Open Access Highly Accessed Methodology article

"Per cell" normalization method for mRNA measurement by quantitative PCR and microarrays

Jun Kanno1*, Ken-ichi Aisaki1, Katsuhide Igarashi1, Noriyuki Nakatsu1, Atsushi Ono1, Yukio Kodama1 and Taku Nagao2

Author Affiliations

1 Division of Cellular and Molecular Toxicology, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan

2 President, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan

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BMC Genomics 2006, 7:64  doi:10.1186/1471-2164-7-64

Published: 29 March 2006

Additional files

Additional File 1:

Excel spreadsheet file containing 15 Affymetrix Mouse 430–2 GeneChip raw data of five LBM samples in triplicate (cf. Figure 1). The column name LBM-100-0-X_Signal indicates the component percentages, i.e. 100% liver 0% brain, and X = 1,2,3 indicates the triplicates. The LBM-100-0-X_Detection column indicates P for present, A for absent and M for marginal calls by Affymetrix MAS 5.0 system.

Format: ZIP Size: 5.4MB Download file

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Additional File 2:

Excel spreadsheet file containing Percellome data of the same LBM samples, of which raw data is listed in 1 (cf. Figure 1).

Format: ZIP Size: 8.6MB Download file

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Additional File 3:

Excel spreadsheet file containing 2 Affymetrix MG-U74v2 raw data of a blank sample with the GSC (horizontal axis of Figure 2a) and blank with the five spike RNAs at a high dosage (vertical axis of Figure 2a).

Format: ZIP Size: 278KB Download file

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Additional File 4:

Excel spreadsheet file containing 2 Affymetrix MG-U74v2 raw data of a liver sample with GSC (horizontal axis of Figure 2b) and without GSC (vertical axis of Figure 2b).

Format: ZIP Size: 337KB Download file

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Additional File 5:

(first quarter of a data set consisting of 2 hr, 4 hr, 8 hr, and 24 hr data, divided because of the upload file size limitation)]: an Excel spreadsheet file containing 2 hr data (15 GeneChip data) of the total of 60 Affymetrix Mouse 430-2 GeneChip raw data of the TCDD study consisting of 20 different treatment groups in triplicate (cf. Figure 5). The column name DoseXXX-TimeYY-Z_Signal indicates the dosage and sampling time after TCDD administration in hours, e.g. XXX = 001 indicates 1 microgram/kg group, YY = 02 indicates two hours after administration, and Z = 1,2,3 indicates animal triplicate. The DoseXXX-TimeYY-Z_Detection column indicates P for present, A for absent and M for marginal calls by Affymetrix MAS 5.0 system.

Format: ZIP Size: 5.3MB Download file

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Additional File 6:

(second quarter of a data set consisting of 2 hr, 4 hr, 8 hr, and 24 hr data, divided because of the upload file size limitation)]: an Excel spreadsheet file containing 4 hr data (15 GeneChip data) of the total of 60 Affymetrix Mouse 430-2 GeneChip raw data of the TCDD study consisting of 20 different treatment groups in triplicate (cf. Figure 5). The column name DoseXXX-TimeYY-Z_Signal indicates the dosage and sampling time after TCDD administration in hours, e.g. XXX = 001 indicates 1 microgram/kg group, YY = 02 indicates two hours after administration, and Z = 1,2,3 indicates animal triplicate. The DoseXXX-TimeYY-Z_Detection column indicates P for present, A for absent and M for marginal calls by Affymetrix MAS 5.0 system.

Format: ZIP Size: 5.3MB Download file

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Additional File 7:

(third quarter of a data set consisting of 2 hr, 4 hr, 8 hr, and 24 hr data, divided because of the upload file size limitation)]: an Excel spreadsheet file containing 8 hr data (15 GeneChip data) of the total of 60 Affymetrix Mouse 430-2 GeneChip raw data of the TCDD study consisting of 20 different treatment groups in triplicate (cf. Figure 5). The column name DoseXXX-TimeYY-Z_Signal indicates the dosage and sampling time after TCDD administration in hours, e.g. XXX = 001 indicates 1 microgram/kg group, YY = 02 indicates two hours after administration, and Z = 1,2,3 indicates animal triplicate. The DoseXXX-TimeYY-Z_Detection column indicates P for present, A for absent and M for marginal calls by Affymetrix MAS 5.0 system.

Format: ZIP Size: 5.3MB Download file

Open Data

Additional File 8:

(last quarter of a data set consisting of 2 hr, 4 hr, 8 hr, and 24 hr data, divided because of the upload file size limitation)]: an Excel spreadsheet file containing 24 hr data (15 GeneChip data) of the total of 60 Affymetrix Mouse 430-2 GeneChip raw data of the TCDD study consisting of 20 different treatment groups in triplicate (cf. Figure 5). The column name DoseXXX-TimeYY-Z_Signal indicates the dosage and sampling time after TCDD administration in hours, e.g. XXX = 001 indicates 1 microgram/kg group, YY = 02 indicates two hours after administration, and Z = 1,2,3 indicates animal triplicate. The DoseXXX-TimeYY-Z_Detection column indicates P for present, A for absent and M for marginal calls by Affymetrix MAS 5.0 system.

Format: ZIP Size: 5.3MB Download file

Open Data

Additional File 9:

(first quarter of a data set consisting of 2 hr, 4 hr, 8 hr, and 24 hr data, divided because of the upload file size limitation)]: an Excel spreadsheet file containing 2 hr Percellome data (15 sample data) of the 60 samples of the TCDD study (cf. Figure 5), of which corresponding raw data is listed in 5.

Format: ZIP Size: 8.5MB Download file

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Additional File 10:

(second quarter of a data set consisting of 2 hr, 4 hr, 8 hr, and 24 hr data, divided because of the upload file size limitation)]: an Excel spreadsheet file containing 4 hr Percellome data (15 sample data) of the 60 samples of the TCDD study (cf. Figure 5), of which corresponding raw data is listed in 6.

Format: ZIP Size: 8.5MB Download file

Open Data

Additional File 11:

(third quarter of a data set consisting of 2 hr, 4 hr, 8 hr, and 24 hr data, divided because of the upload file size limitation)]: an Excel spreadsheet file containing 8 hr Percellome data (15 sample data) of the 60 samples of the TCDD study (cf. Figure 5), of which corresponding raw data is listed in 7.

Format: ZIP Size: 8.5MB Download file

Open Data

Additional File 12:

(last quarter of a data set consisting of 2 hr, 4 hr, 8 hr, and 24 hr data, divided because of the upload file size limitation)]: an Excel spreadsheet file containing 24 hr Percellome data (15 sample data) of the 60 samples of the TCDD study (cf. Figure 5), of which corresponding raw data is listed in 8.

Format: ZIP Size: 8.4MB Download file

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Additional File 13:

Excel spreadsheet file containing 15 Affymetrix MG-U74v2 A GeneChip raw data of the uterotrophic response study (cf. Figure 6). The column name X-Y_Signal indicates the treatment (V = vehicle, Low = low dose, etc) and animal triplicate (Y = 1,2,3). The X-Y_Detection column indicates P for present, A for absent and M for marginal calls by Affymetrix MAS 5.0 system.

Format: ZIP Size: 1.5MB Download file

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Additional File 14:

Excel spreadsheet file containing Percellome data of the same 15 samples of the uterotrophic response study (cf. Figure 6), of which raw data is listed in 13.

Format: ZIP Size: 2.4MB Download file

Open Data