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Sample GSM2432289 Query DataSets for GSM2432289
Status Public on Jan 24, 2018
Title Control_21d_female_rep1
Sample type RNA
 
Source name distal colon, vehicle, 21 days, female
Organism Mus musculus
Characteristics tissue: distal colon
strain: Balb/c
treatment: vehicle
gender: female
time point: 21 days
Treatment protocol Gavage of vehicle (water)
Extracted molecule total RNA
Extraction protocol Isolation of RNA was performed using the miRNeasy Mini Kit (Qiagen, The Netherlands) including a DNase treatment, according to the manufacturer’s protocols for “Animal Cells and Animal Tissues”
Label Cy3
Label protocol Total RNA was synthesized into cRNA and labelled according to the One-Color Microarray-Based Gene Expression Analysis protocol version 6.6
 
Hybridization protocol Hybridization was performed according to the manufacturer’s protocol on SurePrint G3 mouse Gene exp 60kv2 microarrays slides
Scan protocol After hybridization, the microarray slides were scanned using an Agilent DNA Microarray Scanner with Surescan High-resolution Technology (Agilent Technologies, The Netherlands) with scanner settings to Dye Channel: G, Profile: AgilentG3_GX_1Color, Scan region: Agilent HD (61 x 21.3 mm), Scan resolution 3 µm, Tiff file dynamic range: 20 bit, Red PMT gain: 100%, Green PMT gain: 100%.
Data processing First the quality of the microarrays was checked by the quality control pipeline provided by Agilent (Feature extraction software (FES) version 10.7.3.1). All samples met the quality criteria of the FES. In order to have a thorough quality check and normalize the data, an in-house QC pipeline was developed and is publically available (github.com/BiGCAT-UM/arrayQC_Module). All samples met the in-house quality check. Raw data with expression values and genes were selected for data analysis based on flags and missing values. Height groups were defined: E171 2 days, 7 days, 14 days, 21 days for the exposed samples and control 2 days, 7 days, 14 days, 21 days for the controls. Within each group, at least four out of six or five out of seven samples had to have a pass for the spot. Also, within each group, unique identifiers passed when there were less than three missing values out of six or seven values. The unique identifiers with an average expression less than four in all of the groups were omitted. The missing values were pre-processed using the GenePattern ImputeMissingValues.KNN module v13, with standard settings. Unique identifiers were removed and identical Agilent probe identifiers were merged with Babelomics 5, using the median method for pre-processing data. Next, the data was re-annotated from Agilent probe identifiers to EntrezGene identifiers (EntrezGene IDs). The expression data for all genes with an identical EntrezGeneIDs were subsequently merged with Babelomics 5, using the median method for pre-processing data. Using an R-script, a Linear Mixed Model Analysis for Microarrays (LIMMA) (version 1.0) was performed to extract differentially expressed genes (DEG). The data of each control time point (control) was subtracted from the time-matched exposed mice to E171. The standard cut-off values of a fold-change (FC) of 1.5 and a p-value of 0.05 were used in LIMMA. The DEG for each time point were subsequently used in Consensus Pathway Database (CPDB) for an over-expression gene set analysis. All the available databases from CPDB were used (release 31, 1 sept. 2015) with a p<0.01.
 
Submission date Dec 19, 2016
Last update date Jan 24, 2018
Contact name Héloïse Proquin
Organization name Maastricht University
Street address Universiteitssingel 50
City Maastricht
ZIP/Postal code 6229 ER
Country Netherlands
 
Platform ID GPL21163
Series (1)
GSE92563 Transcriptomics effects of ingestion of food additive titanium dioxide (E171) in the colon of BALB/c mice

Data table header descriptions
ID_REF
VALUE normalized signal intensity

Data table
ID_REF VALUE
A_30_P01017428 9.256663767
A_30_P01017437 10.53510743
A_30_P01017440 7.589808941
A_30_P01017445 7.542634516
A_30_P01017447 8.654445027
A_30_P01017454 7.909861851
A_30_P01017455 5.647562745
A_30_P01017468 6.039512817
A_30_P01017473 5.7863985
A_30_P01017482 12.1743581
A_30_P01017490 8.772506572
A_30_P01017495 8.235015226
A_30_P01017505 7.763746072
A_30_P01017524 6.126982123
A_30_P01017525 8.593872763
A_30_P01017535 7.798676433
A_30_P01017541 8.0398998
A_30_P01017550 9.760258015
A_30_P01017560 4.690752277
A_30_P01017564 11.17399545

Total number of rows: 42568

Table truncated, full table size 1057 Kbytes.




Supplementary file Size Download File type/resource
GSM2432289_US10063773_257480910495_S01_GE1_107_Sep09_2_1.txt.gz 12.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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