Expression in Superior Frontal Gyrus of normal individuals or females of different ages affected by Rett syndrome
From ArrayWiki
| PubMed ID: | 17309881 |
|---|---|
| Contact: | valerie matagne
|
| Species: | Homo sapiens |
| Platform: | Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A |
| Number of Samples: | 6 |
| Date Range: | 08/30/2001 - 12/17/2001 |
| Experiment Quality: | 49.47 9.43 % 70.02 |
| Link to Repository: | GSE6955 |
| Original Intensity Data: | Download |
| Clean Intensity Data: | Download |
| Original PLIER Data: | Download |
| Clean PLIER Data: | Download |
| Clean CEL Files: | Download |
| Data Rank: | 
|
Rett syndrome (RTT, OMIM #312750) is a severe X-linked neurodevelopmental disorder linked to heterozygous de novo mutations in the MECP2 gene. MECP2 encodes methyl-CpG-binding protein 2 (MeCP2), which represses gene transcription by binding to 5-methylcytosine residues in symmetrically positioned CpG dinucleotides. The disorder is almost exclusively diagnosed in females, because males affected by the disease usually die perinatally due to severe encephalopathy. Direct MeCP2 target genes underlying the neuropathogenesis of RTT remain largely unknown.
To identify genes involved in the neuropathogenesis of RTT we assessed the gene expression profile of postmortem brains affected by RTT and that of age-matched normal brains using Affymetrix arrays.
Design: samples of the Superior Frontal Gyrus from normal and RTT patients of different ages were obtained from the Krieger Research Institute and the Harvard Brain Tissue Ressource Center. Samples from RTT-affected girls (2-4, 6 and 8 year-old) were compared with aged-matched normal brain tissue (2, 5 and 10 year-old). To ensure the quality of hybridization , labeled RNA was hybridized to a Test Array containing probe sets for all Affymetrix Expression Array controls. Background, noise, average Avg Diff, and ratio of Avg Diff values for probe sets representing the 5’ and 3’ ends of actin and GAPDH transcripts were used to determine target quality. Targets that did not meet empirically determined cut-off values within the project were remade. Quality tested samples were then hybridized to the HU_U95Av2 array. Quality-tested samples were then hybridized in the HU_U95Av2 array containing 12,625 human probes.
Type: comparison between Rettsyndrome suffering and non-suffering patients
Contents |
[edit] Contributors
- Vivianne Deng
- Valerie Matagne
- Sergio R Ojeda
[edit] Protocols
[edit] References
[edit] Links
GEO Accession for this experiment: GSE6955. (Public on Feb 05 2007)
PubMed abstract: 17309881
RAW data: tar file.
[edit] Analysis
Awcaba33c43900c7a51960828a403c74fa-gelplot.png
Before Normalization |
Awcaba33c43900c7a51960828a403c74fa-cleangelplot.png
After Normalization & Cleaning |
[edit] Samples/Quality Control
| Sample | Date Scanned | Source Link | Probe Variance Data | Artifact Mask | Quality Score |
|---|---|---|---|---|---|
| Superior Frontal Gyrus_2y_normal | 12/17/01 14:44:23 | GSM160306 | 
| 
| 69.6421 0.22 % 84.71 |
| Superior Frontal Gyrus_2-4y_RTT | 12/17/01 14:18:31 | GSM160307 | 
| 
| 70.3066 0.07 % 85.12 |
| Superior Frontal Gyrus_5y_normal | 11/01/01 11:01:11 | GSM160308 | 
| 
| 68.6204 1.52 % 83.55 |
| Brain area 8/9_6y_RTT | 08/30/01 13:00:29 | GSM160309 | 
| 
| 69.4022 0.23 % 84.59 |
| Superior Frontal Gyrus_10y_normal | 12/17/01 14:54:42 | GSM160310 | 
| 
| -0.016039 63.88 % 18.0496 |
| Brain area 8/9_8yp_RTT | 12/17/01 14:28:57 | GSM160311 | 
| 
| 69.908 0.01 % 84.9256 |
