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Sample GSM3309884 Query DataSets for GSM3309884
Status Public on Jan 01, 2019
Title N025_ROC10055
Sample type RNA
 
Source name nasal_N025_RNA
Organism Homo sapiens
Characteristics gender: F
age (months): 4
infection: picornavirus (rhinovirus)
symptomatic: No
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) jyu@wustl.edu
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

Data table header descriptions
ID_REF
VALUE Quantification

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 1.62272
AFFX-BkGr-GC04_st 1.47078
AFFX-BkGr-GC05_st 1.54158
AFFX-BkGr-GC06_st 1.51745
AFFX-BkGr-GC07_st 1.56966
AFFX-BkGr-GC08_st 1.62471
AFFX-BkGr-GC09_st 1.65139
AFFX-BkGr-GC10_st 1.7847
AFFX-BkGr-GC11_st 1.90445
AFFX-BkGr-GC12_st 2.14577
AFFX-BkGr-GC13_st 2.40968
AFFX-BkGr-GC14_st 2.74715
AFFX-BkGr-GC15_st 3.29568
AFFX-BkGr-GC16_st 3.96483
AFFX-BkGr-GC17_st 4.48552
AFFX-BkGr-GC18_st 4.99348
AFFX-BkGr-GC19_st 5.50687
AFFX-BkGr-GC20_st 5.75131
AFFX-BkGr-GC21_st 6.01278
AFFX-BkGr-GC22_st 6.39653

Total number of rows: 138745

Table truncated, full table size 3533 Kbytes.




Supplementary file Size Download File type/resource
GSM3309884_27957.CEL.gz 22.2 Mb (ftp)(http) CEL
GSM3309884_27957.np.rma-gene-full.chp.gz 893.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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