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Human gene 1.0 st array chips

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The Human Gene 1.0 ST Array chips are a high-density oligonucleotide microarray designed for the analysis of gene expression in human samples. The chips contain probes targeting over 28,000 well-annotated genes, providing comprehensive coverage of the human transcriptome.

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Lab products found in correlation

Agencourt ampure magnetic bead, by Beckman Coulter (2 mentions) Genechip scanner 3000 7g, by Thermo Fisher Scientific (2 mentions) Fluidics station 450, by Thermo Fisher Scientific (1 mentions) Genechip wt plus reagent kit, by Thermo Fisher Scientific (1 mentions) Trizol reagent, by Thermo Fisher Scientific (1 mentions) Affymetrix fluidics station 450, by Thermo Fisher Scientific (1 mentions) Genechip command console, by Thermo Fisher Scientific (1 mentions)

5 protocols using human gene 1.0 st array chips

1

Transcriptomic Profiling of Gene Expression

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Total RNA was extracted using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions and then purified with Agencourt AMPure magnetic beads (Beckman Coulter, USA). Target preparation for microarray processing was performed according to the instructions provided in the GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific, USA). After hybridization with Affymetrix Human Gene 1.0ST Array chips, the microarrays were washed, stained with streptavidin-phycoerythrin on Affymetrix Fluidics Station 450 (Affymetrix, USA), and then scanned using an Affymetrix® GeneChip Command Console installed in a GeneChip® Scanner 3000 7G (Affymetrix, USA). The microarray data were analyzed by the robust multichip analysis (RMA) algorithm using the default analysis settings and global scaling as the normalization method with Partek® Genomics Suite 6.6. The log2-transformed values of the RMA signal intensities were calculated, and differential expression analysis was further performed by one-way analysis of variance (ANOVA).
Hu M., Zheng Y., Liao J., Wen L., Cheng J., Huang J., Huang B., Lin L., Long Y., Wu Y., Ye X., Fu Y., Qi H., Baker P.N, & Tong C. (2022). miR21 modulates the Hippo signaling pathway via interference with PP2A Bβ to inhibit trophoblast invasion and cause preeclampsia. Molecular Therapy. Nucleic Acids, 30, 143-161.
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2

Placental Microarray Data Processing

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Our entire 157 placenta dataset was previously hybridized against Human Gene 1.0 ST Array chips from Affymetrix [3 (link)]. The resulting microarray CEL files for the 48 placentas assessed for methylation in the current study were loaded into R, and normalized and converted to log2 values using the affy library [25 (link)]. Expression values annotated to the same gene symbol were merged to a mean value, and genes with expression in the lowest quartile were filtered out to reduce confounding by background noise, using the varFilter function.
Leavey K., Wilson S.L., Bainbridge S.A., Robinson W.P, & Cox B.J. (2018). Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsia. Clinical Epigenetics, 10, 28.
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3

Harmonization of Microarray Datasets

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The dataset ‘GSE75010-157’ was generated with the Human Gene 1.0 ST Array chips (Affymetrix). The dataset ‘GSE75010-173’ was a combination of the microarray data from seven different studies, in which five different commercial microarray kits from Applied Biosystems, Agilent Technologies, Affymetrix, Roche NimbleGen Arrays, and Illumina were applied44 (link). According to Leavey et al., both datasets were harmonized by normalization and batch effect correction with the virtual Array R package52 to improve the reproducibility of the downstream statistical analyses. Finally, all data were converted into log2 values using R Affy library53 (link). A total of 14,651 genes with expression values were detectable in both datasets44 (link). The harmonized datasets ‘GSE75010-157’ and ‘GSE75010-173’ were used as discovery set and replication set, respectively.
Zhou G., Winn E., Nguyen D., Kasten E.P., Petroff M.G, & Hoffmann H.M. (2022). Co-alterations of circadian clock gene transcripts in human placenta in preeclampsia. Scientific Reports, 12, 17856.
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4

Transcriptome Analysis via Microarray

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Total RNA was extracted using TRIzol/chloroform, and then purified with Agencourt Ampure magnetic beads (Beckman Coulter, USA). Target preparation for microarray processing was performed according to the instructions provided in the GeneChip® WT PLUS Reagent Kit. After hybridization with Affymetrix Human Gene 1.0ST Array chips, the microarrays were washed and stained with streptavidin-phycoerythrin on the Affymetrix Fluidics Station 450 (Affymetrix Inc., USA), and then scanned using an Affymetrix® GeneChip Command Console, which was installed in a GeneChip® Scanner 3000 7G (Affymetrix Inc., USA).
Tian J., Liu Y., Hu M., Zheng Y., Xu P., Zhang L., Liao J., Wu Y., Wen L., Tong C., Yan J., Qi H., Saffery R., Baker P.N, & Kilby M.D. (2020). Upregulated LncZBTB39 in pre-eclampsia and its effects on trophoblast invasion and migration via antagonizing the inhibition of miR-210 on THSD7A expression. European journal of obstetrics, gynecology, and reproductive biology, 248.
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5

Placental Profiling for N-SGA Transcriptome

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Similar to our previous preeclampsia profiling study, 38 placental sampling for messenger RNA assessment was performed by the BioBank, such that 1 biopsy sample was collected, midway between the umbilical cord insertion and disc periphery, from each quadrant in the placenta. All 4 biopsy samples from each placenta were immediately rinsed in phosphate-buffered saline solution, pooled, snap-frozen in liquid nitrogen, and crushed into a powder. Messenger RNA was extracted from the 20 N-SGA snap-frozen tissues with the use of Trizol and RNAeasy spin columns, as well as from 4 average-for-gestational-age (AGA) control placentas previously purchased and used in our preeclampsia study 38 to serve as technical replicates. Extracted messenger RNA for all 24 placentas was hybridized against Human Gene 1.0 ST Array chips (Affymetrix, Santa Clara, CA) by the Princess Margaret Genomics Centre (Toronto, Canada). The generated microarray dataset for the 20 new N-SGA samples is available on the Gene Expression Omnibus, under the accession number GSE100415.
Gibbs I., Leavey K., Benton S.J., Grynspan D., Bainbridge S.A, & Cox B.J. (2019). Placental transcriptional and histologic subtypes of normotensive fetal growth restriction are comparable to preeclampsia. American journal of obstetrics and gynecology, 220(1).
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