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Sample GSM5099876 Query DataSets for GSM5099876
Status Public on Feb 24, 2021
Title LS042
Sample type RNA
 
Source name induced sputum
Organism Homo sapiens
Characteristics disease state: allergy
season: in season
ait treatment: SCIT
Extracted molecule total RNA
Extraction protocol Induced sputum samples were processed and isolated cells were directly transferred into RNAcell protect reagent (Qiagen) and stored at -80°C until RNA extraction. Total RNA was extracted using RNeasy Mini Kit (Cat.-No. 74104, Qiagen, Hilden, Germany) with on-column DNase digestion (Cat.-No. 79254, DNase-Free DNase Set, Qiagen) for avoiding DNA contaminations {Zissler, 2016 #317}. RNA quantification was performed by ultraviolet–visible spectrophotometry (Nanodrop Technologies, Wilmington, DE, USA), for assessment of the RNA integrity by the RNA 6000 Nano Chip Kit with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 17 ng RNA using the One-Color Agilent Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, GER). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and 20 bit Tiff.
Data processing The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Agilent.SingleColor.28004 microarray, Software GeneSpring 14.5; Threshold: 1.0, Logbase: 2; Normalization: Quantile; Baseline Transformation: None; Filtered on Expression (20.0-100.0); Filtered on Flags (Detected, Not Detected); T test unpaired , P<=:0.05, FC>=1.5
 
Submission date Feb 22, 2021
Last update date Feb 24, 2021
Contact name Ulrich M Zissler
E-mail(s) ulrich.zissler@tum.de
Phone +49 (0)89 4140 3472
Organization name Technical University of Munich & Helmholtz Center Munich
Department Center of Allergy & Environment (ZAUM)
Lab Airway Immunology
Street address Biedersteiner Str. 29
City Munich
ZIP/Postal code 80802
Country Germany
 
Platform ID GPL13607
Series (1)
GSE167225 Allergen-specific immunotherapy induces the suppressive secretoglobin 1A1 in cells of the lower airways

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1 54899.6
2 -3.92888
3 -0.164623
4 223.092
5 47.2518
6 28.2228
7 862.803
8 1542.42
9 17.7385
10 12.5408
11 2.568
12 778.673
13 550.997
14 564.309
15 118.432
16 -2.45318
17 57.6398
18 0.135871
19 10.6313
20 240.308

Total number of rows: 62976

Table truncated, full table size 851 Kbytes.




Supplementary file Size Download File type/resource
GSM5099876_US11073879_252800421914_S01_GE1_1100_Jul11_1_3.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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