|
| Status |
Public on Feb 22, 2016 |
| Title |
In-vivo iHep, rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
In-vivo iHep
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: mT/mG (Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)
cell type: in-vivo myofibroblasts-derived induced hepatocytes
reprogrammed: yes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the cells.
|
| Label |
Alexa Fluor 555
|
| Label protocol |
100 ng of total DNA-free RNA was used as input to prepare the aminoallyl-UTP-modified (aaUTP) cRNAs (Amino Allyl MessageAmp II Kit, #AM1753, Life Technologies) as directed by the company. The aaUTP-cRNAs were labelled with Alexa Fluor 555 Reactive Dye (#A32756, LifeTechnologies). Prior to the reverse transcription reaction, 1μl of a 1:5000 dilution of Agilent's One-Color spike-in Kit stock solution (#5188-5282, Agilent Technologies) was added to 100ng of total RNA of each analyzed sample.
|
| |
|
| Hybridization protocol |
The cRNA fragmentation, hybridization, and washing steps were carried out according to Agilent's One-Color Microarray-Based Gene Expression Analysis Protocol V5.7 except that 500ng of each labelled cRNA sample were used for hybridization.
|
| Scan protocol |
Slides were scanned on the Agilent Micro Array Scanner G2565 CA (pixel resolution 5 micrometers, bit depth 20). Data extraction was performed with the Feature Extraction Software V10.7.3.1.
|
| Description |
Replicate 2
|
| Data processing |
Variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.
|
| |
|
| Submission date |
Jan 13, 2016 |
| Last update date |
Jan 15, 2022 |
| Contact name |
Marcos J. Araúzo-Bravo |
| E-mail(s) |
mararabra@yahoo.co.uk
|
| Phone |
+34 943 00 6108
|
| Organization name |
Max Planck Institute for Molecular Biomedicine
|
| Department |
Cell and Developmental Biology
|
| Lab |
Computational Biology and Bionformatics
|
| Street address |
Rogentstrasse
|
| City |
Muenster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE76843 |
Direct reprogramming of hepatic myofibroblasts into hepatocytes in vivo attenuates liver fibrosis |
|
