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Series GSE235926 Query DataSets for GSE235926
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
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.
 
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.
 
Contributor(s) Yang J, Luo Y
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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
Phone +86-13606052637
Organization name Xiamen University
Department School of Life Sciences
Lab Molecular Medicine
Street address Xiang'an South Road
City Xiamen
State/province Fujian
ZIP/Postal code 361102
Country China
 
Platforms (1)
GPL15491 NimbleGen Human Gene Expression 12x135K Array [2007-09-12_HG18_opt_expr, 070925_HG18_expr]
Samples (6)
GSM7512042 Control_1
GSM7512043 Control_2
GSM7512044 Control_3
Relations
BioProject PRJNA988045

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE235926_RAW.tar 46.9 Mb (http)(custom) TAR (of CALLS, PAIR)
Processed data included within Sample table
Processed data provided as supplementary file

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