NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5624854 Query DataSets for GSM5624854
Status Public on Oct 15, 2021
Title mir-4423 overexpression, 24 h post-transfection, replicate 1
Sample type RNA
 
Source name HeLa cells + mir-4423 plasmid
Organism Homo sapiens
Characteristics cell line: HeLa
plasmid: mir-4423 expression plasmid
time point: 24 h
Treatment protocol The cells were transiently transfected with the mir-199a-1 expression plasmid (HmiR0296-MR04, GeneCopoeia), the mir-4423 expression plasmid (HmiR1083-MR04, GeneCopoeia) or the negative control plasmid (CmiR0001-MR04, GeneCopoeia) using the FuGENE HD transfection reagent (Promega).
Growth protocol The HeLa cells were cultured in DMEM (Thermo Fisher Scientific) supplemented with 10% FBS (Sigma-Aldrich) and 50 U/ml penicillin-streptomycin (Thermo Fisher Scientific) in T25 flasks (Greiner Bio-One).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated 24 h and 48 h after transfection with the miRNeasy Mini Kit (Qiagen).
Label Biotin
Label protocol According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 210 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.
 
Hybridization protocol Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D microarrays. The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Thermo Fisher Scientific.
Scan protocol The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).
Description Transcriptome data for HeLa cell culture after transfection of mir-4423 plasmid
Data processing Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.2 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background adjustment, quantile normalization, gene-level probe set summarization and log2 transformation. The TAC software was also utilized for differential gene expression analysis.
 
Submission date Oct 13, 2021
Last update date Oct 16, 2021
Contact name Michael Hecker
E-mail(s) michael.hecker@rocketmail.com
Organization name University of Rostock
Department Department of Neurology
Lab Division of Neuroimmunology
Street address Gehlsheimer Str. 20
City Rostock
ZIP/Postal code 18147
Country Germany
 
Platform ID GPL23126
Series (1)
GSE185859 Screening for potential target genes of hsa-mir-199a-1 and hsa-mir-4423 using Clariom D arrays

Data table header descriptions
ID_REF
VALUE SST-RMA signal intensity

Data table
ID_REF VALUE
TC0100006432.hg.1 3.06324
TC0100006433.hg.1 2.9
TC0100006434.hg.1 2.38286
TC0100006435.hg.1 3.13684
TC0100006436.hg.1 3.46042
TC0100006437.hg.1 3.44804
TC0100006438.hg.1 5.6123
TC0100006439.hg.1 3.21659
TC0100006440.hg.1 3.98464
TC0100006441.hg.1 3.57863
TC0100006442.hg.1 3.22794
TC0100006443.hg.1 3.78829
TC0100006444.hg.1 3.51275
TC0100006445.hg.1 3.72099
TC0100006446.hg.1 3.37748
TC0100006447.hg.1 16.41256
TC0100006448.hg.1 3.30575
TC0100006449.hg.1 3.0633
TC0100006450.hg.1 3.35012
TC0100006451.hg.1 3.7147

Total number of rows: 135750

Table truncated, full table size 3446 Kbytes.




Supplementary file Size Download File type/resource
GSM5624854_mir-4423_24h_replicate1.CEL.gz 19.9 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap