title: IGTB1622.14


title: IGTB1592.14

status: Public on May 02 2014

type: RNA

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

country: USA

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: healthy individual_monocytes from PBMCs

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: age (yrs)

tag: Sex

value: Female

tag: cell type

value: monocytes from peripheral blood mononuclear cells (PBMCs)

tag: batch

tag: inclusion markers

tag: exclusion markers

tag: phenotype markers

tag: separation method

value: Aria Sorter


title: IGTB1617.14


title: IGTB1639.F14

value: Male


title: IGTB1601.F14


title: IGTB1572.F14


title: IGTB1568.14TR2


title: IGTB1573.14


title: IGTB1559.F14


title: IGTB1557.14


title: IGTB1600.14


title: IGTB1567.14


title: IGTB1575.F14


title: IGTB1570.14


title: IGTB1616.14


title: IGTB1597.14


title: IGTB1565.14


title: IGTB1605.14


title: IGTB1568.14TR1


title: IGTB1556.F14


title: IGTB1550.F14


title: IGTB1542.14


title: IGTB1538.F14


title: IGTB1506.14


title: IGTB1548.14


title: IGTB1514.14


title: IGTB1523.14


title: IGTB1519.F14


title: IGTB1515.14


title: IGTB1511.14


title: IGTB1521.F14


title: IGTB1547.14


title: IGTB1509.14


title: IGTB1499.14


title: IGTB1474.14


title: IGTB1476.14


title: IGTB1491.14


title: IGTB1475.14


title: IGTB1467.14


title: IGTB1479.14


title: IGTB1477.14


title: IGTB1453.14


title: IGTB1458.14


title: IGTB1459.14


title: IGTB1465.14


title: IGTB1488.14


title: IGTB1450.F14


title: IGTB1449.14


title: IGTB1498.14


title: IGTB1472.14


title: IGTB1451.F14


title: IGTB1452.F14


title: IGTB1469.14


title: IGTB1447.14


title: IGTB1442.14


title: IGTB1448.14


title: IGTB1438.14


title: IGTB1440.14


title: IGTB1434.14


title: IGTB1430.14


title: IGTB1417.14


title: IGTB1433.14


title: IGTB1419.14


title: IGTB1435.14


title: IGTB1439.F14


title: IGTB1405.14


title: IGTB1412.F14


title: IGTB1400.14


title: IGTB1403.F14


title: IGTB1406.F14


title: IGTB1446.F14


title: IGTB1424.14


title: IGTB1385.14


title: IGTB1397.F14


title: IGTB1384.14TR2


title: IGTB1396.F14


title: IGTB1416.14


title: IGTB1399.14


title: IGTB1384.14TR1


title: IGTB1370.F14


title: IGTB1375.14


title: IGTB1369.14


title: IGTB1361.14


title: IGTB1380.F14


title: IGTB1374.14


title: IGTB1363.F14


title: IGTB1360.14


title: IGTB1378.14


title: IGTB1360.F14


title: IGTB1343.14


title: IGTB1372.14


title: IGTB1348.F14


title: IGTB1339.14


title: IGTB1336.14


title: IGTB1349.14


title: IGTB1350.F14


title: IGTB1345.14


title: IGTB1357.14


title: IGTB1320.14


title: IGTB1344.14


title: IGTB1314.14


title: IGTB1331.F14TR1


title: IGTB1310.14


title: IGTB1353.14


title: IGTB1327.14


title: IGTB1308.14TR1


title: IGTB1305.14


title: IGTB1335.14


title: IGTB1340.14


title: IGTB1342.14


title: IGTB1331.F14TR2


title: IGTB1300.F14


title: IGTB1356.14


title: IGTB1313.14


title: IGTB1323.14


title: IGTB1299.14


title: IGTB1308.14TR2


title: IGTB1295.14


title: IGTB1292.14


title: IGTB1276.14


title: IGTB1290.14


title: IGTB1278.14


title: IGTB1302.F14


title: IGTB1270.F14


title: IGTB1274.F14


title: IGTB1263.14


title: IGTB1265.F14


title: IGTB1272.14


title: IGTB1268.14


title: IGTB1248.14


title: IGTB1252.F14


title: IGTB1250.14


title: IGTB1259.14


title: IGTB1232.F14


title: IGTB1231.14


title: IGTB1215.14


title: IGTB1200.14


title: IGTB1211.14


title: IGTB1205.F14


title: IGTB1242.14


title: IGTB1217.F14


title: IGTB1237.14


title: IGTB1219.14


title: IGTB1197.14


title: IGTB1196.F14


title: IGTB1195.14


title: IGTB1220.14


title: IGTB1228.14


title: IGTB1202.14


title: IGTB1246.14


title: IGTB1187.14


title: IGTB1189.14


title: IGTB1172.14


title: IGTB1179.14


title: IGTB1199.14


title: IGTB1168.14


title: IGTB1166.14


title: IGTB1156.F14


title: IGTB1159.F14


title: IGTB1154.14


title: IGTB1155.14


title: IGTB1144.14


title: IGTB1142.F14


title: IGTB1140.14


title: IGTB1137.14


title: IGTB1145.14


title: IGTB1151.14


title: IGTB1170.14


title: IGTB1135.14


title: IGTB1148.14


title: IGTB1135.F14


title: IGTB1134.14


title: IGTB1130.14


title: IGTB1133.14


title: IGTB1131.14


title: IGTB1128.14


title: IGTB1123.14


title: IGTB1108.14


title: IGTB1097.14


title: IGTB1114.14


title: IGTB1107.14


title: IGTB1105.F14


title: IGTB1111.14


title: IGTB1088.14


title: IGTB1070.14


title: IGTB1067.14


title: IGTB1066.14


title: IGTB1075.14


title: IGTB1078.14


title: IGTB1086.14


title: IGTB1060.14


title: IGTB1059.14


title: IGTB1052.F14TR1


title: IGTB1051.F14


title: IGTB1057.14


title: IGTB1037.14BR1


title: IGTB1034.14


title: IGTB1052.F14TR2


title: IGTB1042.14


title: IGTB1046.14


title: IGTB1037.14


title: IGTB1030.14


title: IGTB1038.14


title: IGTB1040.14


title: IGTB1029.14


title: IGTB1056.14


title: IGTB1026.F14


title: IGTB1020.14


title: IGTB1016.14


title: IGTB1021.14


title: IGTB1007.14


title: IGTB1018.14


title: IGTB1004.14


title: IGTB998.14


title: IGTB1032.14


title: IGTB998.14BR1


title: IGTB993.14


title: IGTB997.14


title: IGTB987.14


title: IGTB1009.F14


title: IGTB982.14


title: IGTB992.14


title: IGTB1021.F14


title: IGTB981.14


title: IGTB948.14


title: IGTB945.14


title: IGTB940.14


title: IGTB935.14


title: IGTB930.14


title: IGTB910.F14


title: IGTB950.14


title: IGTB944.14


title: IGTB969.14


title: IGTB916.14


title: IGTB899.14


title: IGTB885.14


title: IGTB874.14


title: IGTB880.14


title: IGTB863.14


title: IGTB844.14


title: IGTB876.14


title: IGTB839.14TR2


title: IGTB906.14


title: IGTB1245.14


title: IGTB842.14


title: IGTB943.14


title: IGTB825.14


title: IGTB836.14


title: IGTB814.14


title: IGTB811.14


title: IGTB816.14


title: IGTB809.14


title: IGTB822.14


title: IGTB806.14


title: IGTB802.F14


title: IGTB788.14


title: IGTB777.14


title: IGTB797.14


title: IGTB794.14


title: IGTB784.14


title: IGTB775.14


title: IGTB773.14


title: IGTB793.14


title: IGTB752.14


title: IGTB763.14


title: IGTB772.14


title: IGTB760.14


title: IGTB750.14BR1


title: IGTB751.14


title: IGTB744.F14


title: IGTB751.F14


title: IGTB783.F14


title: IGTB750.14


title: IGTB736.14


title: IGTB723.14


title: IGTB734.F14


title: IGTB707.14


title: IGTB839.14TR1


title: IGTB700.F14


title: IGTB713.14


title: IGTB668.14


title: IGTB665.14


title: IGTB670.F14


title: IGTB655.14


title: IGTB698.14


title: IGTB684.14


title: IGTB697.F14


title: IGTB641.14


title: IGTB627.14


title: IGTB725.14


title: IGTB684.14BR1


title: IGTB717.14


title: IGTB624.14


title: IGTB616.14


title: IGTB605.14


title: IGTB603.14


title: IGTB582.14


title: IGTB612.F14


title: IGTB565.14


title: IGTB568.14


title: IGTB575.14


title: IGTB578.F14


title: IGTB581.14


title: IGTB559.14


title: IGTB578.14


title: IGTB536.14


title: IGTB604.14


title: IGTB520.14


title: IGTB510.14


title: IGTB546.14


title: IGTB547.14


title: IGTB498.14


title: IGTB523.14


title: IGTB508.14


title: IGTB490.14


title: IGTB493.14TR1


title: IGTB493.14TR2


title: IGTB502.14


title: IGTB472.14


title: IGTB469.14


title: IGTB441.14


title: IGTB412.14


title: IGTB422.14


title: IGTB468.14


title: IGTB611.14


title: IGTB425.14


title: IGTB453.F14


title: IGTB448.F14


title: IGTB430.14


title: IGTB371.14


title: IGTB533.14


title: IGTB406.14


title: IGTB358.14


title: IGTB351.14


title: IGTB329.14


title: IGTB369.14


title: IGTB312.F14TR2


title: IGTB372.14


title: IGTB398.14


title: IGTB373.F14


title: IGTB310.14


title: IGTB332.F14


title: IGTB369.14BR1


title: IGTB282.14


title: IGTB277.F14


title: IGTB283.14


title: IGTB274.14


title: IGTB337.14


title: IGTB330.14


title: IGTB266.F14


title: IGTB576.F14


title: IGTB312.F14TR1


title: IGTB256.F14


title: IGTB247.14


title: IGTB501.14


title: IGTB239.14


title: IGTB285.14


title: IGTB240.14


title: IGTB258.14


title: IGTB235.14


title: IGTB234.14


title: IGTB227.F14


title: IGTB230.14


title: IGTB218.F14


title: IGTB263.14


title: IGTB227.14


title: IGTB214.14


title: IGTB170.14


title: IGTB190.14


title: IGTB176.14


title: IGTB178.14


title: IGTB148.F14


title: IGTB155.14


title: IGTB136.F14


title: IGTB174.14


title: IGTB143.14


title: IGTB141.14TR1


title: IGTB133.14


title: IGTB197.14


title: IGTB126.F14


title: IGTB141.14TR2


title: IGTB125.F14


title: IGTB125.14BR1


title: IGTB187.F14


title: IGTB107.F14


title: IGTB104.14


title: IGTB107.14


title: IGTB108.14


title: IGTB125.14


title: IGTB72.14


title: IGTB119.14


title: IGTB182.F14


title: IGTB97.14


title: IGTB67.14


title: IGTB92.14


title: IGTB64.F14


title: IGTB32.14


title: IGTB40.14


title: IGTB28.14


title: IGTB10.14BR1


title: IGTB30.14


title: IGTB100.14


title: IGTB18.14


title: IGTB8.14


title: IGTB4.14


title: IGTB19.14


title: IGTB998.4BR1 [CD4]

source_name: healthy individual_CD4 T-Cells from PBMCs

tag: gender

value: female

value: T4 Naive cells from human peripheral blood mononuclear cells (PBMCs)

value: CD3+ CD4+ CD62L+


title: IGTB4.F14TR1


title: IGTB998.4 [CD4]


title: IGTB3.14


title: IGTB4.F14TR2


title: IGTB993.4 [CD4]


title: IGTB992.4 [CD4]


title: IGTB982.4 [CD4]


title: IGTB981.4 [CD4]

value: male


title: IGTB969.4 [CD4]


title: IGTB948.4 [CD4]


title: IGTB987.4 [CD4]


title: IGTB997.4 [CD4]


title: IGTB10.14


title: IGTB945.4 [CD4]


title: IGTB92.4 [CD4]


title: IGTB940.4 [CD4]


title: IGTB930.4 [CD4]


title: IGTB935.4 [CD4]


title: IGTB910.F4 [CD4]


title: IGTB944.4 [CD4]


title: IGTB917.4 [CD4]


title: IGTB916.4 [CD4]


title: IGTB906.4 [CD4]


title: IGTB885.4 [CD4]


title: IGTB880.4 [CD4]


title: IGTB822.4 [CD4]


title: IGTB888.4 [CD4]


title: IGTB811.4 [CD4]


title: IGTB816.4 [CD4]


title: IGTB943.4 [CD4]


title: IGTB809.4 [CD4]


title: IGTB8.4 [CD4]


title: IGTB806.4 [CD4]


title: IGTB794.4 [CD4]


title: IGTB802.F4 [CD4]


title: IGTB793.4 [CD4]


title: IGTB842.4 [CD4]


title: IGTB792.4 [CD4]


title: IGTB804.4 [CD4]


title: IGTB797.4 [CD4]


title: IGTB844.4 [CD4]


title: IGTB876.4 [CD4]


title: IGTB777.4 [CD4]


title: IGTB866.4 [CD4]


title: IGTB784.4 [CD4]


title: IGTB783.F4 [CD4]


title: IGTB773.4 [CD4]


title: IGTB763.4 [CD4]


title: IGTB751.F4 [CD4]


title: IGTB751.4 [CD4]


title: IGTB313.14


title: IGTB760.4 [CD4]


title: IGTB772.4 [CD4]


title: IGTB750.4BR1 [CD4]


title: IGTB747.4 [CD4]


title: IGTB750.4 [CD4]


title: IGTB736.4 [CD4]


title: IGTB775.4 [CD4]


title: IGTB734.F4 [CD4]


title: IGTB744.F4 [CD4]


title: IGTB725.4 [CD4]


title: IGTB717.4 [CD4]


title: IGTB695.4 [CD4]


title: IGTB697.F4 [CD4]


title: IGTB706.4 [CD4]


title: IGTB72.4 [CD4]


title: IGTB723.4 [CD4]


title: IGTB670.F4 [CD4]


title: IGTB698.4 [CD4]


title: IGTB678.4 [CD4]


title: IGTB679.F4 [CD4]


title: IGTB665.4 [CD4]


title: IGTB659.4 [CD4]


title: IGTB668.4 [CD4]


title: IGTB700.F4 [CD4]


title: IGTB67.4 [CD4]


title: IGTB627.4 [CD4]


title: IGTB684.4 [CD4]


title: IGTB624.4 [CD4]


title: IGTB641.4 [CD4]


title: IGTB604.4 [CD4]


title: IGTB616.4 [CD4]


title: IGTB578.F4 [CD4]


title: IGTB603.4 [CD4]


title: IGTB578.4 [CD4]


title: IGTB575.4 [CD4]


title: IGTB64.F4 [CD4]


title: IGTB565.4 [CD4]


title: IGTB568.4 [CD4]


title: IGTB570.4 [CD4]


title: IGTB523.4 [CD4]


title: IGTB536.4 [CD4]


title: IGTB533.4 [CD4]


title: IGTB502.4 [CD4]


title: IGTB612.F4 [CD4]


title: IGTB517.4 [CD4]


title: IGTB510.4 [CD4]


title: IGTB559.4 [CD4]


title: IGTB520.4 [CD4]


title: IGTB502.F4 [CD4]


title: IGTB547.4 [CD4]


title: IGTB453.F4 [CD4]


title: IGTB469.4 [CD4]


title: IGTB501.4 [CD4]


title: IGTB468.4 [CD4]


title: IGTB472.4 [CD4]


title: IGTB546.4 [CD4]


title: IGTB508.4 [CD4]


title: IGTB448.F4 [CD4]


title: IGTB493.4TR2 [CD4]


title: IGTB448.4 [CD4]


title: IGTB498.4 [CD4]


title: IGTB447.4 [CD4]


title: IGTB490.4 [CD4]


title: IGTB430.4 [CD4]


title: IGTB412.4 [CD4]


title: IGTB581.4 [CD4]


title: IGTB4.F42 [CD4]


title: IGTB40.4 [CD4]


title: IGTB374.4 [CD4]


title: IGTB4.4 [CD4]


title: IGTB358.4 [CD4]


title: IGTB371.4 [CD4]


title: IGTB442.4 [CD4]


title: IGTB351.4 [CD4]


title: IGTB369.4BR1 [CD4]


title: IGTB373.F4 [CD4]


title: IGTB430.4BR1 [CD4]


title: IGTB369.4 [CD4]


title: IGTB4.F41 [CD4]


title: IGTB332.F4 [CD4]


title: IGTB312.F4TR2 [CD4]


title: IGTB35.4 [CD4]


title: IGTB329.4 [CD4]


title: IGTB32.4 [CD4]


title: IGTB337.4 [CD4]


title: IGTB313.4 [CD4]


title: IGTB312.F4TR1 [CD4]


title: IGTB30.4 [CD4]


title: IGTB274.4 [CD4]


title: IGTB493.4TR1 [CD4]


title: IGTB310.4 [CD4]


title: IGTB272.4 [CD4]


title: IGTB283.4 [CD4]


title: IGTB266.F4 [CD4]


title: IGTB256.F4 [CD4]


title: IGTB277.F4 [CD4]


title: IGTB258.4 [CD4]


title: IGTB263.4 [CD4]


title: IGTB240.4 [CD4]


title: IGTB227.4 [CD4]


title: IGTB235.4 [CD4]


title: IGTB19.4 [CD4]


title: IGTB230.4TR1 [CD4]


title: IGTB197.4 [CD4]


title: IGTB187.F4 [CD4]


title: IGTB18.4 [CD4]


title: IGTB214.4 [CD4]


title: IGTB752.4 [CD4]


title: IGTB227.F4BR1 [CD4]


title: IGTB174.4 [CD4]


title: IGTB1686.4 [CD4]


title: IGTB1684.4 [CD4]


title: IGTB176.4 [CD4]


title: IGTB239.4 [CD4]


title: IGTB1688.4 [CD4]


title: IGTB247.4 [CD4]


title: IGTB1683.4 [CD4]


title: IGTB230.4TR2 [CD4]


title: IGTB1674.4 [CD4]


title: IGTB1679.4 [CD4]


title: IGTB1671.F4 [CD4]


title: IGTB1667.F4 [CD4]


title: IGTB1669.4 [CD4]


title: IGTB182.F4 [CD4]


title: IGTB1667.4 [CD4]


title: IGTB1698.4 [CD4]


title: IGTB1663.4 [CD4]


title: IGTB1662.4TR1 [CD4]


title: IGTB1662.4TR2 [CD4]


title: IGTB1652.4 [CD4]


title: IGTB1654.4 [CD4]


title: IGTB1650.F41 [CD4]


title: IGTB1656.F4 [CD4]


title: IGTB1650.F42 [CD4]


title: IGTB1649.4TR2 [CD4]


title: IGTB1647.4 [CD4]


title: IGTB1639.F4 [CD4]


title: IGTB1640.4 [CD4]


title: IGTB1627.4 [CD4]


title: IGTB1646.F4 [CD4]


title: IGTB1626.4TR1 [CD4]


title: IGTB1626.4TR2 [CD4]


title: IGTB1623.F4 [CD4]


title: IGTB1616.4 [CD4]


title: IGTB1619.F4 [CD4]


title: IGTB162.4 [CD4]


title: IGTB1622.4 [CD4]


title: IGTB1649.4TR1 [CD4]


title: IGTB1608.4 [CD4]


title: IGTB1610.4 [CD4]


title: IGTB1605.4 [CD4]


title: IGTB1597.4 [CD4]


title: IGTB1603.4 [CD4]


title: IGTB1592.4 [CD4]


title: IGTB1590.F4 [CD4]


title: IGTB1600.4 [CD4]


title: IGTB1577.4 [CD4]


title: IGTB1617.4 [CD4]


title: IGTB1570.4 [CD4]


title: IGTB1573.4 [CD4]


title: IGTB1575.F4 [CD4]


title: IGTB1568.4 [CD4]


title: IGTB1566.F4 [CD4]


title: IGTB1572.F4 [CD4]


title: IGTB1567.4 [CD4]


title: IGTB1565.4 [CD4]


title: IGTB1559.F4 [CD4]


title: IGTB1557.4 [CD4]


title: IGTB1550.F4 [CD4]


title: IGTB1556.F4 [CD4]


title: IGTB1542.4 [CD4]


title: IGTB154.4 [CD4]


title: IGTB1523.4 [CD4]


title: IGTB1524.F4 [CD4]


title: IGTB1532.4 [CD4]


title: IGTB1519.F4 [CD4]


title: IGTB155.4 [CD4]


title: IGTB1535.4 [CD4]


title: IGTB1521.F4TR1 [CD4]


title: IGTB1521.F4TR2 [CD4]


title: IGTB1514.4 [CD4]


title: IGTB1548.4 [CD4]


title: IGTB1574.4 [CD4]


title: IGTB1512.4 [CD4]


title: IGTB1506.4 [CD4]


title: IGTB1509.4 [CD4]


title: IGTB1531.4 [CD4]


title: IGTB1488.4 [CD4]


title: IGTB148.F4 [CD4]


title: IGTB1479.4 [CD4]


title: IGTB1476.4 [CD4]


title: IGTB1515.4 [CD4]


title: IGTB1489.F4 [CD4]


title: IGTB1475.4 [CD4]


title: IGTB1465.4 [CD4]


title: IGTB1472.4 [CD4]


title: IGTB1499.4 [CD4]


title: IGTB1459.4 [CD4]


title: IGTB1467.4 [CD4]


title: IGTB1469.4 [CD4]


title: IGTB1491.4 [CD4]


title: IGTB1453.4 [CD4]


title: IGTB1474.4 [CD4]


title: IGTB1466.4 [CD4]


title: IGTB419.4 [CD4]


title: IGTB1448.4 [CD4]


title: IGTB1447.4 [CD4]


title: IGTB1446.F4 [CD4]


title: IGTB1449.4 [CD4]


title: IGTB1450.F4 [CD4]


title: IGTB1442.4 [CD4]


title: IGTB1439.F4 [CD4]


title: IGTB1440.4 [CD4]


title: IGTB422.4 [CD4]


title: IGTB1433.4 [CD4]


title: IGTB1435.4 [CD4]


title: IGTB1452.F4 [CD4]


title: IGTB1430.4 [CD4]


title: IGTB1451.F4 [CD4]


title: IGTB1438.4 [CD4]


title: IGTB1416.4 [CD4]


title: IGTB1417.4 [CD4]


title: IGTB1406.F4 [CD4]


title: IGTB1434.4 [CD4]


title: IGTB1419.4 [CD4]


title: IGTB1400.4 [CD4]


title: IGTB1403.F4 [CD4]


title: IGTB1405.4 [CD4]


title: IGTB1412.F4 [CD4]


title: IGTB1399.4 [CD4]


title: IGTB1384.4 [CD4]


title: IGTB1411.F4 [CD4]


title: IGTB143.4 [CD4]


title: IGTB1397.F4 [CD4]


title: IGTB1385.4 [CD4]


title: IGTB1396.F4 [CD4]


title: IGTB1375.4 [CD4]


title: IGTB1393.4 [CD4]


title: IGTB1374.4TR1 [CD4]


title: IGTB1369.4 [CD4]


title: IGTB1378.4 [CD4]


title: IGTB1374.4TR2 [CD4]


title: IGTB1366.F4 [CD4]


title: IGTB1370.F4 [CD4]


title: IGTB1380.F4 [CD4]


title: IGTB1372.4 [CD4]


title: IGTB1363.F42 [CD4]


title: IGTB1363.F41 [CD4]


title: IGTB1357.4 [CD4]


title: IGTB136.F4 [CD4]


title: IGTB1361.4 [CD4]


title: IGTB1360.F4 [CD4]


title: IGTB1350.F4 [CD4]


title: IGTB1348.F4 [CD4]


title: IGTB1356.4 [CD4]


title: IGTB1353.4 [CD4]


title: IGTB1349.4 [CD4]


title: IGTB1360.4 [CD4]


title: IGTB1344.4 [CD4]


title: IGTB1343.4 [CD4]


title: IGTB1339.4 [CD4]


title: IGTB1342.4 [CD4]


title: IGTB1336.4 [CD4]


title: IGTB1320.4 [CD4]


title: IGTB1340.4 [CD4]


title: IGTB1327.4 [CD4]


title: IGTB1313.4 [CD4]


title: IGTB1331.F41 [CD4]


title: IGTB1331.F42 [CD4]


title: IGTB1314.4 [CD4]


title: IGTB1319.F4 [CD4]


title: IGTB1345.4 [CD4]


title: IGTB133.4 [CD4]


title: IGTB1355.4 [CD4]


title: IGTB1308.4TR2 [CD4]


title: IGTB1300.F4 [CD4]


title: IGTB1295.4 [CD4]


title: IGTB1299.4 [CD4]


title: IGTB1297.F4 [CD4]


title: IGTB1302.F4 [CD4]


title: IGTB1290.4 [CD4]


title: IGTB1278.4 [CD4]


title: IGTB1305.4 [CD4]


title: IGTB1268.4 [CD4]


title: IGTB1292.4 [CD4]


title: IGTB1265.F4 [CD4]


title: IGTB1276.4 [CD4]


title: IGTB1281.4 [CD4]


title: IGTB126.F4TR4 [CD4]


title: IGTB1274.F4 [CD4]


title: IGTB1272.4 [CD4]


title: IGTB1308.4TR1 [CD4]


title: IGTB1263.4 [CD4]


title: IGTB1270.F4 [CD4]


title: IGTB126.F4TR1 [CD4]


title: IGTB126.F4TR2 [CD4]


title: IGTB1294.F4 [CD4]


title: IGTB1477.4 [CD4]


title: IGTB1259.4 [CD4]


title: IGTB126.F4TR3 [CD4]


title: IGTB1256.4 [CD4]


title: IGTB1277.4 [CD4]


title: IGTB1266.4 [CD4]


title: IGTB1257.4 [CD4]


title: IGTB1255.4 [CD4]


title: IGTB1250.4TR2 [CD4]


title: IGTB1498.4 [CD4]


title: IGTB1250.4TR1 [CD4]


title: IGTB125.F4 [CD4]


title: IGTB125.4 [CD4]


title: IGTB125.4BR1 [CD4]


title: IGTB1511.4 [CD4]


title: IGTB1237.4 [CD4]


title: IGTB1228.4 [CD4]


title: IGTB1232.F4 [CD4]


title: IGTB1248.4 [CD4]


title: IGTB1242.4 [CD4]


title: IGTB1246.4 [CD4]


title: IGTB1245.4 [CD4]


title: IGTB1224.4TR2 [CD4]


title: IGTB1215.4 [CD4]


title: IGTB1217.F4 [CD4]


title: IGTB1252.4 [CD4]


title: IGTB1224.4TR1 [CD4]


title: IGTB1219.4 [CD4]


title: IGTB1200.4 [CD4]


title: IGTB1220.4 [CD4]


title: IGTB1196.F4 [CD4]


title: IGTB1202.4 [CD4]


title: IGTB1195.4 [CD4]


title: IGTB119.4 [CD4]


title: IGTB1211.4 [CD4]


title: IGTB1205.F4 [CD4]


title: IGTB1231.4 [CD4]


title: IGTB1223.F4 [CD4]


title: IGTB1171.42 [CD4]


title: IGTB1172.4 [CD4]


title: IGTB1171.41 [CD4]


title: IGTB1192.4 [CD4]


title: IGTB1168.4 [CD4]


title: IGTB1166.4 [CD4]


title: IGTB1162.4BR1 [CD4]


title: IGTB1151.4 [CD4]


title: IGTB1159.F4 [CD4]


title: IGTB1157.4 [CD4]


title: IGTB1156.F4 [CD4]


title: IGTB1144.4 [CD4]


title: IGTB1162.4 [CD4]


title: IGTB1148.4 [CD4]


title: IGTB1142.F4 [CD4]


title: IGTB1187.4 [CD4]


title: IGTB1154.4 [CD4]


title: IGTB1137.4 [CD4]


title: IGTB1135.F4 [CD4]


title: IGTB1130.4 [CD4]


title: IGTB1114.4 [CD4]


title: IGTB1142.F4BR1 [CD4]


title: IGTB1134.4 [CD4]


title: IGTB1128.4 [CD4]


title: IGTB1112.4 [CD4]


title: IGTB1133.4 [CD4]


title: IGTB1155.4 [CD4]


title: IGTB1111.4 [CD4]


title: IGTB1107.4 [CD4]


title: IGTB1108.4 [CD4]


title: IGTB1105.F4 [CD4]


title: IGTB1088.4 [CD4]


title: IGTB1131.4 [CD4]


title: IGTB1086.4 [CD4]


title: IGTB1078.4 [CD4]


title: IGTB1070.4 [CD4]


title: IGTB1067.4 [CD4]


title: IGTB107.4 [CD4]


title: IGTB108.4 [CD4]


title: IGTB1066.4 [CD4]


title: IGTB107.F4 [CD4]


title: IGTB1060.4 [CD4]


title: IGTB1057.4BR1 [CD4]


title: IGTB1059.4 [CD4]


title: IGTB1042.4 [CD4]


title: IGTB1038.4 [CD4]


title: IGTB1037.4BR1 [CD4]


title: IGTB111.4 [CD4]


title: IGTB1097.4 [CD4]


title: IGTB1052.F4 [CD4]


title: IGTB1034.4 [CD4]


title: IGTB1030.4 [CD4]


title: IGTB1075.4 [CD4]


title: IGTB1056.4 [CD4]


title: IGTB1037.4 [CD4]


title: IGTB1029.4 [CD4]


title: IGTB1032.4 [CD4]


title: IGTB1026.F4 [CD4]


title: IGTB1021.F4 [CD4]


title: IGTB1021.4 [CD4]


title: IGTB1057.4 [CD4]


title: IGTB1016.4 [CD4]


title: IGTB1018.4 [CD4]


title: IGTB10.4 [CD4]


title: IGTB10.4BR1 [CD4]


title: IGTB1004.4 [CD4]


title: IGTB1020.4 [CD4]


title: ECFC_Scramble_Rep3

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

description: Gene expression of Endothelial Colony Forming-Cell treated with a scramble shRNA

hyb_protocol: Affymetrix standard protocol for GeneChip for cartridge arrays. Hybridization performed at the StemCore Laboratories Affymetrix Microarray facility at the Ottawa Hospital Research Institute (Ottawa, Ontario, Canada)

scan_protocol: Affymetrix standard protocol for GeneChip for cartridge arrays. Scan performed at the StemCore Laboratories Affymetrix Microarray facility at the Ottawa Hospital Research Institute (Ottawa, Ontario, Canada).

data_processing: CEL files were imported into R/Bioconductor package 'affy'. The data was normalized using the RMA algorithm. Probes with variance under the 25th quantile were removed. Differential expression  analysis was performed with the R/Bioconductor 'limma' package. Probes with Benjamini-Hochberg adjusted p-value lower than 0.05 were deemed as significant.

source_name: Human primary endothelial colony-forming cells

label_protocol: Affymetrix standard protocol for GeneChip Whole Transcript Expression Arrays. Labeling performed at the StemCore Laboratories Affymetrix Microarray facility at the Ottawa Hospital Research Institute (Ottawa, Ontario, Canada).

growth_protocol: Human umbilical cord blood from normal full-term deliveries were obtained after informed consent. Light-density mononuclear cell (MNC) fractions were isolated by Ficoll density and resuspended in complete EGM-2 medium (EBM-2 Endothelial Cell basal Medium-2, Lonza, Cat# CC-3156, supplemented with EGM-2 SingleQuot Kit Supplements & Growth Factors, Lonza, Cat# CC-4176)  and 10% fetal bovine serum and plated on to CellBIND 6 well plates at 1x10^7 cells/well. Individual ECFC colonies were isolated with 0.05% trypsin and expanded in EGM-2 medium. ECFCs at passage 3 were used.

extract_protocol: DNA-free total RNA was isolated with the RNeasy Mini Kit following the manufacturer's protocol.

treatment_protocol: Paired samples were infected with lentiviruses expressing an anti-TAL1 shRNA or a scrambled shRNA as a negative control. Infection was done at a multiplicity of infection (MOI) of 100 twice at 24 hours interval in presence of 4μg/ml Hexadimethrine bromide.

tag: source

value: ECFCs derived from umbilical cord blood

tag: treatment

value: Scramble shRNA


title: ECFC_Tal1KD_Rep3

description: Gene expression of Endothelial Colony Forming-Cell treated with an shRNA against Tal1

value: Tal1 shRNA


title: fluorosed maturation ameloblasts, rep 2

city: San Francisco

first: Yan

last: Zhang

state: CA

address: 513 Parnassus Avenue

department: Orofacial Sciences

institute: UCSF

description: gene expression data from flurosed maturation ameloblasts

hyb_protocol: The recovered biotinylated cDNA probes were hybridized onto a GeneChip® Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 16 hours at 45°C.

scan_protocol: The array chips were imaged using an Affymetrix Gene Chip Scanner 3000.

data_processing: The Robust Multichip Average (RMA) method was used for background adjustment, quantile normalization, and median polish summarization using Affymetrix Expression Console software.

organism: Mus musculus

source_name: maturation ameloblasts from incisors of mice drinking water supplemented with 50 ppm NaF

label_protocol: Fragmented ST-cDNA product was biotinylated using an Encore Biotin Module according to the manufacturer’s instructions (NuGEN Technologies).

growth_protocol: Three weeks' old A/J female mice were purchased from JAX. Upon arrival, the mice were housed in the animal facility at University of California, San Francisco, and all handling was followed an IACUC approved protocol.

extract_protocol: Total RNA was purified from microdissected cells using QIAGEN RNeasy Micro Kit following the manufacturer’s instruction.

treatment_protocol: The mice were given either deionized water or 50 ppm NaF supplemented water for 4 weeks.

tag: strain

value: A/J

tag: tissue

value: mandibular incisor

tag: genotype

value: wild type

tag: age


title: fluorosed maturation ameloblasts, rep 3


title: control secretory ameloblasts, rep3

description: gene expression data from control secretory ameloblasts

source_name: secretory ameloblasts from incisors of mice drinking normal water


title: IGTB1007.4 [CD4]


title: control maturation ameloblasts, rep 3

description: gene expression data from control maturation ameloblasts

source_name: maturation ameloblasts from incisors of mice drinking normal water


title: fluorosed maturation ameloblasts, rep 1


title: fluorosed secretory ameloblasts, rep 2

description: gene expression data from flurosed secretory ameloblasts

source_name: secretory ameloblasts from incisors of mice drinking water supplemented with 50 ppm NaF


title: IGTB100.4 [CD4]


title: ECFC_Scramble_Rep2


title: ECFC_Tal1KD_Rep2


title: control secretory ameloblasts, rep 2


title: control secretory ameloblasts, rep 1


title: fluorosed secretory ameloblasts, rep 3


title: WP_ni

status: Public on May 01 2014

city: Munich

first: Kilian

last: Eyerich

address: Biedersteiner Strasse 29

department: Department of Dermatology and Allergy

country: Germany

institute: Technische Universität München

description:
Gene expression
MQ_63

hyb_protocol: Samples were hybridized to a SurePrint G3 Human GE 8X60K BeadChip (Agilent Technologies).

scan_protocol: Fluorescence signals were detected by reading the arrays in the microarray scanner system iScan (Agilent Technology).

data_processing: The Agilent Feature Extraction software was used to read and process microarray image files.

source_name: non-involved skin

label_protocol: Samples were amplified and Cy3 labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions

extract_protocol: Total RNA was isolated with the PAXgene Tissue RNA Kit (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: Lesional and non-involved skin was directly investigated without in vitro modifications

tag: individual

value: WP

tag: disease state

value: control (non-involved)

value: skin


title: control maturation ameloblasts, rep 1


title: ECFC_Tal1KD_Rep1


title: SP_pso

description:
Gene expression
MQ_61

value: SP


title: ECFC_Scramble_Rep1


title: WP_pso

description:
Gene expression
MQ_64

source_name: Lesional skin, psoriasis

value: psoriasis


title: MPG_pso

description:
Gene expression
MQ_60

value: MPG


title: MPG_ni

description:
Gene expression
MQ_59


title: WP_ecz

description:
Gene expression
MQ_62

source_name: Lesional skin, eczema

value: eczema


title: MPG_ecz

description:
Gene expression
MQ_58

value: female


title: SP_ecz

description:
Gene expression
MQ_56


title: control maturation ameloblasts, rep 2


title: BS_pso (MQ_55)

description:
Gene expression
MQ_55


title: fluorosed secretory ameloblasts, rep 1


title: BS_ecz (MQ_53)

description:
Gene expression
MQ_53


title: BA_ni

description:
Gene expression
MQ_50

value: BA


title: BA_pso

description:
Gene expression
MQ_51


title: BA_ACD

description:
Gene expression
MQ_52


title: VI_ACD

description:
Gene expression
MQ_49

value: VI


title: BS_ni (MQ_44)

description:
Gene expression
MQ_44


title: BC_ACD

description:
Gene expression
MQ_43

value: BC


title: BS_ni (MQ_54)

description:
Gene expression
MQ_54


title: BS_pso (MQ_45)

description:
Gene expression
MQ_45


title: VI_pso

description:
Gene expression
MQ_48


title: SM_ni

description:
Gene expression
MQ_38

value: SM


title: VI_ni

description:
Gene expression
MQ_47


title: IGTB1179.4 [CD4]

tag: age (yrs)

value: male

value: T4 Naive cells from human peripheral blood mononuclear cells (PBMCs)

value: CD3+ CD4+ CD62L+

value: Aria Sorter


title: SM_ACD

description:
Gene expression
MQ_40


title: LI_ACD

description:
Gene expression
MQ_34

value: LI


title: BS_ACD

description:
Gene expression
MQ_46


title: LI_pso

description:
Gene expression
MQ_33


title: HI_ACD

description:
Gene expression
MQ_37

value: HI


title: JB_pso

description:
Gene expression
MQ_30

value: JB


title: JB_ni

description:
Gene expression
MQ_29

value: control (non-involved)

value: skin


title: JB_ACD

description:
Gene expression
MQ_31


title: Klose_ACD

description:
Gene expression
MQ_28

value: Klose


title: LI_ni

description:
Gene expression
MQ_32


title: SP_ni

description:
Gene expression
MQ_57

value: SP


title: Klose_ni

description:
Gene expression
MQ_26


title: SM_pso

description:
Gene expression
MQ_39

value: psoriasis


title: HI_pso

description:
Gene expression
MQ_36

value: female


title: SS2_ACD

description:
Gene expression
MQ_25

value: eczema


title: Klose_pso

description:
Gene expression
MQ_27


title: SS2_pso

description:
Gene expression
MQ_24


title: SS2_ni

description:
Gene expression
MQ_23


title: Mattes_pso

description:
Gene expression
MQ_21

value: Mattes


title: MOF_pso

description:
Gene expression
MQ_18

value: MOF


title: MOF_ecz

description:
Gene expression
MQ_19


title: Mattes_ni

description:
Gene expression
MQ_20


title: Mattes_ecz

description:
Gene expression
MQ_22


title: MOF_ni

description:
Gene expression
MQ_17


title: LA_ni

description:
Gene expression
MQ_14

value: LA


title: ZA_pso

description:
Gene expression
MQ_12

value: ZA


title: MM_ecz

description:
Gene expression
MQ_11

value: MM


title: LA_ecz

description:
Gene expression
MQ_16

value: male


title: SI_ecz

description:
Gene expression
MQ_9

value: SI


title: MM_pso

description:
Gene expression
MQ_10


title: Patient ID_225

city: Sinjuku-ku

first: Masami

last: Tanaka

state: Tokyo

address: Sinjuku 6-1-1

country: Japan

institute: Tokyo Medical University

hyb_protocol: labeled RNA was hybridized to Agilent miRNA array ( 8 arrays per slide) at 55°C for 20h in rotisserie in a hybridization oven. Disassembled arrays was washed in GE wash buffer 1&2 for 5 minutes each.

scan_protocol: Images was scanned with Agilent scanner at 5µm resolution

data_processing: The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate Gene view file, providing expression data for each gene probed on the array. Features interogating same miRNA were summarized together based on their weight. No interarray normalization method was employed.

source_name: Liver, ID_225

label_protocol: 100ng total RNA was dephosphorylated at the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was then ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 1.0

extract_protocol: Total RNA was extracted by using mirVana™ miRNA Isolation Kit (Ambion) according to manufacturer’s instruction

value: liver (chronic hepatitis)

tag: drug-response

value: sustained virological responder

tag: Sex

value: Male

tag: type of hcv

tag: degree of inflammation/fibrosis


title: LA_pso

description:
Gene expression
MQ_15


title: Patient ID_227

source_name: Liver, ID_227

value: stopping dosage


title: Patient ID_226

source_name: Liver, ID_226

value: not determined


title: KK_pso

description:
Gene expression
MQ_3

value: KK

value: skin


title: SI_pso

description:
Gene expression
MQ_8

value: psoriasis


title: ZA_ecz

description:
Gene expression
MQ_13

value: female


title: KP_pso

description:
Gene expression
MQ_6

value: KP


title: BC_pso

description:
Gene expression
MQ_42

value: BC


title: Patient ID_224

source_name: Liver, ID_224

value: Female


title: Patient ID_193

source_name: Liver, ID_193


title: Patient ID_212

source_name: Liver, ID_212

value: non-virological responder


title: EP_pso

description:
Gene expression
MQ_1

value: EP


title: KK_ecz

description:
Gene expression
MQ_4

value: eczema


title: KP_ni

description:
Gene expression
MQ_5

value: control (non-involved)

value: male


title: KP_ecz

description:
Gene expression
MQ_7


title: EP_ecz

description:
Gene expression
MQ_2


title: LNCaP_bicalutamide+SAHA_biological replicate 1

status: Public on Mar 27 2014

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: Gene expression data from LNCaP human prostate cancer cells treated with bicalutamide and SAHA for 6 hours

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Data were analysed using Partek Genomics Suite. Briefly, .cel files were normalised using RMA background correction, Partek's own GC content correction, and mean probe summarization.

source_name: human prostate cancer cells, bicalutamide+SAHA, 6 hours

label_protocol: Affymetrix protocol

growth_protocol: LNCaP human prostate cancer cells were cultured in tissue culture flasks or plates at 37 degrees celsius in a 5% carbon dioxide atmosphere prior to drug treatment.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions after 6 hours of culture with the drug treatments.

tag: cell line

value: LNCaP


title: CCM3 shRNA cells passage 11, rep 4

status: Public on Apr 10 2014

city: Santiago de Compostela

first: Juan

last: Zalvide

state: A Coruña

address: CIMUS, Avda de Barcelona s/n

department: Physiology

country: Spain

institute: Universidad de Santiago de Compostela

description: Gene expression data from late passage CCM3-knockdown endothelial cells.

hyb_protocol: Hybridization was performed as recommended in GeneChip Hybridization, Wash and Stain kit (Affimetrix), incubating the samples for 17 h at 45º C in a GeneChip Hybridization Oven 640 (Affimetrix). GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affimetrix).

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000 (Affimetrix).

data_processing: Microarray data were normalized using the Affimetrix Expression Console. Subsequent analysis was made using the MeV software. Cutoff intensity was set on 6. Sample comparisons between late and early passage control cells were made using SAM algorithm with delta2 as a cutoff. Genes that were considered overexpressed when log2 (shNTp11/shNTp7)>0.5 (senescence genes).

label: Biotin

source_name: CCM3 shRNA cells, passage 11

label_protocol: Single-stranded cDNA was obtained from 250 ng total RNA using Ambion WT Expression kit (Life Technologies). Then, ss cDNA was fragmented and labeled using the Affimetrix GeneChip WT Terminal Labeling and Hybridization kit.

growth_protocol: Human Coronary Artery Endothelial Cells (HCAEC) were obtained from European Collection of Cell Cultures, and were grown as recommended.

extract_protocol: RNA extracts were obtained using Trizol reagent and quantified with a Nanodrop 2000 (Thermo Scientific). RNA quality was assesed using a RNA 6000 Nano kit (Agilent Biotechnologies).

treatment_protocol: Stable cell populations with silenced CCM3 or control were obtained via puromycin selection after lentiviral transduction using MISSION lentiviral shRNA transduction particles against human CCM3 or MISSION lentiviral non-target shRNA transduction particles, from Sigma-Aldrich (TRC).

tag: cell type

value: Endothelial cells


title: CCM3 shRNA cells passage 7, rep 3

description: Gene expression data from early passage CCM3-knockdown endothelial cells.

source_name: CCM3 shRNA cells, passage 7


title: CCM3 shRNA cells passage 7, rep 4


title: Control shRNA cells passage 11, rep 2

description: Gene expression data from late passage endothelial cells.

source_name: Endothelial control cells, passage 11


title: LNCaP_17-AAG+SAHA_biological replicate 6

description: Gene expression data from LNCaP human prostate cancer cells treated with 17-AAG and SAHA for 6 hours

source_name: human prostate cancer cells, 17-AAG+SAHA, 6 hours


title: LNCaP_bicalutamide+SAHA_biological replicate 2


title: LNCaP_bicalutamide+SAHA_biological replicate 4


title: CCM3 shRNA cells passage 11, rep 3


title: Control shRNA cells passage 7, rep 1

description: Gene expression data from early passage endothelial cells.

source_name: Endothelial control cells, passage 7


title: LNCaP_bicalutamide+SAHA_biological replicate 5


title: CCM3 shRNA cells passage 11, rep 5


title: CCM3 shRNA cells passage 7, rep 2


title: LNCaP_bicalutamide+SAHA_biological replicate 3


title: CCM3 shRNA cells passage 11, rep 1


title: Control shRNA cells passage 11, rep 3


title: CCM3 shRNA cells passage 7, rep 1


title: LNCaP_bicalutamide+SAHA_biological replicate 6


title: Control shRNA cells passage 7, rep 2


title: LNCaP_17-AAG+SAHA_biological replicate 5


title: Control shRNA cells passage 11, rep 1


title: Control shRNA cells passage 11, rep 5


title: Control shRNA cells passage 7, rep 3


title: Control shRNA cells passage 7, rep 4


title: CCM3 shRNA cells passage 11, rep 2


title: LNCaP_17-AAG+SAHA_biological replicate 2


title: LNCaP_17-AAG+SAHA_biological replicate 4


title: Control shRNA cells passage 11, rep 4


title: LNCaP_17-AAG+SAHA_biological replicate 3


title: LNCaP_17-AAG+SAHA_biological replicate 1


title: LNCaP_17-AAG+bicalutamide_biological replicate 5

description: Gene expression data from LNCaP human prostate cancer cells treated with 17-AAG and bicalutamide for 6 hours

source_name: human prostate cancer cells, 17-AAG+bicalutamide, 6 hours


title: LNCaP_17-AAG_biological replicate 4

description: Gene expression data from LNCaP human prostate cancer cells treated with 17-AAG for 6 hours

source_name: human prostate cancer cells, 17-AAG, 6 hours


title: LNCaP_17-AAG_biological replicate 3


title: LNCaP_SAHA_biological replicate 3

description: Gene expression data from LNCaP human prostate cancer cells treated with SAHA for 6 hours

source_name: human prostate cancer cells, SAHA, 6 hours


title: LNCaP_17-AAG+bicalutamide_biological replicate 2


title: LNCaP_17-AAG+bicalutamide_biological replicate 4


title: LNCaP_vehicle control_biological replicate 5

description: Gene expression data from LNCaP human prostate cancer cells treated with vehicle control for 6 hours

source_name: human prostate cancer cells, vehicle control, 6 hours


title: LNCaP_bicalutamide_biological replicate 6

description: Gene expression data from LNCaP human prostate cancer cells treated with bicalutamide for 6 hours

source_name: human prostate cancer cells, bicalutamide, 6 hours


title: LNCaP_bicalutamide_biological replicate 5


title: LNCaP_SAHA_biological replicate 6


title: LNCaP_bicalutamide_biological replicate 3


title: LNCaP_bicalutamide_biological replicate 4


title: LNCaP_17-AAG+bicalutamide_biological replicate 1


title: LNCaP_17-AAG_biological replicate 6


title: LNCaP_SAHA_biological replicate 5


title: LNCaP_vehicle control_biological replicate 4


title: LNCaP_bicalutamide_biological replicate 2


title: LNCaP_bicalutamide_biological replicate 1


title: LNCaP_vehicle control_biological replicate 3


title: LNCaP_17-AAG+bicalutamide_biological replicate 6


title: LNCaP_SAHA_biological replicate 1


title: LNCaP_SAHA_biological replicate 4


title: LNCaP_17-AAG+bicalutamide_biological replicate 3


title: LNCaP_17-AAG_biological replicate 1


title: LNCaP_17-AAG_biological replicate 5


title: LNCaP_SAHA_biological replicate 2


title: LNCaP_vehicle control_biological replicate 6


title: LNCaP_17-AAG_biological replicate 2


title: LNCaP_vehicle control_biological replicate 2


title: LNCaP_vehicle control_biological replicate 1


title: Naïve CD4.RORC.DMSO.60h

status: Public on Mar 07 2014

city: Cambridge

first: Scott

last: Davis

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

description: CD4+CD45RA+ T cells stimulated with anti-CD3/CD28 beads (1 bead/cell) and infected with RORC lentiviruses in the presence of DMSO for 60 h

hyb_protocol: The labeled fragmented DNA was hybridized to the Gene Arrays 1.0ST for 16-18 hours in GeneChip Hybridization oven 640 at 45 °C with rotation (60 rpm).  The hybridized samples were washed and stained using Affymetrix fluidics station 450. The first stain with streptavidin-R-phycoerythrin (SAPE) was followed by signal amplification using a biotinilated goat anti-streptavidin antibody and another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix).

scan_protocol: Standard Affymetrix protocol on an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix).

data_processing: Samples were RMA normalized using Affymetrix Power Tools (gcbg background correction, quantile normalization, median polish) on the annotated set of probesets. Unannotated probesets were removed prior to normalization (see supplemental .mps file)

label_protocol: biotin

growth_protocol: Human CD4+ T cells  were cultured in standard T cell culture medium (10% FBS IMDM, 2 mM L-glutamine, 1 mM Pyruvate,0.1 mM NEAA, 0.05 mM 2-mercaptoethonol, 10 U/10 mg Penicillin/Streptomycin) at a density of 1 x1 0^6 per mL.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy with on-column DNase treatment method.

treatment_protocol: RORgt inhibitor (200 nM) or vehicle control (0.1% v/v DMSO) were added to the T cells in culture immediately before the addition of anti-CD3/anti-CD28 beads for diffferent time point.


title: Memory CD4.CCR6-.RORC.DMSO.60h #1

description: CCR6- CD45RO+ CD4+ T cells stimulated with anti-CD3/CD28 beads (1 bead/cell) and infected with RORC lentiviruses in the presence of DMSO for 60 h

value: CD4+ CCR6-


title: Naïve CD4.RORC.TMP778.60h

description: CD4+CD45RA+ T cells stimulated with anti-CD3/CD28 beads (1 bead/cell) and infected with RORC lentiviruses in the presence of TMP778 for 60 h


title: Memory CD4.CCR6+.TMP778.20h #2

description: CCR6+ CD45RO+ CD4+ T cells purified by cell sorting were stimulated with anti-CD3/28 beads plus TMP778 for 20 h

value: CD4+ CCR6+


title: Memory CD4.CCR6+.TMP778.20h #1

value: stimulated with anti-CD3/28 beads plus TMP778 for 20 h


title: Naïve CD4.Th17.TMP776.60h #2

description: Naïve CD4+ T cells, purified by Naïve CD4+ T cells Isolation Kit II (human) from Miltenyi Biotec (cat No.: 130-094-131), skewed under Th17 conditions (Cytokine and Ab Cocktail (Final concentrations): IL-1b(10 ng/ml); IL-6 (20 ng/ml), IL-23 (10 ng/ml); TGFb (2 ng/ml); IL-2 (1ng/ml), a IL-4 (2 ug/ml); a IFNg (2 ug/ml)) plus TMP776 for 60 h

value: skewed under Th17 conditions plus plus TMP776 for 60 h


title: Naïve CD4.Th17.TMP778.60h #2

description: Naïve CD4+ T cells, purified by Naïve CD4+ T cells Isolation Kit II (human) from Miltenyi Biotec (cat No.: 130-094-131), skewed under Th17 conditions (Cytokine and Ab Cocktail (Final concentrations): IL-1b(10 ng/ml); IL-6 (20 ng/ml), IL-23 (10 ng/ml); TGFb (2 ng/ml); IL-2 (1ng/ml), a IL-4 (2 ug/ml); a IFNg (2 ug/ml)) plus TMP778 for 60 h

value: skewed under Th17 conditions plus plus TMP778 for 60 h


title: Memory CD4.CCR6+.DMSO.20h #2

description: CCR6+ CD45RO+ CD4+ T cells purified by cell sorting were stimulated with anti-CD3/28 beads plus DMSO for 20 h


title: Memory CD4.CCR6-.RORC.TMP778.60h #1

description: CCR6- CD45RO+ CD4+ T cells stimulated with anti-CD3/CD28 beads (1 bead/cell) and infected with RORC lentiviruses in the presence of TMP778 for 60 h


title: Memory CD4.CCR6+.TMP776.20h #1

description: CCR6+ CD45RO+ CD4+ T cells purified by cell sorting were stimulated with anti-CD3/28 beads plus TMP776 for 20 h


title: Naïve CD4.Th17.TMP776.60h #1


title: Memory CD4.CCR6+.DMSO.20h #1

value: stimulated with anti-CD3/28 beads plus DMSO for 20 h


title: Memory CD4.CCR6+.TMP776.20h #2

value: stimulated with anti-CD3/28 beads plus TMP776 for 20 h


title: Naïve CD4.Th17.DMSO.60h #1

description: Naïve CD4+ T cells, purified by Naïve CD4+ T cells Isolation Kit II (human) from Miltenyi Biotec (cat No.: 130-094-131), skewed under Th17 conditions (Cytokine and Ab Cocktail (Final concentrations): IL-1b(10 ng/ml); IL-6 (20 ng/ml), IL-23 (10 ng/ml); TGFb (2 ng/ml); IL-2 (1ng/ml), a IL-4 (2 ug/ml); a IFNg (2 ug/ml)) plus DMSO control for 60 h

value: skewed under Th17 conditions plus DMSO control for 60 h


title: Naïve CD4.Th17.DMSO.60h #2


title: Memory CD4.CCR6-.DMSO.20h #1

description: CCR6- CD45RO+ CD4+ T cells purified by cell sorting were stimulated with anti-CD3/28 beads plus DMSO for 20 h


title: Memory CD4.CCR6-.DMSO.16h #1

description: CCR6- CD45RO+ CD4+ T cells purified by cell sorting were stimulated with anti-CD3/28 beads for 16 h


title: Memory CD4.CCR6+.DMSO.16h #1

description: CCR6+ CD45RO+ CD4+ T cells purified by cell sorting were stimulated with anti-CD3/28 beads for 16 h


title: Memory CD4.CCR6+.DMSO.20h #3


title: L15_rep [217697]

status: Public on Mar 01 2014

first: Nir

last: Hacohen

address: 7 Cambridge Center

institute: Broad Institute

hyb_protocol: cDNA synthesis, labeling, hybridization, and scanning were performed by the company Expression Analysis (Durham, NC).

data_processing:
Data were processed using Bioconductor RMA package.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

growth_protocol: Monocyte-derived dendritic cells from each donor were cultured for 7 days in RPMI supplemented with 10% FBS, 100 ng/mL GM-CSF and 40 ng/mL IL-4.

extract_protocol: Total RNA was isolated using Qiagen RNeasy columns.

treatment_protocol: MoDCs were stimulated with 15 ng/mL LPS for 5 h, influenza virus for 10 h, or left unstimulated.

tag: stimulation

value: LPS

tag: total rna (ug)

tag: rna concentration (ug/ul)

tag: cd4 %

tag: age (years)

tag: million modc

tag: million monocyte

tag: million pbmc

tag: ethnicity

value: Caucasian

value: F

tag: individual id


title: L14_rep [217694]

scan_protocol: cDNA synthesis, labeling, hybridization, and scanning were performed by the company Expression Analysis (Durham, NC).

value: M


title: L16_rep [217700]

label_protocol: cDNA synthesis, labeling, hybridization, and scanning were performed by the company Expression Analysis (Durham, NC).

value: African American


title: V15_rep [217698]


title: 16_unstim_rep [217699]

value: Unstim


title: Naïve CD4.Th17.TMP778.60h #1

tag: treatment


title: 15_unstim_rep [217696]


title: V14_rep [217695]


title: 14_unstim_rep [217693]


title: V16_rep [217701]


title: V13_rep [217692]


title: 9_unstim_rep [217678]


title: L10_rep [217682]

value: Asian


title: 10_unstim_rep [217681]


title: L12_rep [217688]


title: V8_rep [217677]


title: L13_rep [217691]


title: 8_unstim_rep [217675]


title: L11_rep [217685]


title: V11_rep [217686]


title: L9_rep [217679]


title: V12_rep [217689]


title: 12_unstim_rep [217687]


title: L7_rep [217673]


title: 13_unstim_rep [217690]


title: V7_rep [217674]


title: V9_rep [217680]


title: V6_rep [217671]


title: 11_unstim_rep [217684]


title: 7_unstim_rep [217672]


title: 6_unstim_rep [217669]


title: 5_unstim_rep [217666]


title: V3_rep [217662]


title: L5_rep [217667]


title: L6_rep [217670]


title: V5_rep [217668]


title: L4_rep [217664]


title: L8_rep [217676]


title: L3_rep [217661]


title: V4_rep [217665]


title: 4_unstim_rep [217663]


title: V2_rep [217659]


title: 2_unstim_rep [217657]


title: V1_rep [217656]


title: 3_unstim_rep [217660]


title: L2_rep [217658]


title: 1_unstim_rep [217654]


title: L1_rep [217655]


title: 29_unstim [209609]


title: 7L [209607]


title: 7V [209608]


title: 29V [209611]


title: 18L [209587]


title: 18_unstim [209586]


title: 41_unstim [209581]


title: 40V [209580]


title: 39V [209577]


title: 37V [209571]


title: 40L [209579]


title: 39L [209576]


title: 38L [209573]


title: 40_unstim [209578]


title: 38_unstim [209572]


title: 41V [209583]


title: 7_unstim [209606]


title: 36V [209568]


title: 38V [209574]


title: 35_unstim [209563]


title: 35V [209565]


title: 35L [209564]


title: 36_unstim [209566]


title: 37_unstim [209569]


title: 36L [209567]


title: 30V [209562]


title: 26L [209552]


title: 30_unstim [209560]


title: 26_unstim [209551]


title: 28_unstim [209557]


title: 27L [209555]


title: 28L [209558]


title: 30L [209561]


title: 37L [209570]


title: 25V [209550]


title: 27V [209556]


title: 28V [209559]


title: 26V [209553]


title: 22V [209541]


title: 24V [209547]


title: 25_unstim [209548]


title: 24_unstim [209545]


title: 23V [209544]


title: 23L [209543]


title: 22L [209540]


title: 22_unstim [209539]


title: 25L [209549]


title: 23_unstim [209542]


title: 20_unstim [209533]


title: 20L [209534]


title: 15_unstim [209524]


title: 19L [209531]


title: 19_unstim [209530]


title: 10V [209520]


title: 9L [209516]


title: 21V [209538]


title: 15L [209525]


title: 21L [209537]


title: 10L [209519]


title: 3V [209514]


title: 1L [209510]


title: 1_unstim [209509]


title: 3_unstim [209512]


title: 1V [209511]


title: 3L [209513]


title: small unilamellar vesicles, biological rep 3

status: Public on Feb 27 2014

city: Nashville

first: Kasey

middle: C

last: Vickers

state: TN

address: 2220 Pierce Ave   358 PRB

department: Medicine

institute: Vanderbilt Univ. School of Medicine

hyb_protocol: Samples were hybridized to GeneChip Human Gene 1.0 ST whole genome arrays (28,869 genes) (Affymetrix), washed, stained (Affymetrix Fluidics Station)

data_processing:
High-level and low-level transcriptomics analyses were carried out using GeneSpring GX12.0 (Agilent) (www.genomics.agilent.com). ExonPLIER16 summarization algorithm, quantile normalization, baseline transformation to all samples.
ExonExprChip.HuGene-1_0-st-v1_na30_1_hg19

source_name: 1-palmitoyl-2-linoleoyl phosphatidylcholine (PLPC; Avanti Polar Lipids, Alabaster, AL)

label_protocol: Gene expression profiling was assessed using Affymetrix GeneChip microarray assays according to the manufacturer’s protocol (Affymetrix). Briefly, 1 ug of total RNA was reverse transcribed (T-7 dT primers), amplified and biotinylated (Affymetrix IVT Labeling Kit).

growth_protocol: Human coronary artery endothelial cells (HCAEC) and human umbilical vein endothelial cells (HUVEC), passages 3 to 6, were grown in MesoEndo Growth Medium (Cell Applications, Inc. San Diego CA) containing 5% (v/v) serum and plated 24 hours before use in 12 well plates at a density of 1x105 cells per well.

extract_protocol: The cells were harvested and total RNA was isolated using Qiazol miRNAeasy kits (Qiagen) and quantified by spectrophotometry

treatment_protocol: HCAEC were incubated at 37 °C for 16-24 h with SUV (final PLPC concentration 3 mmol/L), lipid-free apoA-I (final concentration 1 mg /ml), rHDL (final apoA-I concentration 1 mg/ml), native HDL (final total protein concentration 1 mg/ml) or PBS.

value: Human Coronary Artery Endothelial Cells

tag: agent

value: small unilamellar vesicles


title: control, biological rep 5

source_name: PBS

value: control


title: rHDL, biological rep 4

source_name: Human plasma (apoA-I) & 1-palmitoyl-2-linoleoyl phosphatidylcholine (PLPC; Avanti Polar Lipids, Alabaster, AL)

value: rHDL


title: small unilamellar vesicles, biological rep 1


title: Native HDL, biological rep 4

source_name: Human plasma

value: Native HDL


title: Native HDL, biological rep 5


title: small unilamellar vesicles, biological rep 2


title: Native HDL, biological rep 2


title: control, biological rep 4


title: Lipid-free apolipoprotein A-I, biological rep 4

value: Lipid-free apolipoprotein A-I


title: rHDL, biological rep 2


title: Native HDL, biological rep 3


title: control, biological rep 3


title: small unilamellar vesicles, biological rep 4


title: Lipid-free apolipoprotein A-I, biological rep 5


title: rHDL, biological rep 3


title: control, biological rep 2


title: rHDL, biological rep 1


title: small unilamellar vesicles, biological rep 5


title: rHDL, biological rep 5


title: control, biological rep 1


title: Native HDL, biological rep 1


title: BC4885 CD40-activated B cell

status: Public on Jan 14 2014

city: Cologne

first: Alexander

last: Shimabukuro-Vornhagen

address: Kerpener Str. 62

department: Department I of Internal Medicine

institute: University Hospital of Cologne

hyb_protocol: Hybridization and washing was performed following standard procedures for Affymetrix HG-U133A arrays (www.affymetrix.com) on a GeneChip Fluidic station 400, using the EukGe-WS2v4 protocol.

scan_protocol: Scanning was performed twice with filter set at 570 nm on an Agilent gene array scanner (Affymetrix).

data_processing: MAS5.0 (Affymetrix) was used for raw data measurement and quality control. dChip 2006 was used for data normalization, quality control and data analysis.

source_name: peripheral blood

label_protocol: Synthesis of biotin labeled cRNA was performed with BioArray HighYield RNA TranscriptLabeling Kit (ENZO) following standard procedures.

growth_protocol: For CD40-activation the purified CD19-positive B cells were stimulated via CD40 by means of  NIH3T3 cells transfected with CD40L in 6-well plates in medium containing 45% Dulbecco modified Eagle medium supplemented with 10% fetal calf serum, 2 mM glutamine, and 15 ug/mL gentamicin.

extract_protocol: Immature monocyte-derived DC were harvested on day 7, lyzed in TRIzol and stored at 80°C until further processing. RNA was extracted from cell lyzates with chloroform/isopropanol method, and was clean-uped in silica columns (Qiagen). The quality of the isolated RNA was determined by measuring the A260/280 ratio and the integrity of the ribosomal 28s and 18s bands were determined by agarose-gel electrophoresis.

treatment_protocol: Human B cells were purified from buffy coats using CD19 MACS.

tag: donor id

tag: tissue

value: peripheral blood

value: CD19-positive B cells

tag: stimulated with

tag: cell status


title: Lipid-free apolipoprotein A-I, biological rep 1

tag: cell type


title: BC4884 CD40-activated B cell


title: BC4870 resting B cells

value: Resting


title: Lipid-free apolipoprotein A-I, biological rep 2


title: BC4884 resting B cells


title: BC4869 CD40-activated B cell


title: BC4869 resting B cells


title: BC4870 CD40-activated B cell


title: Lipid-free apolipoprotein A-I, biological rep 3


title: 4F_Day8, biological rep1

status: Public on Jan 11 2014

city: Barcelona

first: Miki

last: Ebisuya

address: PRBB Building, C/ Dr. Aiguader, 88

department: EMBL Barcelona

institute: EMBL

description:
4F_Day8-1
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 8.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol with Affymetrix Scanner 3000 7G

data_processing: The probeset signals were calculated using Agilent GeneSpring software.

label_protocol: Biotinylated cRNAs were prepared from 120 ng (rep1) or 300 ng (the others) total RNAs according to the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay manual.

growth_protocol: MEFs were maintained in Dulbecco's Modified Eagle's medium (DMEM) containing 10% foetal bovine serum (FBS).

extract_protocol: Total RNAs were extracted using the Qiagen RNeasy kit according to the manufacturer's protocol. On-column DNase digestion was performed.

treatment_protocol: MEFs were infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), three transcription factors (Oct4, Sox2 and Klf4) or GFP (control) at day 0.

value: mouse embryonic fibroblasts (MEFs)

tag: retrovirus

value: 4 transcription factors (Oct4, Sox2, Klf4 and c-Myc)

tag: time

value: day 8


title: 4F_Day6, biological rep1

description:
4F_Day6-1
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 6.

value: day 6


title: GFP_Day3, biological rep1

description:
GFP_Day3-1
Gene expression data from MEFs infected with retroviruses encoding GFP, day 3.

value: GFP

value: day 3


title: GFP_Day5, biological rep1

description:
GFP_Day5-1
Gene expression data from MEFs infected with retroviruses encoding GFP, day 5.

value: day 5


title: GFP_Day8, biological rep1

description:
GFP_Day8-1
Gene expression data from MEFs infected with retroviruses encoding GFP, day 8.


title: 4F_Day4, biological rep2

description:
4F_Day4-2
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 4.

value: day 4


title: 4F_Day4, biological rep1

description:
4F_Day4-1
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 4.


title: GFP_Day1, biological rep1

description:
GFP_Day1-1
Gene expression data from MEFs infected with retroviruses encoding GFP, day 1.

value: day 1


title: 4F_Day3, biological rep2

description:
4F_Day3-2
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 3.


title: 4F_Day6, biological rep2

description:
4F_Day6-2
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 6.


title: 4F_Day2, biological rep2

description:
4F_Day2-2
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 2.

value: day 2


title: GFP_Day3, biological rep2

description:
GFP_Day3-2
Gene expression data from MEFs infected with retroviruses encoding GFP, day 3.


title: 4F_Day8, biological rep2

description:
4F_Day8-2
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 8.


title: 4F_Day5, biological rep2

description:
4F_Day5-2
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 5.


title: GFP_Day5, biological rep2

description:
GFP_Day5-2
Gene expression data from MEFs infected with retroviruses encoding GFP, day 5.


title: 4F_Day1, biological rep2

description:
4F_Day1-2
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 1.


title: 4F_Day1, biological rep1

description:
4F_Day1-1
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 1.


title: 4F_Day2, biological rep1

description:
4F_Day2-1
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 2.


title: 4F_Day5, biological rep1

description:
4F_Day5-1
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 5.


title: 4F_Day0, biological rep2

description:
4F_Day0-2
Gene expression data from MEFs, day 0.

source_name: MEFs, day 0

value: day 0


title: GFP_Day1, biological rep2

description:
GFP_Day1-2
Gene expression data from MEFs infected with retroviruses encoding GFP, day 1.


title: GFP_Day8, biological rep2

description:
GFP_Day8-2
Gene expression data from MEFs infected with retroviruses encoding GFP, day 8.


title: 4F_Day3, biological rep1

description:
4F_Day3-1
Gene expression data from MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), day 3.


title: 4F_Day0, biological rep1

description:
4F_Day0-1
Gene expression data from MEFs, day 0.


title: E2-2

status: Public on Jan 01 2014

city: Tokyo

first: zhu

last: yun

address: takanawa 4-21-12

institute: scinet company

hyb_protocol: The arrays were hybridized at 65℃ overnight

scan_protocol: The arrays were scaned using FLA-8000 (FUJIFILM).

data_processing: The signal intensities were quantified using ArrayGauge software (FUJIFILM). The ratio of the signal intensity for E2- or ABE-treated sample to that for the control sample was calculated for each gene, and then normalized using control genes .

source_name: E2-treated Cells

label_protocol: Five mg of total RNA was reverse-transcribed and labeled with cy3 (GE Healthcare) using SuperScript Indirect cDNA labeling system (Invitrogen).

extract_protocol: Total RNA was extracted using RNeasy plus mini kit (QIAGEN).

value: breast cancer


title: naïve B cells CD40L/IL-21; donor 4

status: Public on Jan 09 2014

city: Darlinghurst

first: Stuart

last: Tangye

state: NSW

address: 384 Victoria St

department: Immunology

institute: Garvan Institute for Medical Research

description: RNA from normal naïve B cells stimulated with CD40L + IL-21

hyb_protocol: Hybridization was performed using the Affymetrix GeneChip® Hybridization, Wash and Stain kit.

scan_protocol: Scanning was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia) according to the Affymetrix GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731).

data_processing: Microarray data was analysed using GenePettern software (v3.2.3, Broad Institute). A custom contrast was then created to display genes with increased expression in the presence of IL-21 in normal B cells, but not in STAT3 deficient B cells

source_name: naïve B cells from normal donors

label_protocol: The Affymetrix GeneChip Whole Transcript Sense Target Labelling Assay was performed to generate amplified and biotinylated sense-strand DNA targets from mRNA. Briefly, cDNA was synthesised and amplified from RNA samples, then antisense RNA (cRNA) transcribed. The transcribed cRNA was then purified and used as a template for the synthesis of single-stranded DNA in the sense orientation. The sense strand DNA underwent further purification, fragmentation and labelling steps according to the Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay protocol.

growth_protocol: Human naïve B cells were cultured in RPMI1640 containing 10% FCS for 4 days

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: B cells were stimulated with recombinant CD40 ligand alone or together with IL-21 (50 ng/mL)

tag: diagnosis

value: healthy

value: naïve B cells


title: E2-1


title: naïve B cells CD40L/IL-21; AD-HIES pt 2

description: RNA from AD-HIES patient naïve B cells stimulated with CD40L + IL-21

source_name: naïve B cells from AD-HIES patients

value: Autosomal dominant hyper IgE syndrome (AD-HIES)


title: E2-3


title: 21_unstim [209536]

tag: stimulation

value: Unstim

tag: total rna (ug)

tag: rna concentration (ug/ul)

tag: cd4 %

value: Caucasian

tag: Sex

value: F


title: naïve B cells CD40L alone; donor 1

description: RNA from normal naïve B cells stimulated with CD40L alone


title: naïve B cells CD40L/IL-21; AD-HIES pt 3


title: naïve B cells CD40L alone; AD-HIES pt 1

description: RNA from AD-HIES patient naïve B cells stimulated with CD40L alone


title: naïve B cells CD40L/IL-21; donor 3


title: naïve B cells CD40L alone; donor 2


title: naïve B cells CD40L/IL-21; AD-HIES pt 1


title: naïve B cells CD40L alone; AD-HIES pt 3


title: naïve B cells CD40L alone; donor 4


title: naïve B cells CD40L/IL-21; donor 2


title: naïve B cells CD40L/IL-21; donor 1


title: naïve B cells CD40L alone; AD-HIES pt 2


title: naïve B cells CD40L alone; donor 3


title: Human Th0 cell clone,16h, biological rep5

status: Public on Dec 20 2013

city: Pula

first: Mauro

last: Pala

state: Cagliari

address: Parco Scientifico Polaris Loc. Pixinamanna

country: Italy

hyb_protocol: Following fragmentation, biotinylated cRNA probe (25 ng/uL in 100 uL hybridizationconcktail) were hybridized for 17 hr at 45C on GeneChip Human 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (protocol FS450_0007).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console, R and Bioconductor.

label_protocol: Biotinylated cRNA probes were synthesized using the GeneChip Whole Transcript Sense Target Labeling Assay Kit (Affymetrix) following the manufacturer's instructions.

growth_protocol: T cell clones from CD4+ cells by limiting dilution at 0.3 cells/well in the presence of a feeder cell mixture and soluble anti-CD3 mAbs growth in X-vivo15 medium (BioWhittaker, Verviers, Belgium) supplemented with 5% pooled human AB serum (BioWhittaker), 100 U/mL penicillin/streptomycin (BioWhittaker). At day 3, IL-2 (40 U/mL; Chiron, Italia, Milan, Italy) was added.  T cell clones were restimulated every 14 days with feeder cell mixture and soluble anti-CD3 mAbs (1 µg/mL). Between stimulations with feeder cells,  T cell clones were expanded with rhIL-2 (40 U/mL). Once the T cell clones had been established, rhIL-15 (5 ng/mL, R&D System, Minneapolis, MN, USA) was added at every change of medium as a Tr1 cell growth factor

extract_protocol: RNA from Tr1 and TH0 cell clones unstimulated  or stimulated  was extracted with RNeasy Mini kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions.

treatment_protocol: Human Tr1 and Th0 cell clones were left unstimulated or were for 6 and 16 h with immobilized anti-CD3 mAb (10 µg/mL; Jansen-Cilag) and soluble anti-CD28 mAb (1 µg/mL, BD Pharmingen) in complete medium at a concentration of 10^6 T cells/ml

value: peripheral blood

value: Human Th0 cell clone

value: stimulated with immobilized anti-CD3 and soluble anti-CD28 mAbs


title: Human Th0 cell clone, 6h,biological  rep6

description: T cell clones from CD4+ cells by limiting dilution at 0.3 cells/well in the presence of a feeder cell mixture and soluble anti-CD3 mAbs


title: Human Tr1 cell clone, 6h, biological rep4

value: Human Tr1 cell clone


title: Human Th0 cell clone,16h, biological rep6


title: Human Th0 cell clone,16h, biological rep4


title: Human Tr1 cell clone, 6h, biological rep3


title: Human Th0 cell clone, 6h, biological rep3


title: Human Th0 cell clone, 6h, biological rep2


title: Human Tr1 cell clone, 16h, biological rep3


title: Human Th0 cell clone, 6h, biological rep1


title: Human Tr1 cell clone, 6h, biological rep2


title: Human Tr1 cell clone, 16h, biological rep1


title: Human Th0 cell clone, 0 min, biological rep10

value: 0 min


title: Human Th0 cell clone, 6h, biological rep5


title: Human Th0 cell clone,16h, biological rep1


title: Human Tr1 cell clone, 16h, biological rep4


title: Human Th0 cell clone, 0 min, biological rep9


title: Human Th0 cell clone, 0 min, biological rep11


title: Human Th0 cell clone,16h, biological rep2


title: Human Tr1 cell clone, 0 min, biological rep3


title: Human Tr1 cell clone, 16h, biological  rep2


title: Human Tr1 cell clone, 6h, biological rep1


title: Human Th0 cell clone, 0 min, biological rep8


title: Human Th0 cell clone,16h, biological rep3


title: Human Th0 cell clone, 6h,biological  rep4


title: Human Tr1 cell clone, 0 min, biological rep4


title: Human Tr1 cell clone, 0 min, biological rep5


title: Human Th0 cell clone, 0 min, biological rep7


title: Human Th0 cell clone, 0 min,biological  rep6


title: Human Th0 cell clone, 0 min, biological rep3


title: Human Th0 cell clone, 0 min, biological rep1


title: Human Th0 cell clone, 0 min, biological rep5


title: Human Th0 cell clone, 0 min, biological rep4


title: Human Tr1 cell clone, 0 min, biological rep1


title: Human Tr1 cell clone, 0 min, biological rep2


title: A0R_d0_rep1

status: Public on Dec 18 2013

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

description: Gene expression data from A459 cell line

hyb_protocol: Arrays were hybridized and washed according to the manufacturer's specifications (Affymetrix Inc., Santa Clara, CA, USA)

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Expression data was normalized, background corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console software Build 1.3.1.187.

source_name: A549 cell line

label_protocol: The samples were labeled according to the Affymetrix GeneChip WT Terminal Labeling protocol (Affymetrix UK Ltd., High Wycombe, UK).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAgen Hilden). RNA quality was approved using the Agilent RNA 6000 Nano Kit (Agilent Technologies).

tag: cell line

tag: rounds of in vivo selection

tag: 5-azacytidine status

value: untreated


title: H3R_d0_rep1

description: Gene expression data from highly metastatic HTB56 cell line

source_name: HTB56 cell line


title: H0R_d0_rep2

description: Gene expression data from HTB56 cell line


title: H3R_d0_rep3


title: H3R_d0_rep2


title: A3R_d0_rep3

description: Gene expression data from highly metastatic A459 cell line


title: H0R_d0_rep3


title: A0R_d0_rep3


title: A3R_d0_rep1


title: Th2_Media#2

status: Public on Dec 17 2013

description: Aria sorted CCR7Lo CD45RO+ CD25- cells stimulated with anti-CD3/CD28 beads (2 beads/cell) for 36hrs at 2e5c/well

data_processing: Samples were RMA normalized using Affymetrix Power Tools (gcbg background correction, quantile normalization, median polish) on the annotated set of probesets. Unannotated probesets were removed prior to normalization (see supplemental .MPS file)

growth_protocol: Human CD45RO+ CCR7lo CD25- effector memory subsets (FACS-sorted as detailed above in summary section) were cultured in IMDM media supplemented with 10% FBS, 1% L-glutamine, 1% non-essential amino acids, 1% sodium pyruvate, 1% HEPES, and 1% Pen-Strep. 2e5 cells were activated using anti-CD3/anti-CD28-coated beads at a ratio of 1 bead: 1 cell. No other cytokines or additives were included in the cultures. Cells were cultured for 36 hours prior to harvest and cell lysis.

tag: cell subset

value: CCR6- CCR4hi CXCR3+


title: H0R_d0_rep1


title: Th2_Media#3


title: Th17.1_Media#3

value: CCR6+ CCR4lo CXCR3-


title: A0R_d0_rep2


title: Th17.1_Media#2


title: A3R_d0_rep2


title: Th1_Media#2

value: CCR6- CCR4lo CXCR3+


title: Th17_Media#3

value: CCR6+ CCR4hi CXCR3-


title: Th1_Media#3


title: Human Th0 cell clone, 0 min, biological rep2

tag: treatment


title: germinal center B cells 3

status: Public on Dec 01 2013

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: unsupported Human Gene 1.0 ST Array CDF Files
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

source_name: germinal center B cells

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

extract_protocol: RNA was amplified using the One-direct-Kit from NUGEN applied for 250 microdissected cells

treatment_protocol: Cells were microdissected from HE stained kryosections

value: germinal center B cells


title: germinal center B cells 5


title: Infected with H37Rv and treated with 1,25D, replicate 2

status: Public on Nov 28 2013

city: Montreal

first: John

last: White

state: QC

address: 3655 Prom. Sir William Osler

institute: McGill University

description:
Monocyte cell line terminally differentated into macrophages by PMA treatment
Gene expression data from macrophages

hyb_protocol: cDNA was hybridized onto Affymetrix Human Gene 1.0 ST chips

scan_protocol: Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm

data_processing: Data was processed using Flexarray v1.6.1

label_protocol: Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.

growth_protocol: Cells were grown and infected in RPMI-1640 with 10%FBS

extract_protocol: Trizol-choloform extraction

treatment_protocol: Cells were differentiated with PMA


title: Infected with H37Rv and treated with 1,25D, replicate 1


title: Th17_Media#2


title: germinal center B cells 4


title: Infected with H37Rv and treated with 1,25D, replicate 3


title: germinal center B cells 2


title: Infected with H37Rv, replicate 3

source_name: Infected with H37Rv, replicate 3


title: Infected with H37Rv, replicate 1

source_name: Infected with H37Rv, replicate 1


title: Uninfected, replicate 3

source_name: Uninfected, replicate 3


title: germinal center B cells 1


title: Uninfected treated with 1,25D, replicate 2


title: Uninfected treated with 1,25D, replicate 3


title: Uninfected, replicate 1

source_name: Uninfected, replicate 1


title: Uninfected, replicate 2

source_name: Uninfected, replicate 2


title: Uninfected treated with 1,25D, replicate 1


title: Infected with H37Rv, replicate 2

source_name: Infected with H37Rv, replicate 2


title: Monocyte Donor 6

status: Public on Nov 22 2013

city: Omaha

first: Jessica

last: Winkler

address: 985800 Nebraska Medical Center- DRC I

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

description: Gene expression data from monocytes not stimulated with M-CSF

hyb_protocol: Overnight hybridization using the Affymetrix hybridization over at 42oC. 500ng of cDNA was used

scan_protocol: Affymetrix GeneChip Scanner 3000 7G generated the resulting array image

data_processing: RMA normalization followed by Partek analysis

source_name: Monocyte isolated from human PMCs

label_protocol: Biotin labled using definded Affymetrix protocol

growth_protocol: primary human monocytes were cultured Macrophage serum free media (Invitrgen) supplemented with 5% Nutridoma (Roche) and 10mM HEPES.

extract_protocol: trizol

treatment_protocol: Monocytes were differentiated by adding 10uM Macrophage colony stimulating factor

value: Immune cell

tag: source

value: Human blood samples

value: not stimulated with M-CSF


title: Macrophage Donor 5

description: Gene expression data from monocytes stimulated with M-CSF

source_name: Monocyte derived macrophage

value: stimulated with M-CSF


title: Monocyte Donor 2


title: Macrophage Donor 2


title: Macrophage Donor 3


title: Monocyte Donor 4


title: Macrophage Donor 6


title: Monocyte Donor 1


title: Monocyte Donor 3


title: Monocyte Donor 5


title: Fibroblast HFFF2 cocultured with epithelial MDAMB231 cells replicate-4

status: Public on Nov 21 2013

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

description: human cells cell cultured- tumors cell lines, human fibroblast strains

hyb_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc.  using standard Affymetrix protocols.

data_processing: We used R package aroma.affymetrix to analyze raw data. Chip type is HuGene-1_0-st-v1, and we used HuGene-1_0-st-v1.r3 as annotation CDF. After RMA background correction and quantile normalization we got probe-level intensity values as shown in the data matrix. We ran quality assessment to check data (not shown). In the further analysis we averaged intensity values for genes with multiple probes, then took log2 tranformed values for each gene.

extract_protocol: Total RNA was isolated using the miRNeasy Mini kit (Qiagen) according to the manufacturer's protocol. The optional on-column DNA digestion was performed, using the RNase-free DNase Set (Qiagen).

tag: cell


title: Macrophage Donor 1


title: Fibroblast HFFF2 cocultured with epithelial MDAMB231 cells replicate-3

scan_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc.  using standard Affymetrix protocols.


title: Fibroblast HFFF2 cocultured with epithelial MDAMB231 cells replicate-1

label_protocol: cDNA synthesis, labeling, hybridization and scanning was performed by Expression Analysis Inc.  using standard Affymetrix protocols.


title: Fibroblast HFFF2 cocultured with epithelial Cal51 cells replicate-2


title: Fibroblast HFFF2 monocultured replicate-4

value: Fibroblast HFFF2 monocultured


title: Fibroblast HFFF2 cocultured with epithelial MDAMB231 cells replicate-2


title: Macrophage Donor 4


title: Fibroblast HFFF2 cocultured with epithelial Cal51 cells replicate-4


title: Fibroblast HFFF2 monocultured replicate-2


title: Fibroblast HFFF2 cocultured with epithelial Cal51 cells replicate-3


title: Fibroblast HFF1 cocultured with epithelial Cal51 cells replicate-3


title: Fibroblast HFF1 cocultured with epithelial Cal51 cells replicate-4


title: Fibroblast HFF1 cocultured with epithelial MDAMB231 cells replicate-1


title: Fibroblast HFF1 monocultured replicate-4

value: Fibroblast HFF1 monocultured


title: Fibroblast HFFF2 monocultured replicate-3


title: Fibroblast HFFF2 cocultured with epithelial Cal51 cells replicate-1


title: Fibroblast HFF1 monocultured replicate-2


title: Fibroblast HFF1 monocultured replicate-3


title: Fibroblast HFFF2 monocultured replicate-1


title: Fibroblast HFF1 monocultured replicate-1


title: Fibroblast HFF1 cocultured with epithelial MDAMB231 cells replicate-3


title: Fibroblast HFF1 cocultured with epithelial MDAMB231 cells replicate-2


title: Fibroblast HFF1 cocultured with epithelial Cal51 cells replicate-1


title: Fibroblast Wi38 cocultured with epithelial MDAMB231 cells replicate-4


title: Fibroblast Wi38 cocultured with epithelial Cal51 cells replicate-3


title: Fibroblast Wi38 cocultured with epithelial Cal51 cells replicate-2


title: Fibroblast Wi38 monocultured replicate-4

value: Fibroblast Wi38 monocultured


title: Fibroblast Wi38 cocultured with epithelial Cal51 cells replicate-1


title: Fibroblast Wi38 monocultured replicate-3


title: Fibroblast CCD1112Sk cocultured with epithelial MDAMB231 cells replicate-1


title: Fibroblast Wi38 cocultured with epithelial MDAMB231 cells replicate-1


title: Fibroblast Wi38 monocultured replicate-1


title: Fibroblast Wi38 cocultured with epithelial MDAMB231 cells replicate-2


title: Fibroblast CCD1112Sk cocultured with epithelial MDAMB231 cells replicate-2


title: Fibroblast Wi38 monocultured replicate-2


title: Fibroblast CCD1112Sk cocultured with epithelial MDAMB231 cells replicate-3


title: Fibroblast CCD1112Sk monocultured replicate-3

value: Fibroblast CCD1112Sk monocultured


title: Fibroblast CCD1112Sk cocultured with epithelial Cal51 cells replicate-2


title: ∆pfap2-g, 9h post-invasion cDNA

status: Public on Nov 06 2013

city: New York

first: Bjorn

middle: FC

last: Kafsack

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine

description: Shared cDNA reference pool

hyb_protocol: See Kafsack et al. Malaria J 2012 (PMID: 22681930 ) and Painter et al. Methods Mol Biol 2013 (PMID: 22990780) for detailed methods

data_processing:
The data were normalized using the Agilent Feature Extractor protocol 9.5.3.1 for two color gene expression (GE2-v5_95_Feb07_no_spikein).
The specific settings are included in the header for each supplementary file.

organism: Plasmodium falciparum

source_name: ∆pfap2-g, 9h post-invasion cDNA

growth_protocol: Parasites were double synchronized and used to intiate cultures at ~10% parasitemia, media was changed every 12h

tag: strain

tag: timepoint

value: 9h post-invasion

source_name: Shared cDNA reference pool

tag: reference

value: Shared cDNA reference pool


title: ∆pfap2-g, 39h post-invasion cDNA

description: Shared cDNA reference pool

scan_protocol: See Kafsack et al. Malaria J 2012 (PMID: 22681930 ) and Painter et al. Methods Mol Biol 2013 (PMID: 22990780) for detailed methods

source_name: ∆pfap2-g, 39h post-invasion cDNA

value: 39h post-invasion


title: Fibroblast CCD1112Sk monocultured replicate-1


title: Fibroblast CCD1112Sk monocultured replicate-2


title: ∆pfap2-g, 15h post-invasion cDNA

description: Shared cDNA reference pool

source_name: ∆pfap2-g, 15h post-invasion cDNA

label_protocol: See Kafsack et al. Malaria J 2012 (PMID: 22681930 ) and Painter et al. Methods Mol Biol 2013 (PMID: 22990780) for detailed methods

value: 15h post-invasion


title: ∆pfap2-g, 21h post-invasion cDNA

description: Shared cDNA reference pool

source_name: ∆pfap2-g, 21h post-invasion cDNA

extract_protocol: See Kafsack et al. Malaria J 2012 (PMID: 22681930 ) and Painter et al. Methods Mol Biol 2013 (PMID: 22990780) for detailed methods

value: 21h post-invasion


title: Fibroblast CCD1112Sk cocultured with epithelial Cal51 cells replicate-3


title: ∆pfap2-g, 33h post-invasion cDNA

description: Shared cDNA reference pool

source_name: ∆pfap2-g, 33h post-invasion cDNA

value: 33h post-invasion


title: ∆pfap2-g, 45h post-invasion cDNA

description: Shared cDNA reference pool

source_name: ∆pfap2-g, 45h post-invasion cDNA

value: 45h post-invasion


title: 3D7-A clone E5, 33h post-invasion cDNA

description: Shared cDNA reference pool

source_name: 3D7-A clone E5, 33h post-invasion cDNA


title: 3D7-A clone E5, 45h post-invasion cDNA

description: Shared cDNA reference pool

source_name: 3D7-A clone E5, 45h post-invasion cDNA


title: clone F12, 45h post-invasion cDNA

description: Shared cDNA reference pool

source_name: clone F12, 45h post-invasion cDNA


title: 3D7-A clone E5, 39h post-invasion cDNA

description: Shared cDNA reference pool

source_name: 3D7-A clone E5, 39h post-invasion cDNA


title: ∆pfap2-g, 3h post-invasion cDNA

description: Shared cDNA reference pool

source_name: ∆pfap2-g, 3h post-invasion cDNA

value: 3h post-invasion


title: ∆pfap2-g, 27h post-invasion cDNA

description: Shared cDNA reference pool

source_name: ∆pfap2-g, 27h post-invasion cDNA

value: 27h post-invasion


title: 3D7-A clone E5, 27h post-invasion cDNA

description: Shared cDNA reference pool

source_name: 3D7-A clone E5, 27h post-invasion cDNA


title: Fibroblast CCD1112Sk cocultured with epithelial Cal51 cells replicate-1


title: Fibroblast Wi38 cocultured with epithelial MDAMB231 cells replicate-3


title: clone F12, 33h post-invasion cDNA

description: Shared cDNA reference pool

source_name: clone F12, 33h post-invasion cDNA


title: clone F12, 3h post-invasion cDNA

description: Shared cDNA reference pool

source_name: clone F12,3h post-invasion cDNA


title: clone F12, 39h post-invasion cDNA

description: Shared cDNA reference pool

source_name: clone F12, 39h post-invasion cDNA


title: clone F12, 9h post-invasion cDNA

description: Shared cDNA reference pool

source_name: clone F12, 9h post-invasion cDNA


title: clone F12, 27h post-invasion cDNA

description: Shared cDNA reference pool

source_name: clone F12, 27h post-invasion cDNA

source_name: Shared cDNA reference pool


title: 3D7-A clone E5, 21h post-invasion cDNA

description: Shared cDNA reference pool

source_name: 3D7-A clone E5, 21h post-invasion cDNA


title: 3D7-A clone E5, 15h post-invasion cDNA

description: Shared cDNA reference pool

source_name: 3D7-A clone E5, 15h post-invasion cDNA


title: clone F12, 15h post-invasion cDNA

description: Shared cDNA reference pool

source_name: clone F12, 15h post-invasion cDNA


title: clone F12, 21h post-invasion cDNA

description: Shared cDNA reference pool

source_name: clone F12, 21h post-invasion cDNA


title: 3D7-A clone E5, 3h post-invasion cDNA

description: Shared cDNA reference pool

source_name: 3D7-A clone E5, 3h post-invasion cDNA


title: trout_18_rep1

status: Public on Nov 04 2013

city: Madrid

first: Mónica

last: Aguado-Urda

address: Avda. Puerta de Hierro s/n

department: Animal Health

institute: Complutense University of Madrid

description: Biological replicate 1 of 3. L. Garvieae str.8831 grown at 18 degrees celsius

hyb_protocol: Hybridization protocol followed was that suggested by Agilent´s according to the Two-color microarray-based prokaryote analysis protocol

scan_protocol: Image acquisition and scanning was done following Agilent's instruction and protocols (GE2_107_Sep09) on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS Normalization was done using BRB Array Express software

organism: Lactococcus garvieae

source_name: L. Garvieae 8831, 18C

label_protocol: A total of 5 ug of total RNA of each sample replicate was reverse transcripted and labeled by using the FairPlay III labeling kit (Agilent ) and according to the two color microarray-based prokaryote analysis protocol provided by the manufacturer except for the following: purification of the dye-coupled cDNA was performed by using QIAquick PCR purification kit (Qiagen). The yield and the specific activity of each labelling reaction were determined in a NanoDrop 1000 spectrophotometer.

growth_protocol: L. garvieae strains were grown aerobically in MRS broth at different temperatures (18ºC, 29ºC and 37ºC) and harvested at the mid-log phase (OD600 ~ 0.9) for RNA extraction.

extract_protocol: Total RNA from L. garvieae strains was isolated from three independent biological replicates of each temperature condition by using RNeasy protect bacteria mini kit (Qiagen) according to the manufacturer’s protocol. The quality and concentration of RNA was determined by using the RNA 6000 NanoKit on the Bioanalyzer 2100 (Agilent). Only high- quality RNA samples (RIN > 9) were used for labeling and hybridization.

tag: temperature

value: 18 degrees celsius

source_name: Reference control

value: Equimolar mixture of 21881 & 8831 strains at 29C


title: trout_18_rep3

description: Biological replicate 3 of 3. L. Garvieae str.8831 grown at 18 degrees celsius


title: trout_18_rep2

description: Biological replicate 2 of 3. L. Garvieae str.8831 grown at 18 degrees celsius


title: CD103+ Sirpa+ intestinal DC 3

status: Public on Nov 01 2013

city: Palo Alto

first: Katharina

last: Lahl

address: 3801 Miranda Avenue

institute: Stanford University

description: Transcriptional profiling of sorted human intestinal dendritic cells

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Human Exon 1.0 ST Arrays and scanned by Expression Analysis, Inc.

scan_protocol: Array scanning was performed by Expression Analysis, Inc. according to the manufacturer's instruction

data_processing: GeneSpring GX 11.5 and Partek Genomic Suite (6.6) were used for processing and analyzing the data. Genespring preprocessing and default normalization (RMA-16) was applied to each dataset. Chp files were generated by Expression Analysis, Inc.

source_name: De-identified human subject

label_protocol: Single-stranded cDNA was generated from amplified cRNA (using Ambion WT Expression Kit) and then fragmented/labeled with the Affymetrix GeneChip WT Terminal Labeling and Controls Kit, performed by Expression Analysis, Inc.

extract_protocol: Total RNA was isolated from sorted human gut DC subsets using Qiagen RNeasy Plus Micro kit following manufacturer’s protocol

tag: tissue

value: Small Intestine


title: CD103+ Sirpa+ intestinal DC 5


title: CD103+ Sirpa- intestinal DC 2


title: CD103+ Sirpa- intestinal DC 3


title: SB-KMS-KS1

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

institute: Charité - Universitätsmedizin Berlin

description: primary Ewing sarcoma cell line SB-KMS-KS1, passage 22

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: RMA normalization.

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol: Cell lines were grown in plastic cell culture flasks in a humidified incubator at 37°C in 5% CO2 atmosphere in RPMI 1640 media containing 10% heat-inactivated fetal bovine serum, 1% glutamine, 100 µg/mL gentamycin and 200 mg/dl D-glucose .

extract_protocol: RNA was isolated using the RNeasy RNA isolation kit according to the manufacturer´s instructions.


title: CD103+ Sirpa+ intestinal DC 2


title: CD103+ Sirpa- intestinal DC 1


title: CD103+ Sirpa+ intestinal DC 4


title: CD103- Sirpa+ intestinal DC 1


title: SB-KMS-MJ3

description: primary Ewing sarcoma cell line SB-KMS-MJ3, passage 6


title: CD103+ Sirpa+ intestinal DC 1


title: A673 rep1

description: Ewing sarcoma cell line A673 with control siRNA treatment

source_name: Ewing sarcoma cell line A673

value: Ewing sarcoma cell line A673, treated with control siRNA


title: CD103- Sirpa+ intestinal DC 3


title: SB-KMS-DA1

description: primary Ewing sarcoma cell line SB-KMS-DA1, passage 3


title: CD103- Sirpa+ intestinal DC 2


title: S2085_MuTG-AS

description: stomach associated sarcoma

source_name: stomach associated sarcoma

value: stomach associated sarcoma


title: A673 rep2

description: Ewing sarcoma cell line A673, passage 14

value: Ewing sarcoma cell line A673, wild type


title: MPI-932_post_GC_B_cells

city: Leipzig

first: Maciej

last: Rosolowski

address: Härtelstr. 16-18

institute: Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

hyb_protocol: Affymetrix hybridization was carried on U133A GeneChips according to the manufacturer's recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter

scan_protocol: After hybridization of night (16 hours, 45° C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500)

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260)

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation

extract_protocol: Post GC memory B cells were isolated from peripheral blood samples of healthy individuals. For the isolation, FACS sorting employing antibodies against CD19 and CD27 was used. RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)

tag: type

tag: tumor


title: MPI-935_post_GC_B_cells


title: MPI-934_post_GC_B_cells


title: MPI-937_post_GC_B_cells


title: MPI-936_post_GC_B_cells


title: MPI-930_post_GC_B_cells


title: MPI-933_post_GC_B_cells


title: MPI-931_post_GC_B_cells


title: MPI-928_naive_B_cells

extract_protocol: Naive B cells were isolated from peripheral blood samples of healthy individuals. For the isolation, FACS sorting employing antibodies against CD19 and IgD was used. RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)


title: 3D7-A clone E5, 9h post-invasion cDNA

description: Shared cDNA reference pool

source_name: 3D7-A clone E5, 9h post-invasion cDNA


title: MPI-924_naive_B_cells


title: MPI-922_GC_B_cells

extract_protocol: GC B cells were isolated from suspended tonsillar cells of healthy individuals. For the isolation, FACS sorting employing antibodies against CD20 and CD38 was used. RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)


title: MPI-925_naive_B_cells


title: MPI-916_GC_B_cells


title: MPI-927_naive_B_cells


title: MPI-919_GC_B_cells


title: MPI-917_GC_B_cells


title: MPI-926_naive_B_cells


title: MPI-912_GC_B_cells


title: MPI-918_GC_B_cells


title: MPI-923_naive_B_cells


title: MPI-921_GC_B_cells


title: Fibroblast HFF1 cocultured with epithelial Cal51 cells replicate-2


title: MPI-929_naive_B_cells


title: MPI-911_GC_B_cells


title: MPI-914_GC_B_cells


title: MPI-910_GC_B_cells


title: MPI-913_GC_B_cells


title: MPI-920_GC_B_cells


title: MPI-915_GC_B_cells


title: Th17 cells_Donor 6_Control

city: Måløv

first: Klaus Stensgaard

last: Frederiksen

address: Novo Nordisk Park F9.1.07

department: Molecular Genetics

country: Denmark

institute: Novo Nordisk A/S

hyb_protocol: Affymetrix EukGE-WS2v5

scan_protocol: Affymetrix cel analysis

data_processing: Bioconductor/R RMA

source_name: Th17 cells

label_protocol: Affymetrix in vitro transcription

extract_protocol: Total RNA was isolated using the standard TRIzol protocol (Invitrogen, Carlsbad, CA), but with subsequent RNA clean-up of the water phase using the RNeasy Qiagen MinElute kit (Qiagen, Germantown, MD). The quality of the RNA was confirmed on the Agilent Bioanalyzer using RNA Nano chips (Agilent Technologies, Santa Clara, CA).

tag: donor

value: Donor 6

value: Control

tag: cell type


title: Th17 cells_Donor 8_Control

value: Donor 8


title: Th17 cells_Donor 7_Adalimumab

value: Donor 7

value: Adalimumab


title: Th17 cells_Donor 6_Adalimumab


title: Th17 cells_Donor 9_Control

value: Donor 9


title: Th17 cells_Donor 7_Control


title: Th17 cells_Donor 9_Adalimumab


title: Th17 cells_Donor 8_Adalimumab


title: Th17 cells_Donor 2_Adalimumab

value: Donor 2


title: Th17 cells_Donor 5_Control

value: Donor 5


title: Th17 cells_Donor 4_Control

value: Donor 4


title: Th17 cells_Donor 3_Adalimumab

value: Donor 3


title: Th17 cells_Donor 5_Adalimumab


title: Th17 cells_Donor 2_Control


title: Th17 cells_Donor 1_Control

value: Donor 1


title: Th17 cells_Donor 1_Adalimumab


title: Bcell_activated-gp120m_6hrs, AJ4

status: Public on Oct 17 2013

city: Frederick

first: Richard

last: Lempicki

state: MD

address: 1050 Boyles Street / P.O. Box B

institute: NCI-Frederick

hyb_protocol: Labeled cRNA was hybridized to the Affymetrix Human Gene 1.0 ST microarray according to the manufacturer's recommended standard protocol.

scan_protocol: Hybridized Affymetrix human gene microarrays were scanned according to the manufacturer's recommended standard protocol.

data_processing: Gene expression profiles were analyzed using Partek Genomic Suite 6.6.

source_name: Bcell, activated, gp120-, 6hrs

label_protocol: cRNA was labelled according to the manufacturer's recommended standard protocol for the Affymetrix Human Gene 1.0 ST microarray.

growth_protocol: Freshly isolated PBMCs were obtained from healthy donors and separated by Ficoll-Hypaque. Purified CD4+ T cells or B cells were obtained by negative selection using magnetic beads (StemCell Technologies, Vancouver, Canada). Cultured CD4+ cells were activated with OKT3, IL2 (20IU/ml) and all-trans retinoic acid (RA, 10nM) unless otherwise specified. RA was obtained from Sigma (St. Louis, MO) and discarded 1 month after reconstitution.

extract_protocol: cDNA of each sample was generated with Ambion WT Expression Kit.

treatment_protocol: Isolated B cells were treated with gp120 proteins of different affinity or mock protein. The exposure time points included 30min, 3hrs and 6hrs.

tag: disease status

value: healthy

value: B cells

tag: gp120 treatment

tag: time point


title: Th17 cells_Donor 4_Adalimumab


title: Bcell_mock_6hrs, AJ1

source_name: Bcell, mock, 6hrs

value: mock


title: Th17 cells_Donor 3_Control


title: Bcell_activated-gp120PP_6hrs, AJ3

source_name: Bcell, activated, gp120++, 6hrs


title: Bcell_activated-gp120m_6hrs, AH4


title: Bcell_activated_6hrs, AH2

source_name: Bcell, activated, 6hrs


title: Bcell_activated_6hrs, AJ2


title: Bcell_activated-gp120PP_6hrs, AG3


title: Bcell_mock_6hrs, AH1


title: Bcell_activated-gp120PP_6hrs, AH3


title: Bcell_activated-gp120m_6hrs, AG4


title: Bcell_mock_6hrs, AG1


title: Bcell_activated-gp120m_6hrs, AF10


title: Bcell_activated_6hrs, AG2


title: Bcell_activated_6hrs, AF8


title: Bcell_activated-gp120m_3hrs, AF7

source_name: Bcell, activated, gp120-, 3hrs


title: Bcell_activated_3hrs, AF5

source_name: Bcell, activated, 3hrs


title: Bcell_activated-gp120pp_6hrs, AF9


title: Bcell_activated-gp120m_30min, AF4

source_name: Bcell, activated, gp120-, 30min