|
| Status |
Public on Jan 01, 2019 |
| Title |
N003_ROC10005 |
| Sample type |
RNA |
| |
|
| Source name |
nasal_N003_RNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
age (months): 6
infection: picornavirus (rhinovirus)
symptomatic: Yes
|
| Treatment protocol |
The blood samples obtained by venipuncture were drawn into a Tempus tube (Applied Biosystems, Foster City, CA). The nasopharynx was washed with normal saline by a trained study coordinator and a nasal swab was obtained using a mid-turbinate flocked swab (Copan Diagnostics, Inc., Murrieta, CA). The nasal swab was immediately placed in RNAprotect (Qiagen, Valencia, CA). The nasal swab in RNAprotect was stored for 1-5 days at 4°C, after which cells were pelleted, suspended in lysis buffer containing BME, and homogenized by passing the lysate 10-12 times through a 28- gauge needle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Absolutely RNA Miniprep Kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
RNAs were amplified with the Affymetrix WT Pico whole transcript amplification (WTA) kit to generate cDNA targets labeled with biotin.
|
| |
|
| Hybridization protocol |
Followed Affymetrix standard hybridization protocol for Human Clariom D chips.
|
| Scan protocol |
Chips were scanned with Affymetrix 7G scanner at the standard setting.
|
| Description |
nasal swab
|
| Data processing |
The raw chip data files (.CEL) were processed through Affymetrix standard analysis pipeline for RMA background correction, median-polish summarization and quantile normalization. The .CHP files were generated at gene-level.
|
| |
|
| Submission date |
Jul 27, 2018 |
| Last update date |
Jan 01, 2019 |
| Contact name |
Jinsheng Yu |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University School of Medicine
|
| Department |
Genetics
|
| Lab |
GTAC Lab
|
| Street address |
660 S. Euclid Ave.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE117827 |
Host Gene Expression in Nasal and Blood Samples for the Diagnosis of Viral Respiratory Infection |
|
