|
| Status |
Public on Mar 22, 2013 |
| Title |
Patient3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Normal breeding ground
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: adipose tissue
cell type: preadipocytes
protocol: control
|
| Treatment protocol |
Preadipocytes were treated by secreted factors of macrophages for 10 days
|
| Growth protocol |
Preadipocytes were cultured in DMEM/F12 medium with 50nm Insulin and 100 nM Rosiglitazone
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Rneasy Mini Kit following manufacturer's instructions (Qiagen,Coutaboeuf, France)
|
| Label |
Cy3,Cy5
|
| Label protocol |
Total RNA samples were labelled using Agilent low RNA input linear amplification Kit, according to the manufacturer's protocols. 200ng of total RNA were reversed transcribed by MMLV reverse transcriptase. Amplification and labelling were done by T7-polymerase transcription. cRNA were labelled with cyanine Cy5 or Cy3-CTP dyes.
|
| |
|
| Channel 2 |
| Source name |
Inflammatory breeding ground
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: adipose tissue
cell type: preadipocytes
protocol: macrophage treatment
|
| Treatment protocol |
Preadipocytes were treated by secreted factors of macrophages for 10 days
|
| Growth protocol |
Preadipocytes were cultured in DMEM/F12 medium with 50nm Insulin and 100 nM Rosiglitazone
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Rneasy Mini Kit following manufacturer's instructions (Qiagen,Coutaboeuf, France)
|
| Label |
Cy5,Cy3
|
| Label protocol |
Total RNA samples were labelled using Agilent low RNA input linear amplification Kit, according to the manufacturer's protocols. 200ng of total RNA were reversed transcribed by MMLV reverse transcriptase. Amplification and labelling were done by T7-polymerase transcription. cRNA were labelled with cyanine Cy5 or Cy3-CTP dyes.
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized with Agilent Gene Expression Hybridization Kit and then hybridized for 17 hours at 65°C in a 4 rpm rotary oven. Slides were then washed in buffer 1 and 2, according to manufacturer’s specification.
|
| Scan protocol |
Arrays scanned using an GenePix 4000B scanner and GenePix Pro 6.0.1.00 software
|
| Description |
Analysis used preadipocytes with normal breeding ground as control samples for comparison to preadipocytes with inflammatory breeding ground.Biological replicate 3 of 5.
|
| Data processing |
Data analysis was carried out using the limma package of R software. The mean values from each channel were log2 transformed and normalized using the LOESS algorithm to remove intensity dependent effects within the calculated values. For each patient, dye-swap replicates were combined.
|
| |
|
| Submission date |
Apr 07, 2011 |
| Last update date |
Mar 22, 2013 |
| Contact name |
Danièle Lacasa |
| Organization name |
INSERM
|
| Department |
U872
|
| Lab |
Equipe 7 Nutriomique
|
| Street address |
15 rue de l'Ecole de Médecine
|
| City |
Paris |
| ZIP/Postal code |
75006 |
| Country |
France |
| |
|
| Platform ID |
GPL13379 |
| Series (1) |
| GSE28445 |
Transcriptomic profile of human preadipocyte treated by macrophages from adipose tissue |
|
