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Sample GSM6398562 Query DataSets for GSM6398562
Status Public on Jul 11, 2023
Title SARS-Cov-2 patient with persistent olfactory symptoms (Group 1, P14)
Sample type RNA
 
Source name Olfactory epithelium cells (OE)
Organism Homo sapiens
Characteristics cell type: olfactory epithelium
Extracted molecule total RNA
Extraction protocol Total RNA, including miRNAs, was extracted from the olfactory epithelium cells by using “Monarch® Total RNA Miniprep kit” (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s instructions. Briefly, this kit is a comprehensive solution for sample preservation, cell lysis, gDNA removal, and purification of total RNA from a wide variety of biological samples, including mammalian tissue. Total RNA was quantified by Nanodrop (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity, and the content of miRNAs (%) in each sample were assessed by capillary electrophoresis with the RNA 6000 Nano LabChip and the Small RNA Nano LabChip, respectively, using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Only samples with RNA Integrity Number (R.I.N.) values higher than six were used for gene and miRNA expression analysis.
Label Cy3
Label protocol Total RNA (200 ng) was labeled with pCp Cy3, according to the Agilent’s protocol, and unincorporated dyes were removed with MicroBioSpin6 columns (BioRad, Hercules, CA, USA)
 
Hybridization protocol Probes were hybridized at 55°C for 22 hours using the Agilent's hybridization oven that is suited for bubble-mixing and microarray hybridization processes.
Scan protocol Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 10% sensitivity settings. Agilent Feature Extraction software version 12.0.0.7 was used for image analysis.
Description miRNA expression profiling of patient with persistent olfactory symptoms (Group 1, P14)
Data processing Inter-array normalization of miRNA expression levels was performed with cyclic Lowess for miR [Risso et al., 2009] and the average of replicates was used. Feature Extraction software (Agilent Technologies) was used to obtain spot quality measures in order to evaluate the quality and the reliability of the hybridization. In particular, the flag “glsFound” (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as “not available” (NA). So, in order to perform a more robust and unbiased statistical analysis, probes with a high proportion of NA values were removed from the dataset. NA (44%) was used as threshold in the filtering process, obtaining a total of 210 available human miRNAs.
 
Submission date Jul 26, 2022
Last update date Jul 11, 2023
Contact name Cristiano De Pitta
E-mail(s) [email protected]
Phone +390498276210
Organization name University of Padova
Department Biology
Street address Via U. Bassi, 58/B
City Padova
ZIP/Postal code 35131
Country Italy
 
Platform ID GPL24741
Series (1)
GSE209806 Persistent and transient olfactory deficits in COVID-19 are associated to inflammation and zinc homeostasis

Data table header descriptions
ID_REF
VALUE Normalized and averaged signal intensity.

Data table
ID_REF VALUE
hsa-let-7a-5p 411.8435462
hsa-let-7b-5p 335.8959615
hsa-let-7c-5p 118.1986177
hsa-let-7d-5p 50.69657069
hsa-let-7e-5p 63.00291969
hsa-let-7f-5p 207.6338636
hsa-let-7g-5p 84.47649399
hsa-let-7i-5p 45.48276378
hsa-miR-100-5p 24.72482826
hsa-miR-103a-3p 65.30176605
hsa-miR-106b-5p 7.433241948
hsa-miR-107 33.71005116
hsa-miR-1202 25.62424695
hsa-miR-1207-5p 14.50151023
hsa-miR-1225-5p 8.843078061
hsa-miR-1227-5p null
hsa-miR-1229-5p 22.08088123
hsa-miR-1246 5.040555702
hsa-miR-125a-5p 14.53246656
hsa-miR-125b-5p 34.75949735

Total number of rows: 210

Table truncated, full table size 5 Kbytes.




Supplementary file Size Download File type/resource
GSM6398562_257015617872_S01_2_1_GeneView_P14.txt.gz 9.9 Kb (ftp)(http) TXT
Processed data included within Sample table

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