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Sample GSM3110866 Query DataSets for GSM3110866
Status Public on Jun 01, 2020
Title 1week_control02
Sample type RNA
 
Source name total small intestine
Organism Mus musculus
Characteristics strain: C57BL/6J wild type
group: control
time after infection: -
age: 10 days
Treatment protocol 3-4 day old neonate mice were orally infected by gavage with 2x105 G. lamblia ATCC 5058 (assemblage B, strain GS, clone H7) trophozoites.
Growth protocol G. lamblia was cultured in vitro in medium containing (per liter): Trypticase Peptone 20g, Yeast Extract 10g, D (+) Glucose 10g, NaCl 2g, K2HPO4 1g, KH2PO4 0.6g, L-Cysteine 2g, L(+)Ascorbic Acid 0.2g, Ammonium Citrate 22.8mg, Bile 0.5g, Ampicillin (50ug/ml) 50mg, Kanamycin (100ug/ml) 100mg supplemented with 100ml (10%) of heat Inactivated bovine serum (not fetal bovine serum) and adjusted to pH to 7-7.1 using 5M NaOH and filter sterilzed (0.22um) using a vacuum filter. Prior to infection, parasites were put on ice and parasites released from the flask bottom were counted (Neubauer), washed (2000rpm for 5-7 minutes) and adjusted.
Extracted molecule total RNA
Extraction protocol RNA was isolated with Trizol according to the mansufacturer's protocol and stored at -80°C.
Label Cy3
Label protocol Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.
 
Hybridization protocol cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.
Scan protocol Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).
Description Gene expression in total small intestinal tissue in age-matched control animals
Data processing Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’. gPS values were normalized by global linear scaling. For this, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be scaled (‘Array i’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula: normalized gPSArray i = gPSArray i x (1500 / 75th PercentileArray i) A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.
 
Submission date Apr 25, 2018
Last update date Jun 23, 2023
Contact name Mathias W. Hornef
E-mail(s) mhornef@ukaachen.de
Phone +491702210495
Organization name RWTH Áachen University
Department Medical Microbiology
Street address Steppenbergallee 203
City Aachen
ZIP/Postal code 52074
Country Germany
 
Platform ID GPL10333
Series (2)
GSE113666 Influence of G. lamblia infection on the transcriptional profile in intestinal and liver tissue [small intestinal tissue]
GSE113668 Influence of G. lamblia infection on the transcriptional profile in intestinal and liver tissue

Data table header descriptions
ID_REF
VALUE Normalized processed signal intensity values (non-log).

Data table
ID_REF VALUE
1 12627
2 15
3 15
4 15
5 15
6 15
7 15
8 15
9 15
10 15
11 15
12 541
13 15
14 3312
15 32
16 2585
17 5043
18 15
19 15
20 245

Total number of rows: 44397

Table truncated, full table size 418 Kbytes.




Supplementary file Size Download File type/resource
GSM3110866_M4513.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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