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Sample GSM3111006 Query DataSets for GSM3111006
Status Public on Jun 01, 2020
Title N-ZK152-I2 (LIVER) (12887)
Sample type RNA
 
Source name infected_7 days_total liver tissue
Organism Mus musculus
Characteristics strain: C57BL/6J wild type
age: 10 days
group: infected
time after infection: 7 days
tissue: liver
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 150 ng of total RNA were used as input. Synthesis of Cy3-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit One-Color’ (#5190-2305, 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 V6.7’.
Scan protocol Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).
Description M5704
Gene expression in total liver tissue of infected and of 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’. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5. Averaged 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.
Normalized processed signal intensity values (non-log), averaged across on-chip replicates / quantuplicate measurements. Measurements of control features were removed.
 
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 GPL24228
Series (2)
GSE113668 Influence of G. lamblia infection on the transcriptional profile in intestinal and liver tissue
GSE113679 Influence of G. lamblia infection on the transcriptional profile in intestinal and liver tissue [liver]

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
A_51_P100034 4996
A_51_P100174 696
A_51_P100208 15
A_51_P100289 1522
A_51_P100298 86
A_51_P100309 15
A_51_P100327 1460
A_51_P100347 18
A_51_P100519 15
A_51_P100537 20
A_51_P100573 394
A_51_P100624 15
A_51_P100625 13933
A_51_P100768 15
A_51_P100776 79
A_51_P100787 2907
A_51_P100828 12176
A_51_P100852 744
A_51_P100991 276
A_51_P100997 99

Total number of rows: 39429

Table truncated, full table size 674 Kbytes.




Supplementary file Size Download File type/resource
GSM3111006_M5704.txt.gz 34.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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