|
| Status |
Public on May 24, 2023 |
| Title |
Liver_ZT0_replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
time point: ZT0
replicate: 2
|
| Growth protocol |
13 week old C56bl/6J male mice were ad libitum feed with chow diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Nucleospin RNA kit from Macherey Nagel according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 2,3 microgrammes of ssDNA were hybridized for 16 hr at 45C on Mogen2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using GeneChip Scanner GCS3000.
|
| Data processing |
data were processed using our in-house Galaxy instance with “GIANT” (Galaxy-based interactive tools for Analysis of Transcriptomic data). It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis using apt-probeset-summarize tool (v.2.10.0). Normalization done on probeset level with NetAffx Annotation Release 36, then probeset values were grouped and averaged using gene symbols
MoGene-2_0-st.pgf and MoGene-2_0.clf
MoGene-2_0-st-v1.na36.mm10.probeset.csv
|
| |
|
| Submission date |
Feb 03, 2023 |
| Last update date |
May 24, 2023 |
| Contact name |
Alexandre Berthier |
| E-mail(s) |
[email protected]
|
| Phone |
0320974217
|
| Organization name |
Inserm
|
| Street address |
U1011, Bâtiment J&K, Bd du Pr Leclerc
|
| City |
Lille |
| ZIP/Postal code |
59000 |
| Country |
France |
| |
|
| Platform ID |
GPL18233 |
| Series (1) |
| GSE224446 |
Circadian transcriptomic analysis of mouse liver |
|
