecan (1 mentions)
Affymetrix genechip wt terminal labeling and controls kit, by Thermo Fisher Scientific (1 mentions)
Genechip mirna 2.0 array, by Thermo Fisher Scientific (1 mentions)
Genespring 13, by Agilent Technologies (1 mentions)
Genechip mouse gene 2.0 st array, by Thermo Fisher Scientific (1 mentions)
7 protocols using genearray scanner 3000 7g
1
Microarray Analysis of PBMC in Preeclampsia
2
Gene Expression Profiling of Cells
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To compare the gene expression profiles of the different cells isolated, an Affymetrix Gene Chip Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA, USA) was used. 150 ng of total ribonucleic acid (RNA) was subjected to an Ambion WT Expression Kit (Thermo Fisher Scientific, Waltham, MA, USA) and a GeneChip WT Terminal Labeling Kit (Affymetrix) according to the manufacturers’ protocol, then washed and stained on FS-450 fluidics station (Affymetrix). The signal intensities were detected by Hewlett Packard Gene Array Scanner 3000 7 G (Hewlett Packard, Palo Alto, CA, USA). The scanned images were processed using GeneChip Command Console Software (AGCC) (Affymetrix) and the CEL files were imported into GeneSpring GX 12.6 software (Agilent Technologies Inc, Santa Clara, CA, USA). Robust microarray analysis (RMA) was applied for normalization. Based on the literature, stem cells-related genes were selected and statistical analysis was performed (One-way ANOVA with Tukey post hoc test and Benjamini-Hochberg FDR; fold change cut off being set at 2) to calculate p values and fold change.
3
Transcriptome Analysis of GIGYF2 KO and Overexpression in HeLa Cells
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RNA extracted from control, GIGYF2-KO and GIGYF2 overexpressing HeLa cells (all from three biological replicates) was sent to the GeneCore Facility (EMBL, Heidelberg) for Affymetrix GeneChip array analysis. When comparing to GIGYF2-KO cells, control cells were HeLa-11ht cells that had been transfected with the pSpCas9(BB)-2A-GFP plasmid with no single guide RNA and then underwent the same clonal selection as the KO cells. When comparing to GIGYF2 overexpressing cells, control cells were HeLa-11ht cells that had been transfected with the parental plasmid. RNA samples (500 ng) were processed and labeled for array hybridization using the Ambion WT Expression kit (Life Technologies, catalogue number 4411974). Labeled, fragmented cDNA (Affymetrix GeneChip® WT Terminal Labeling and Controls Kit, catalog number 901524) was hybridized to Affymetrix GeneChip® Human Gene 2.0 ST arrays (catalogue number 902113) for 16 h at 45°C (at 60 rpm) (Affymetrix GeneChip® Hybridization, Wash, and Stain Kit, catalog number 900720). Arrays were washed and stained using the Affymetrix Fluidics Station 450, and scanned using the Hewlett-Packard GeneArray Scanner 3000 7G. Data analysis was performed with the Transcriptome Analysis Console (TAC) 4.0 Software (Affymetrix).
4
RNA Expression Profiling of Sorted Cells
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RNA quality was assessed using a Bioanalyzer for integrity and concentration. For cultured material RNA (200ng) were processed and labeled for array hybridization using the Ambion WT Expression kit (Life Technologies). For sorted material, biotinylated cDNA was synthesized from 1.8ng of total RNA using the Nugen Ovation Pico WTA System V2 kit. Five μg of ssDNA from sorted material was subsequently fragmented and biotinylated (NuGen Encore Biotin Module). Labeled, fragmented cDNA (Affymetrix GeneChip® WT Terminal Labeling and Controls Kit) was hybridized to Mouse Gene 2.0 arrays for 16 hours at 45°C (at 60 rpm) (Affymetrix GeneChip® Hybridization, Wash, and Stain Kit). Arrays were washed and stained using the Affymetrix Fluidics Station 450, and scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.
5
Gene Expression Analysis via Microarray
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Images were scanned using a Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, USA). A 2-fold change in expression level was chosen as a cutoff for categorizing a significant change in expression level.13 (link)
6
Profiling miRNA Expression in Ovarian Cancer
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Global miRNA expression was analyzed in 12 HGSC, 9 CCC and 9 OSE samples. Total RNA (400 ng) was used for biotin labeling of miRNA by the Genisphere FlashTag HSR kit following the manufacturer’s recommendations (Genisphere, Hatfield, PA). Labeled miRNAs were hybridized to the GeneChip miRNA 2.0 Array (Affymetrix, Santa Clara, CA), representing 1,105 mature human miRNAs, as recommended by the manufacturer. Arrays were washed and stained using the FS-450 fluidics station (Affymetrix). Signal intensities were detected by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA). Microarray data were deposited in NCBI’s Gene Expression Omnibus (GEO) [30 (link)] and are accessible through GEO Series accession number GSE47841 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47841 ).
7
Microarray Analysis of 5-ITu Treatment
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Microarray experiments were carried out at the Genomics Core Facility of EMBL. Transcriptional analysis was performed using the Affymetrix GeneChip Mouse Gene 2.0 ST Arrays. Three biological replicates were used in each condition (DMSO only, 0.1 μM and 1.0 μM 5-ITu). Labelling and hybridization were carried out according to the standard Affymetrix protocol. Chips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7 G. The quality and the background of the array data were assessed using the Expression Console (version 1.3) software (Affymetrix). Data analysis was carried out using the GeneSpring 13.0 software (Agilent Technologies). RNA normalization was performed and only probes above the background threshold (=353) were considered for further evaluation. Statistically significant transcripts were obtained based on their one-way Anova p value (<0.05). A cut-off on fold change >1.5 was selected. The data have been deposited in GEO database under the accession number GSE119737.
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