Source Name Comment [Sample_source_name] Comment [Sample_title] Characteristics [cell line] Term Source REF Term Accession Number Characteristics [organism] Term Source REF Term Accession Number Characteristics [sex] Term Source REF Term Accession Number Protocol REF Term Source REF Protocol REF Term Source REF Extract Name Material Type Protocol REF Term Source REF Labeled Extract Name Label Protocol REF Term Source REF Assay Name Array Design REF Term Source REF Technology Type Protocol REF Term Source REF Array Data File Comment [ArrayExpress FTP file] Protocol REF Term Source REF Normalization Name Derived Array Data File Comment [Derived ArrayExpress FTP file] FactorValue [cell line] Term Source REF Term Accession Number GSM1417146 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression SUM225 SUM225 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417146 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417146 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417146 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417146_SUM225.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417146_sample_table.txt norm GSM1417146_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip SUM225 GSM1417145 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression SUM190PT SUM190PT EFO EFO_0001243 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417145 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417145 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417145 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417145_SUM190PT.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417145_sample_table.txt norm GSM1417145_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip SUM190PT EFO EFO_0001243 GSM1417144 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression SKBR3 SKBR3 EFO EFO_0001236 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417144 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417144 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417144 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417144_SKBR3.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417144_sample_table.txt norm GSM1417144_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip SKBR3 EFO EFO_0001236 GSM1417143 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression MDA-MB-453 MDA-MB-453 EFO EFO_0001215 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417143 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417143 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417143 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417143_MDAMB453.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417143_sample_table.txt norm GSM1417143_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip MDA-MB-453 EFO EFO_0001215 GSM1417142 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression KPL4 KPL4 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417142 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417142 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417142 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417142_KPL4.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417142_sample_table.txt norm GSM1417142_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip KPL4 GSM1417141 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression JIMT1 JIMT1 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417141 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417141 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417141 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417141_JIMT1.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417141_sample_table.txt norm GSM1417141_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip JIMT1 GSM1417140 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression HCC202 HCC202 EFO EFO_0001176 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417140 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417140 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417140 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417140_HCC202.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417140_sample_table.txt norm GSM1417140_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip HCC202 EFO EFO_0001176 GSM1417139 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression HCC1954 HCC1954 EFO EFO_0001175 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417139 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417139 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417139 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417139_HCC1954.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417139_sample_table.txt norm GSM1417139_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip HCC1954 EFO EFO_0001175 GSM1417138 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression HCC1569 HCC1569 EFO EFO_0001173 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417138 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417138 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417138 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417138_HCC1569.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417138_sample_table.txt norm GSM1417138_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip HCC1569 EFO EFO_0001173 GSM1417137 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression HCC1419 HCC1419 EFO EFO_0005372 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417137 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417137 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417137 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417137_HCC1419.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417137_sample_table.txt norm GSM1417137_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip HCC1419 EFO EFO_0005372 GSM1417136 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression EFM-192A EFM-192A Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417136 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417136 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417136 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417136_EFM192A.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417136_sample_table.txt norm GSM1417136_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip EFM-192A GSM1417135 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression BT474 BT474 EFO EFO_0001093 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417135 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417135 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417135 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417135_BT474.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417135_sample_table.txt norm GSM1417135_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip BT474 EFO EFO_0001093 GSM1417134 1 HER2 positive breast cancer cell line, untreated Breast cancer cell line untreated gene expression AU565 AU565 EFO EFO_0001087 Homo sapiens EFO http://purl.obolibrary.org/obo/NCBITaxon_9606 female EFO EFO_0001265 P-GSE58700-2 ArrayExpress P-GSE58700-3 ArrayExpress GSM1417134 extract 1 total RNA P-GSE58700-4 ArrayExpress GSM1417134 LE 1 biotin P-GSE58700-5 ArrayExpress GSM1417134 A-GEOD-18850 ArrayExpress array assay P-GSE58700-6 ArrayExpress GSM1417134_AU565.CEL ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.raw.1.zip P-GSE58700-1 ArrayExpress GSM1417134_sample_table.txt norm GSM1417134_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-58700/E-GEOD-58700.processed.1.zip AU565 EFO EFO_0001087