|
| 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 |
| E-mail(s) |
albacostales@gmail.com
|
| 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 |
|
