^SAMPLE=HS-5 cells rep 1 !Sample_title = Human bone marrow stromal cells, HS-5 cells, replicate 1 !Sample_source_name_ch1 = Human bone marrow stromal cells, HS-5 cells !Sample_organism_ch1 = Homo sapiens !Sample_characteristics_ch1 = Human bone marrow stromal cells, HS-5 !Sample_growth_protocol_ch1 = HS-5 cells cultured in RPMI medium 1640 containing 10% fetal calf serum. Cells were plated in T75 flasks at 3,000,000 cells/flask. They were cultured for 3 days and harvested by trypsinization followed by pelleting of the cells. !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (30 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. !Sample_label_ch1 = Cy5 !Sample_label_protocol_ch1 = The cDNA from HS-5 RNA and Human Universal RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray. !Sample_source_name_ch2 = Universal human reference RNA !Sample_organism_ch2 = Homo sapiens !Sample_characteristics_ch2 = As a control RNA, Human Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of human genes was used. !Sample_molecule_ch2 = total RNA !Sample_extract_protocol_ch2 = The RNA (30 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. !Sample_label_ch2 = Cy3 !Sample_label_protocol_ch2 = The cDNA from HS-5 RNA and Human Universal RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray. !Sample_scan_protocol = Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. !Sample_description = Human bone marrow stromal cells, HS-5 cells !Sample_data_processing = After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the data table. !Sample_platform_id = GPL1001 #ID_REF = #VALUE = Normalized log2 ratio of means defined as CH1 divided by CH2 #CH1_Median = Channel 1 median intensity #CH1_Mean = Channel 1 mean intensity #CH1_SD = Channel 1 mean standard deviation #CH1_BKD_ Median = Channel 1 median background intensity #CH1_BKD_ Mean = Channel 1 mean background intensity #CH1_BKD_ SD = Channel 1 background standard deviation #% > CH1_BKD_+2SD = Percent of feature pixels that were greater than two standard deviations of #CH2_Median = Channel 2 median intensity #CH2_Mean = Channel 2 mean intensity #CH2_SD = Channel 2 mean standard deviation #CH2_BKD_ Median = Channel 2 median background intensity #CH2_BKD_ Mean = Channel 2 mean background intensity #CH2_BKD_ SD = Channel 2 background standard deviation #% > CH2_BKD_+2SD = Percent of feature pixels that were greater than two standard deviations of the background over the background signal #Ratio of Means = Unnormalized, untransformed ratio of means #AREA = Number of pixels used to calculate a feature's intensity #BKD_AREA = Number of pixles used to calculate a feature's background #CH1_Median - CH1_BKD_ = Channel 1 median signal #CH2_Median - CH2_BKD_ = Channel 2 median signal #CH1_Mean - CH1_BKD_ = Channel 1 mean signal #CH2_Mean - CH2_BKD_ = Channel 2 mean signal #Flags = 0 denotes satisfactory features, while <0 denotes features that did not meet !Sample_table_begin ID_REF VALUE CH1_Median CH1_Mean CH1_SD CH1_BKD_ Median CH1_BKD_ Mean CH1_BKD_ SD % > CH1_BKD_+2SD CH2_Median CH2_Mean CH2_SD CH2_BKD_ Median CH2_BKD_ Mean CH2_BKD_ SD % > CH2_BKD_+2SD Ratio of Means AREA BKD_AREA CH1_Median - CH1_BKD_ CH2_Median - CH2_BKD_ CH1_Mean - CH1_BKD_ CH2_Mean - CH2_BKD_ Flags 1 17.51 36 38 9 37 38 8 5 45 46 9 46 47 10 0 100000 80 500 -1 -1 1 0 -50 2 -0.10 42 47 19 37 39 11 12 64 65 15 45 47 10 43 0.5 32 176 5 19 10 20 -50 3 -0.42 44 48 18 36 38 8 37 75 75 17 45 46 10 71 0.4 32 176 8 30 12 30 -50 4 17.51 37 40 11 37 39 10 11 42 43 8 43 43 8 2 100000 80 498 0 -1 3 0 -50 5 0.95 147 193 125 37 39 8 98 157 194 109 43 44 9 98 1.033 52 398 110 114 156 151 0 6 0.79 57 62 21 37 39 9 55 69 71 14 44 45 8 76 0.926 52 329 20 25 25 27 -50 7 0.12 45 48 16 37 40 10 28 64 64 14 45 46 9 50 0.579 32 224 8 19 11 19 -50 8 0.68 54 54 17 36 38 9 48 63 64 13 43 44 8 57 0.857 80 510 18 20 18 21 -50 9 -0.10 51 53 16 36 38 9 44 73 77 19 43 44 9 84 0.5 52 406 15 30 17 34 -50 10 0.15 47 50 15 37 39 8 38 65 65 14 43 44 9 63 0.591 52 332 10 22 13 22 -50 11 -1.42 38 40 12 37 39 10 9 58 60 13 45 47 10 31 0.2 32 148 1 13 3 15 -50 12 -0.58 44 47 15 37 39 9 22 70 71 16 43 44 9 70 0.357 80 506 7 27 10 28 -50 13 0.08 63 63 24 36 38 9 63 85 91 21 43 44 9 94 0.563 52 382 27 42 27 48 0 14 -1.05 63 69 23 37 38 9 69 168 167 32 43 45 8 100 0.258 52 382 26 125 32 124 0 15 1.02 439 452 225 37 39 9 98 428 425 198 43 44 8 93 1.086 80 546 402 385 415 382 0 16 2.07 86 91 30 37 39 9 88 66 67 15 43 44 8 70 2.25 80 540 49 23 54 24 0 17 -0.79 40 44 14 36 39 10 11 67 69 15 43 44 9 73 0.308 52 384 4 24 8 26 -50 18 -0.57 50 51 16 37 39 10 37 79 82 22 43 44 9 83 0.359 80 570 13 36 14 39 -50 19 1.90 37 39 10 37 39 10 5 44 44 8 43 44 9 1 2 80 475 0 1 2 1 -50 20 -0.99 42 44 11 37 39 9 9 65 69 16 43 45 9 61 0.269 52 388 5 22 7 26 -50 !Sample_table_end ^SAMPLE=HS-27a cells !Sample_title = HS-27a cells. !Sample_source_name_ch1 = Human bone marrow stromal cells, HS-27a !Sample_organism_ch1 = Homo sapiens !Sample_characteristics_ch1 = Human bone marrow stromal cells, HS-27a !Sample_growth_protocol_ch1 = HS-27a cells cultured in RPMI medium 1640 containing 10% fetal calf serum. Cells were plated in T75 flasks at 3,000,000 cells/flask. They were cultured for 3 days and harvested by trypsinization followed by pelleting of the cells. !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (30 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. !Sample_label_ch1 = Cy5 !Sample_label_protocol_ch1 = The cDNA from HS-27a RNA and Human Universal RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray. !Sample_source_name_ch2 = Universal human reference RNA !Sample_organism_ch2 = Homo sapiens !Sample_characteristics_ch2 = As a control RNA, Human Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of human genes was used. !Sample_molecule_ch2 = total RNA !Sample_extract_protocol_ch2 = The RNA (30 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. !Sample_label_ch2 = Cy3 !Sample_label_protocol_ch2 = The cDNA from HS-27a RNA and Human Universal RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray. !Sample_scan_protocol = Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. !Sample_description = Human bone marrow stromal cells, HS-27a cells !Sample_data_processing = After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the data table. !Sample_platform_id = GPL1001 #ID_REF = #VALUE = Normalized log2 ratio of means defined as CH1 divided by CH2 #CH1_Median = Channel 1 median intensity #CH1_Mean = Channel 1 mean intensity #CH1_SD = Channel 1 mean standard deviation #CH1_BKD_ Median = Channel 1 median background intensity #CH1_BKD_ Mean = Channel 1 mean background intensity #CH1_BKD_ SD = Channel 1 background standard deviation #% > CH1_BKD_+2SD = Percent of feature pixels that were greater than two standard deviations of #CH2_Median = Channel 2 median intensity #CH2_Mean = Channel 2 mean intensity #CH2_SD = Channel 2 mean standard deviation #CH2_BKD_ Median = Channel 2 median background intensity #CH2_BKD_ Mean = Channel 2 mean background intensity #CH2_BKD_ SD = Channel 2 background standard deviation #% > CH2_BKD_+2SD = Percent of feature pixels that were greater than two standard deviations of the background over the background signal #Ratio of Means = Unnormalized, untransformed ratio of means #AREA = Number of pixels used to calculate a feature's intensity #BKD_AREA = Number of pixles used to calculate a feature's background #CH1_Median - CH1_BKD_ = Channel 1 median signal #CH2_Median - CH2_BKD_ = Channel 2 median signal #CH1_Mean - CH1_BKD_ = Channel 1 mean signal #CH2_Mean - CH2_BKD_ = Channel 2 mean signal #Flags = 0 denotes satisfactory features, while <0 denotes features that did not meet !Sample_table_begin ID_REF VALUE CH1_Median CH1_Mean CH1_SD CH1_BKD_ Median CH1_BKD_ Mean CH1_BKD_ SD % > CH1_BKD_+2SD CH2_Median CH2_Mean CH2_SD CH2_BKD_ Median CH2_BKD_ Mean CH2_BKD_ SD % > CH2_BKD_+2SD Ratio of Means AREA BKD_AREA CH1_Median - CH1_BKD_ CH2_Median - CH2_BKD_ CH1_Mean - CH1_BKD_ CH2_Mean - CH2_BKD_ Flags 1 17.07 36 40 11 37 40 12 5 39 38 5 38 39 6 1 100000 80 540 -1 1 3 0 -50 2 -0.25 47 51 18 37 39 10 30 60 62 15 39 39 6 71 0.609 52 408 10 21 14 23 -50 3 -0.53 46 49 16 37 40 12 15 62 62 13 38 39 5 86 0.5 52 318 9 24 12 24 -50 4 17.07 36 40 12 36 40 12 10 39 39 6 39 39 6 5 100000 80 489 0 0 4 0 -50 5 1.28 178 251 175 36 41 12 95 116 161 103 39 39 6 95 1.762 80 476 142 77 215 122 0 6 0.83 56 64 31 37 41 18 32 57 60 18 39 39 7 57 1.286 80 514 19 18 27 21 -50 7 0.86 59 63 32 38 40 12 32 55 58 14 39 39 7 57 1.316 52 382 21 16 25 19 -50 8 2.12 124 144 75 37 40 12 95 72 73 15 39 39 6 88 3.147 80 554 87 33 107 34 0 9 -0.24 59 66 26 36 40 12 48 92 87 19 38 39 6 96 0.612 52 400 23 54 30 49 -50 10 0.64 63 63 20 37 40 11 53 58 61 12 38 39 6 75 1.13 80 502 26 20 26 23 -50 11 0.39 50 57 21 38 41 12 31 57 58 11 38 39 7 62 0.95 32 171 12 19 19 20 -50 12 -0.05 57 59 21 38 42 15 25 69 69 13 39 40 6 96 0.7 52 330 19 30 21 30 -50 13 -0.30 76 77 28 37 40 13 67 106 107 20 39 40 6 100 0.588 52 390 39 67 40 68 0 14 0.11 166 170 60 36 39 12 100 210 210 38 39 39 7 100 0.784 52 380 130 171 134 171 0 15 0.92 1356 1345 447 38 42 15 100 1004 993 331 39 40 10 100 1.37 52 380 1318 965 1307 954 0 16 2.92 183 193 62 39 42 12 100 66 67 14 39 39 6 88 5.5 80 476 144 27 154 28 0 17 -0.12 54 58 17 36 39 12 36 70 71 14 38 39 6 93 0.667 80 535 18 32 22 33 -50 18 -1.08 59 62 24 36 39 11 51 109 114 36 38 39 5 100 0.342 80 466 23 71 26 76 -50 19 17.07 36 41 13 38 41 11 11 39 38 5 38 39 5 1 100000 80 485 -2 1 3 0 -50 20 0.05 50 52 20 37 41 24 5 56 58 16 38 39 7 63 0.75 52 371 13 18 15 20 -50 !Sample_table_end ^SAMPLE=HS-5 cells rep2 !Sample_title = HS-5 cells, replicate 2 !Sample_source_name_ch1 = Human bone marrow stromal cells, HS-5 !Sample_organism_ch1 = Homo sapiens !Sample_characteristics_ch1 = Human bone marrow stromal cells, HS-5 !Sample_growth_protocol_ch1 = HS-5 cells cultured in RPMI medium 1640 containing 10% fetal calf serum. Cells were plated in T75 flasks at 3,000,000 cells/flask. They were cultured for 3 days and harvested by trypsinization followed by pelleting of the cells. !Sample_molecule_ch1 = total RNA !Sample_extract_protocol_ch1 = RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (30 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. !Sample_label_ch1 = Cy5 !Sample_label_protocol_ch1 = The cDNA from HS-5 RNA and Human Universal RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray. !Sample_source_name_ch2 = Universal human reference RNA !Sample_organism_ch2 = Homo sapiens !Sample_characteristics_ch2 = As a control RNA, Human Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of human genes was used. !Sample_molecule_ch2 = total RNA !Sample_extract_protocol_ch2 = The RNA (30 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. !Sample_label_ch2 = Cy3 !Sample_label_protocol_ch2 = The cDNA from HS-5 RNA and Human Universal RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray. !Sample_scan_protocol = Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. !Sample_description = Human bone marrow stromal cells, HS-5 cells !Sample_data_processing = After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the data table. !Sample_platform_id = GPL1001 #ID_REF = #VALUE = Normalized log2 ratio of means defined as CH1 divided by CH2 #CH1_Median = Channel 1 median intensity #CH1_Mean = Channel 1 mean intensity #CH1_SD = Channel 1 mean standard deviation #CH1_BKD_ Median = Channel 1 median background intensity #CH1_BKD_ Mean = Channel 1 mean background intensity #CH1_BKD_ SD = Channel 1 background standard deviation #% > CH1_BKD_+2SD = Percent of feature pixels that were greater than two standard deviations of #CH2_Median = Channel 2 median intensity #CH2_Mean = Channel 2 mean intensity #CH2_SD = Channel 2 mean standard deviation #CH2_BKD_ Median = Channel 2 median background intensity #CH2_BKD_ Mean = Channel 2 mean background intensity #CH2_BKD_ SD = Channel 2 background standard deviation #% > CH2_BKD_+2SD = Percent of feature pixels that were greater than two standard deviations of the background over the background signal #Ratio of Means = Unnormalized, untransformed ratio of means #AREA = Number of pixels used to calculate a feature's intensity #BKD_AREA = Number of pixles used to calculate a feature's background #CH1_Median - CH1_BKD_ = Channel 1 median signal #CH2_Median - CH2_BKD_ = Channel 2 median signal #CH1_Mean - CH1_BKD_ = Channel 1 mean signal #CH2_Mean - CH2_BKD_ = Channel 2 mean signal #Flags = 0 denotes satisfactory features, while <0 denotes features that did not meet !Sample_table_begin ID_REF VALUE CH1_Median CH1_Mean CH1_SD CH1_BKD_ Median CH1_BKD_ Mean CH1_BKD_ SD % > CH1_BKD_+2SD CH2_Median CH2_Mean CH2_SD CH2_BKD_ Median CH2_BKD_ Mean CH2_BKD_ SD % > CH2_BKD_+2SD Ratio of Means AREA BKD_AREA CH1_Median - CH1_BKD_ CH2_Median - CH2_BKD_ CH1_Mean - CH1_BKD_ CH2_Mean - CH2_BKD_ Flags 1 3.74 39 44 16 37 40 13 10 42 42 8 41 42 8 2 7 80 473 2 1 7 1 -50 2 -0.14 46 46 15 37 40 13 10 57 58 14 39 40 7 53 0.474 80 549 9 18 9 19 -50 3 -0.31 47 47 18 36 40 13 16 65 66 18 40 41 7 75 0.423 80 554 11 25 11 26 -50 4 3.74 40 43 12 36 40 12 10 40 40 7 39 40 8 1 7 80 480 4 1 7 1 -50 5 0.60 74 91 55 37 41 14 60 95 108 45 40 41 8 93 0.794 80 532 37 55 54 68 0 6 0.86 60 58 19 38 42 14 33 59 60 14 39 40 8 60 0.952 80 555 22 20 20 21 -50 7 0.67 47 48 14 38 42 14 7 50 52 11 40 41 8 30 0.833 52 392 9 10 10 12 -50 8 0.71 51 56 22 38 41 13 31 62 61 14 40 41 7 66 0.857 80 516 13 22 18 21 -50 9 0.09 49 52 18 37 40 13 21 67 67 18 40 41 7 75 0.556 120 699 12 27 15 27 -50 10 -0.29 45 49 16 40 44 16 9 62 62 14 41 42 10 53 0.429 32 232 5 21 9 21 -50 11 -0.18 42 46 15 40 44 15 10 52 52 11 39 40 8 33 0.462 80 488 2 13 6 13 -50 12 -0.87 45 49 18 39 42 15 10 75 75 15 40 41 8 88 0.286 80 521 6 35 10 35 -50 13 -0.04 64 69 27 37 41 13 51 100 102 23 39 41 8 98 0.508 80 467 27 61 32 63 -50 14 -1.75 58 63 22 37 41 14 38 206 208 43 40 41 8 100 0.155 80 468 21 166 26 168 -50 15 1.32 643 731 413 38 42 15 100 543 569 218 40 41 7 100 1.31 80 537 605 503 693 529 0 16 2.58 162 168 74 37 41 13 98 80 83 22 41 42 8 93 3.119 80 458 125 39 131 42 0 17 -0.75 42 46 15 37 40 12 12 67 69 16 40 41 8 82 0.31 80 470 5 27 9 29 -50 18 -1.39 41 45 16 38 41 13 8 67 75 29 40 41 9 68 0.2 80 555 3 27 7 35 -50 19 0.00 40 42 14 37 40 12 10 39 39 7 40 40 7 2 -5 80 464 3 -1 5 -1 -50 20 -0.65 38 42 15 37 40 14 3 53 55 13 40 41 8 37 0.333 80 549 1 13 5 15 -50 !Sample_table_end