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| Status |
Public on Jul 04, 2023 |
| Title |
Gene expression profiling in miR-574-5p knockdown HeLa cells and the controls |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
To profile gene expression in human HeLa cells follwing the knockdown of miR-574-5p, as compared to control HeLa cells
Gene ontology and clustering analyses revealed that the differentially-expressed genes were highly enriched for the immune system and its related signal transduction pathways.
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| Overall design |
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. The 6 gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Genes that have values greater than or equal to lower cut-off: 50.0 in that at least 3 out of 6 samples (“All Targets Value”) were chosen for data analysis. Significant differentially expressed genes were identified through Volcano Plot filtering.
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| Contributor(s) |
Yang J, Luo Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jun 27, 2023 |
| Last update date |
Jul 05, 2023 |
| Contact name |
James Yunqing Yang |
| E-mail(s) |
jamesyang@xmu.edu.cn
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| Phone |
+86-13606052637
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| Organization name |
Xiamen University
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| Department |
School of Life Sciences
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| Lab |
Molecular Medicine
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| Street address |
Xiang'an South Road
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| City |
Xiamen |
| State/province |
Fujian |
| ZIP/Postal code |
361102 |
| Country |
China |
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| Platforms (1) |
| GPL15491 |
NimbleGen Human Gene Expression 12x135K Array [2007-09-12_HG18_opt_expr, 070925_HG18_expr] |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA988045 |
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