|
| Status |
Public on Mar 27, 2016 |
| Title |
hyb13810 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Liver_male_2month_E109_LKO
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed strain
genotype/variation: conditional liver NIPP1 KO
gender: male
age: 2 months
tissue: liver
treatment: untreated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gen Elute Mammalian total RNA kit (Sigma)
|
| Label |
Cy5
|
| Label protocol |
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) or Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).
|
| |
|
| Channel 2 |
| Source name |
Liver_male_2month_E113_CTR
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed strain
genotype/variation: control
gender: male
age: 2 months
tissue: liver
treatment: untreated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gen Elute Mammalian total RNA kit (Sigma)
|
| Label |
Cy3
|
| Label protocol |
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) or Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).
|
| |
|
| |
| Hybridization protocol |
A mixture of purified and labeled cRNA (Cy3 label: 825ng; Cy5 label: 825ng) was hybridised on Agilent's Whole Mouse Genome (4x44K v2) arrays followed by (manual) washing, according to the manufacturer’s procedures.
|
| Scan protocol |
To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.7.3.1).
|
| Description |
---
|
| Data processing |
Prior to normalization, data from control spots was removed. We used the processed signals obtained with the Agilent Feature extraction software (version 10.7.3.1). The presented values are log2-(Cy5/Cy3)-ratios.
|
| |
|
| Submission date |
Mar 27, 2015 |
| Last update date |
Mar 27, 2016 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL10333 |
| Series (1) |
| GSE67366 |
Conditional liver NIPP1 KO micro array on total liver RNA |
|
