Shaw Lab |
Baylor College of Medicine
All expression data was obtained from Affymetrix MOE 430 2.0 chips. Normalization and expression modeling were performed in the R statistical computing environment, with extensive use of the Bioconductor suite of R packages. In particular, probe level summaries were computed using the GC-RMA method (Wu et. al (2003)). The GC-RMA normalized data for each treatment and for the entire study are available for download through this site.
This link leads to a table showing the schemes used to purify each cell type. All cells were primary cells freshly isolated using a combination of magnetic and flow cytometric sorting with the indicated markers. Initial populations were derived from the tissue indicated in the third column (1)- activated T cells were obtained by stimulation with conconavalin A for 8-11 hours in vitro. Because of the difficulty in obtaining RNA from terminally differentitated erythroid cells, the erythrocyte population is the only one that contains substantial numbers of cell-type specific progenitors. The correlation coefficient (R2) that indicates the similarity between the two arrays for each population is indicated in the leftmost column.
| Purification Schemes | HTML | Excel |
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Shown below is a table of the correlation coefficients between each microarray chip. An R2 of 0.96 or greater was seen between replicates.
| Correlation Coefficients | HTML | Excel |
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The link below contains an Excel worksheet of the normalized data set.
| Normalized Data (Excel) | gzip (3 MB) | bz2 (2 MB) |
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Each link below leads to the raw CEL file for the chip indicated.
Note: .gz files are about 6.2MB and .bz2 files are about 4.6MB.
| HSC 1 | gzip | bz2 |
|---|---|
| HSC 2 | gzip | bz2 |
| NK 1 | gzip | bz2 |
| NK 2 | gzip | bz2 |
| T-CD4-A 1 | gzip | bz2 |
| T-CD4-A 2 | gzip | bz2 |
| T-CD8-A 1 | gzip | bz2 |
| T-CD8-A 2 | gzip | bz2 |
| T-CD4-N 1 | gzip | bz2 |
| T-CD4-N 2 | gzip | bz2 |
| T-CD8-N 1 | gzip | bz2 |
| T-CD8-N 2 | gzip | bz2 |
| B-Cell 1 | gzip | bz2 |
| B-Cell 2 | gzip | bz2 |
| Monocyte 1 | gzip | bz2 |
| Monocyte 2 | gzip | bz2 |
| Granulocyte 1 | gzip | bz2 |
| Granulocyte 2 | gzip | bz2 |
| N-Er 1 | gzip | bz2 |
| N-Er 2 | gzip | bz2 |
| All CEL Files | gzip (124MB) | bz2 (92MB) |
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