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| Scope: Self Platform Samples Series Family Format: HTML SOFT MINiML Amount: Brief Quick GEO accession: |  |
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| Sample GSM5550653 | Query DataSets for GSM5550653 |
| | Status | Public on Dec 31, 2021 | | Title | Subject ID: B0428; Tissue: nasal | | Sample type | RNA | | Source name | nasal | | Organism | Homo sapiens | | Characteristics | subject id: B0428tissue: nasalgender: Femaleage: 48status1: COVIDstatus2: Non_Hospitalizedseverity_sampling: Mildfinal_severity: Mild | | Extracted molecule | total RNA | | Extraction protocol | RNA was isolated using PAXgene blood miRNA extraction kit (Qiagen) following manufacturer recommendations and carrying out the on-column DNase I treatment during the extraction process. RNA from saliva and nasal epithelium specimens was isolated using 500ul of sample and the RNeasy microkit (Qiagen). We used Oragene RNA neutralizer solution (DNA Genotek) to precipitate impurities and inhibitors and slightly modified the protocol provided by the extraction kit as recommended by the Oragene tubes supplier | | Label | n/a | | Label protocol | n/a | | Hybridization protocol | We used the standard gene expression protocol for 12x RNA hybridization with 5ul of RNA as input, a hybridization time of 18h for all samples and mixing control and COVID-19 samples to avoid technical sample bias. | | Scan protocol | SPRINT nCounter machine | | Data processing | Normalization of the gene expression data was carried out for each tissue separately by selecting the optimal number and best reference candidate from the set of housekeeping (HK) genes included in the panel, as well as other endogenous genes that showed high levels of stability between samples. We excluded HK candidate genes with less than 50 raw counts in any of the samples compared from the reference selection analysis. Data normalization was performed through a combined approach using both DESeq2 and RUVSeq as described in Bhattacharya et al. (2021) (https://academic.oup.com/bib/article-abstract/22/3/bbaa163/5891144). Genes with counts below the background (mean + 2 standard deviations (SD) of the negative control spikes in the code set) were not included in the differential expression (DE) analysis. After data normalization and background thresholding, we eliminated lower expressed genes from the list. | | Submission date | Aug 31, 2021 | | Last update date | Dec 31, 2021 | | Contact name | Alberto Gómez-Carballa | | E-mail(s) | [email protected] | | Organization name | GENVIP research group | | Department | Pediatrics | | Street address | Choupana sn | | City | Santiago de Compostela | | State/province | A coruña | | ZIP/Postal code | 15706 | | Country | Spain | | Platform ID | GPL30569 | | Series (1) | | GSE183071 | A multi-tissue study of immune gene expression profiling highlights the key role of the nasal epithelium in COVID-19 severity |
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| Data table header descriptions | | ID_REF | | VALUE | normalized data |
| Data table | | ID_REF | VALUE | | ABCB1 | 5.27683957932139 | | ABCF1 | 8.22706315896516 | | ABL1 | 8.56027654781435 | | ADA | 5.81518350543964 | | AHR | 11.3048764217984 | | AICDA | | AIRE | | ALAS1 | 9.19834817863007 | | APP | 11.4340857770308 | | ARG1 | 5.49987855693273 | | ARG2 | 7.41788622007267 | | ARHGDIB | 9.19162206644683 | | ATG10 | 6.80957334147214 | | ATG12 | 6.33366295674504 | | ATG16L1 | 8.05216063080339 | | ATG5 | 9.50974452521969 | | ATG7 | 8.81498994529263 | | ATM | 5.074980903275 | | B2M | 16.6584369192528 | | B3GAT1 |
Total number of rows: 594Table truncated, full table size 12 Kbytes.| Supplementary file | Size | Download | File type/resource | | GSM5550653_B0428-nasal.RCC.gz | 6.8 Kb | (ftp)(http) | RCC | | Processed data included within Sample table |
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