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Sample GSM2818538 Query DataSets for GSM2818538
Status Public on Jul 21, 2019
Title wt 3 control
Sample type RNA
Source name Colon organoids derived from wt mouse_biological replicate 3_EtOH treated
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: wild type
agent: EtOH
gender: Female
age: 2 months
Treatment protocol 1,25(OH)2D3 was added to culture media to a final concntration of 100nM. The treatment was repeated every 48 hours (coincident with culture media change).
Growth protocol Mouse colonic crypts were isolated and embebbed on Matrigel to establish a 3D stem cell enriched culture as previously decribed in Sato et al 2007
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIZOL and NucleoSpin miRNA extraction kit (Macherey-Nagel)
Label Cy3
Label protocol Amount of nucleic acid labeled: 100ng. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) kit, version 6.7, by following manufacturer instructions. Agilent manual G4140-90040 of Sep2014. Amplification: by RNA polymerases.
Hybridization protocol Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 1.65 µg. Volume: 100 uL. Temperature (ºC): 65. Duration: 17 hours. Further details in One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) kit manual, Agilent version 6.7.
Scan protocol Scanned on a G2505C DNA microarray scanner (Agilent) with Protocol GE1_1105_Oct12 and Grid 028005_D_F_20140728.
Description Colonic organoid gene expression after 62 houres of tretament
Data processing Images were analyzed by Feature Extraction Software (Agilent v11.5), which performed feature quantitation and background subtraction by spatial detrending algorithms. Subsequent processing was performed with GeneSpring 13 software (Agilent), 1) values below 1 were thresholded to 1, and on-chip probe replicates summarized by computing their geometric mean; 2) values were Logbase2 transformed; 3) a global normalization step adjusted then all the probe intensities within an array, by subtracting the 75th percentile of each array from the log transformed signal value of each entity; and 4) in order to visualize relative differences between samples, independently of the abundance level, a Per-gene Baseline Transformation was done by subtracting for each probe signal the median of its intensities among all samples.
Submission date Oct 18, 2017
Last update date Jul 22, 2019
Contact name Alba Costales
Phone 0034647906865
Organization name IIB
Department cancer genetics
Lab 231
Street address Arturo Duperier, 4
City madrid
State/province madrid
ZIP/Postal code 28029
Country Spain
Platform ID GPL13912
Series (1)
GSE105117 1,25(OH)D3 effect on colonic organoids from wt and VDR KO mice

Data table header descriptions
VALUE Normalized value generated after log2 transformation, intra-array [Percentile Shift] normalization and per-gene baseline transformation.

Data table
1 14.36174028
2 5.049823795
3 5.071144883
4 5.41648243
5 6.412987096
6 5.860841973
7 5.308266858
8 11.41453332
9 5.366876904
10 5.629529622
11 5.623718584
12 5.266065182
13 8.277802276
14 12.1333035
15 6.581664767
16 5.216774203
17 12.25283673
18 9.402696227
19 11.36404683
20 15.74135882

Total number of rows: 62976

Table truncated, full table size 1089 Kbytes.

Supplementary file Size Download File type/resource
GSM2818538_252800522081_S01_GE1_1105_Oct12_2_2.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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