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Sample GSM5229885 Query DataSets for GSM5229885
Status Public on Feb 01, 2022
Title Patient 2, WB Pmix stimulation
Sample type RNA
Source name Patient 2, WB Pmix stimulation
Organism Homo sapiens
Characteristics tissue: whole blood
gender: male
age(day): 330
Treatment protocol The diluted blood was divided into each tube by 800 μL and it was incubated with α-casein (100 μg/mL; Sigma-Aldrich) or Pmix (100 μg/mL), which is a mixture of four milk protein components (α-casein, κ-casein, α-lactalbumin, or β-lactoglobulin; 100 µg/mL each; Sigma-Aldrich) at 37°C for 24 h
Growth protocol Heparinized whole blood collected from patients with non-IgE GI-FAs and individuals who did not have non-IgE-GI-FAs or other immune diseases was diluted 4-fold with RPMI-1640 medium (Sigma-Aldrich, St. Louis, MO, USA).
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted from the blood sample, which unstimulated or stimulated with milk protein by using Nucleo Spin® RNA Blood (MACHEREY-NAGEL GmbH & Co. KG, Düren Germany).
Label Cy3
Label protocol One-color spike-mix (Agilent Technology) was added to the total RNA prior to the labeling reaction. Labeling was performed using a Low lnput Quick Amp Labeling Kit (Agilent Technology) in the presence of cyanine-3 (Cy3)-CTP.
Hybridization protocol 600 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25μl of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE Microarray 8 × 60 k ver. 2.0 (Design ID: 039494, Agilent Technologies) for 17 hours at 65°C.
Scan protocol Fluorescence images of the hybridized arrays were generated using the Agilent Scanner (Scan control software ver. 8)
Description Gene expression, whole blood sample from patient2 was stimulated with Pmix for 24 hours
Data processing The intensities were extracted with Agilent Feature Extraction software ver.
Submission date Apr 07, 2021
Last update date Feb 01, 2022
Contact name Yag Hisako
Organization name Department of Pediatrics, Gunma University Graduate School of Medicine
Street address 3-39-22 Showa-machi
City Maebashi
ZIP/Postal code 371-8511
Country Japan
Platform ID GPL13607
Series (1)
GSE171660 Novel Peripheral Blood Allergen Stimulation Test for Non-IgE-mediated Gastrointestinal Food Allergies in Neonates and Infants.

Data table header descriptions
VALUE processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
1 2.448566e+005
2 5.146658e+000
3 5.148336e+000
4 1.939961e+002
5 3.485407e+001
6 9.161332e+001
7 3.005090e+002
8 3.224312e+004
9 5.135080e+000
10 1.378940e+001
11 5.122946e+000
12 1.607377e+003
13 3.586309e+002
14 7.157562e+002
15 4.850374e+001
16 5.077083e+000
17 1.523869e+001
18 5.054604e+000
19 5.042153e+000
20 8.158381e+002

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.

Supplementary file Size Download File type/resource
GSM5229885_US83700204_252800420509_S01_GE1_105_Dec08_1_2.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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