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Status |
Public on Oct 15, 2021 |
Title |
negative control, 48 h post-transfection, replicate 3 |
Sample type |
RNA |
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Source name |
HeLa cells + control plasmid
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Organism |
Homo sapiens |
Characteristics |
cell line: HeLa plasmid: negative control plasmid time point: 48 h
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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).
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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).
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated 24 h and 48 h after transfection with the miRNeasy Mini Kit (Qiagen).
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Label |
Biotin
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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.
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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.
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Scan protocol |
The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).
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Description |
Transcriptome data for HeLa cell culture after transfection of control plasmid
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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.
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Submission date |
Oct 13, 2021 |
Last update date |
Oct 16, 2021 |
Contact name |
Michael Hecker |
E-mail(s) |
michael.hecker@rocketmail.com
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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 |
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Platform ID |
GPL23126 |
Series (1) |
GSE185859 |
Screening for potential target genes of hsa-mir-199a-1 and hsa-mir-4423 using Clariom D arrays |
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