The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia

Additional file 1:

Size distribution of amplified RNA from CA1 and CA3 areas. A, Shown are electropherograms generated with the Agilent Bioanalyzer from 2^nd round amplified RNA from CA1 or CA3 of 4 animals (2 sham, 2 ischemia-treated). B, Marker lane with corresponding sizes (nt, nucleotides), and corresponding curve. C, Shown are the corresponding graphs. There is no difference in size distribution between CA1 and CA3, nor between sham- and ischemia-treated animals. The bulk of the amplified RNA ranges between 200 to 2000 nt.

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Additional file 2:

List of all significantly regulated genes in CA3 vs CA1 (native state). HTML file containing all significantly regulated genes in CA3 vs CA1 in the native state, with Agilent probe numbers, accession numbers, gene names, enrichment factors ("M (CA3/CA1")), and false-discovery-rate corrected p-values. M indicates direction and extent of enrichment: Numbers >1 indicate preferential expression in CA3, numbers <1 in CA1.

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Additional file 3:

Genes with differential expression in CA3 and CA1 under native conditions: Verification by detection in brain mapping projects. Shown are genes which had significantly differing distribution to CA3 and CA1. Selected genes with matches in brain mapping projects (BGEM or Allen Brain Atlas) are given with the gene symbol, gene name, Refseq accession number, Agilent probe number, preference of enrichment, and enrichment factor, and location in or link to microgrpahs of in situ hybridizations. All genes that were found are confirmed by the in-situ hybridizations. There is also general good correlation of the enrichment factors and visual impressions of the staining intensities in CA3 or CA1.

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Additional file 4:

List of all significantly regulated genes in CA3 ischemic vs. sham. HTML file containing all genes significantly regulated in CA3 between the ischemic and the sham group. Given are Agilent probe numbers, accession numbers, gene names, enrichment factors ("M (ICA3/SCA3")), and false-discovery-rate corrected p-values.

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Additional file 5:

List of all significantly regulated genes in CA1 ischemic vs. sham. HTML file containing all genes significantly regulated in CA1 between the ischemic and the sham group. Given are Agilent probe numbers, accession numbers, gene names, enrichment factors ("M (ICA1/SCA1")), and false-discovery-rate corrected p-values.

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Additional file 6:

List of all significantly regulated genes in CA3 vs CA1 (ischemic state). HTML file containing all significantly regulated genes in CA3 vs CA1 in the ischemic state. Given are Agilent probe numbers, accession numbers, gene names, enrichment factors ("M (CA3/CA1")), and false-discovery-rate corrected p-values.

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Additional file 7:

Comparison of regulation factors derived from array analysis and quantitative PCR. Shown are 8 genes that show differential expression between CA3 and CA1 in the native or ischemic state with the regulation factor derived from array analysis, and quantitative PCR: There is a good correlation between both assessments. The Pearson correlation coefficient from these 8 comparisons is 0.75.

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Additional file 8:

Immunohistochemical detection of Synatotagmin-like 4 in the hippocampus. A, Distribution of Sytl4 gene product in the hippocampus of a sham-operated rat (overview), B, and in an animal from the ischemic group. C,D magnification of the CA3 field of a sham (C), and ischemic (D) animal (original magnification 40×). Sytl4 localizes preferentially to the CA3 field (stratum lucidum) under both conditions.

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Additional file 9:

Distribution of standard deviations in the ischemic and sham groups. Plotted are the cumulative number of genes in each group versus the standard deviation. Both distributions are highly similar, although the ischemic group is slightly right-shifted.

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Additional file 10:

Genes that show a significantly different CA3/CA1 distribution under normoxic and ischemic conditions. Shown are 15 genes which had significantly differing distribution to CA3 and CA1 in the normoxic versus the ischemic state. Given are the accession number, gene name, the relative CA3/CA1 ratio shift from normoxic to ischemic conditions (negative values indicate the reverse CA1/CA3 ratio), the raw P values and the FDR-corrected P-values for the siginificance of different behaviour under the two conditions), and the CA3/CA1 ratios under normoxic and ischemic conditions with the respective FDR-corrected P-values. Changes in most genes are caused by an attenuation of differential expression by ischemia. The only gene which shows a true reversal of distribution preference is Inhibin beta A (from CA1 in sham to CA3 in ischemia).

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