|
| Status |
Public on Nov 19, 2012 |
| Title |
Non Infected BalbC macrophages at T3, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Non infected (NI) Mouse Macrophges at 3 hrs
|
| Organism |
Mus musculus |
| Characteristics |
strain: wild type BALB/c (Elevage Janvier)
tissue: Bone Marrow-derived macrophage (BMdM)
|
| Treatment protocol |
BMdM were incubated at a parasite to cell ratio of 10:1 with Ficoll purified metacyclic promastigotes of Leishmania major at 37°C in 5% CO2 during respectively T1,T3,T6,T12 and T24 hours post infection.
|
| Growth protocol |
Bone Marrow cells were grown for 7 days, with re-feeding on day 3, to induce macrophage differentiation. Generated macrophages were assessed by flow cytometry for expression of F4/80 (around 90% were positive).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
100 ng of Total RNA were proceeded according to the GeneChip whole transcript sense target labeling assay manual using the GeneChip WT cDNA Synthesis, amplification Kit and WT terminal labeling Kit. The fragmented and labeled ssDNA was hybridized to a GeneChip Mouse Gene 1.0 ST array, washed with the Fluidics station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Scanner 30007G.
|
| Description |
NI_T3_B5r
Gene expression data from non infected (NI) BalbC macrophages at T3
|
| Data processing |
The data preprocessing step included intrachip and interchip normalisation and summarisation. The intrachip normalisation step corrects for the GC content of the probes, the interchip normalisation step reduces non-biological differences between chips and the summarisation step combines the probe intensities into single gene expression values. For the intrachip normalisation the 'Model-based Analysis of Tiling-arrays' (MAT) was implemented as described by Kapur, Ket al., 2007. Genome Biol 8:R82, since this method provides the most advanced GC correction for whole-transcript prepared samples. As a last step in the preprocessing of the data we applied a summarisation of probe intensities to a probe set expression [Processed/nomalized data and additional data processing details were provided as Series supplementary files].
|
| |
|
| Submission date |
Sep 08, 2011 |
| Last update date |
Nov 20, 2012 |
| Contact name |
lamia Guizani-Tabbane |
| E-mail(s) |
[email protected]
|
| Phone |
0021698311019
|
| Organization name |
Insitut Pasteur de Tunis
|
| Department |
Immunopathology
|
| Street address |
13, Place Pasteur BP74. Tunis-Belvedere
|
| City |
Tunis |
| ZIP/Postal code |
1002 |
| Country |
Tunisia |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE31995 |
Gene Expression data from Mouse Balb/c Bone marrow derived macrophages infected by the promastigote form of Leishmania major parasite (P) or Killed parasite (Kp) during a time course of infection [Balb/c] |
| GSE31997 |
Gene Expression data from mouse bone marrow derived macrophages infected by the promastigote form of Leishmania major parasite (P) or Killed parasite (Kp) during a time course of infection |
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