title: Breast Cancer [BC0200]

description: miRNA


title: Breast Cancer [BC1387]

status: Public on Feb 13 2023

type: RNA

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

country: Japan

institute: Toray Industries, Inc.

description: miRNA

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol were attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

molecule: total RNA

organism: Homo sapiens

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: disease status

value: Breast Cancer

tag: tissue

value: Serum

tag: gender

value: Female

tag: age

tag: tumor stage (the pathological diagnosis of breast cancer

value: TNM Classification 8th edition):Tis

tag: lymphovascular invasion (the pathological diagnosis of breast cancer)

value: No

tag: suspicious lymph node metastasis (ultrasound finding)


title: Breast Cancer [BC0352]

description: miRNA

value: TNM Classification 8th edition):T1


title: Breast Cancer [BC1562]

description: miRNA

value: TNM Classification 8th edition):T2

value: Yes


title: Breast Cancer [BC1220]

description: miRNA


title: Breast Cancer [BC0525]

description: miRNA


title: Breast Cancer [BC0040]

description: miRNA


title: Breast Cancer [BC0589]

description: miRNA


title: Breast Cancer [BC1224]

description: miRNA


title: Breast Cancer [BC1185]

description: miRNA


title: Breast Cancer [BC0988]

description: miRNA


title: Breast Cancer [BC0242]

description: miRNA


title: Breast Cancer [BC1388]

description: miRNA


title: Breast Cancer [BC0419]

description: miRNA


title: Breast Cancer [BC0053]

description: miRNA

value: TNM Classification 8th edition):T3


title: Breast Cancer [BC1339]

description: miRNA


title: Breast Cancer [BC0648]

description: miRNA


title: Breast Cancer [BC1183]

description: miRNA


title: Breast Cancer [BC1160]

description: miRNA


title: Breast Cancer [BC0528]

description: miRNA


title: Breast Cancer [BC0037]

description: miRNA


title: Breast Cancer [BC1580]

description: miRNA


title: Breast Cancer [BC0086]

description: miRNA


title: Breast Cancer [BC0304]

description: miRNA


title: Breast Cancer [BC0309]

description: miRNA


title: Breast Cancer [BC0527]

description: miRNA


title: Breast Cancer [BC1128]

description: miRNA


title: Breast Cancer [BC1265]

description: miRNA


title: Breast Cancer [BC0916]

description: miRNA


title: Breast Cancer [BC0997]

description: miRNA


title: Breast Cancer [BC0804]

description: miRNA


title: Breast Cancer [BC0108]

description: miRNA


title: Breast Cancer [BC0137]

description: miRNA


title: Breast Cancer [BC0803]

description: miRNA


title: Breast Cancer [BC1063]

description: miRNA


title: Breast Cancer [BC0227]

description: miRNA


title: Breast Cancer [BC1543]

description: miRNA


title: Breast Cancer [BC0922]

description: miRNA


title: Breast Cancer [BC0444]

description: miRNA


title: Breast Cancer [BC1493]

description: miRNA


title: Breast Cancer [BC1270]

description: miRNA


title: Breast Cancer [BC0121]

description: miRNA


title: Breast Cancer [BC0476]

description: miRNA


title: Breast Cancer [BC1175]

description: miRNA


title: Breast Cancer [BC1190]

description: miRNA


title: Breast Cancer [BC1569]

description: miRNA


title: Breast Cancer [BC1206]

description: miRNA


title: Breast Cancer [BC0060]

description: miRNA


title: Breast Cancer [BC0243]

description: miRNA


title: Breast Cancer [BC0662]

description: miRNA


title: Breast Cancer [BC1045]

description: miRNA


title: Breast Cancer [BC1547]

description: miRNA


title: Breast Cancer [BC0622]

description: miRNA

value: TNM Classification 8th edition):T4


title: Breast Cancer [BC0967]

description: miRNA


title: Breast Cancer [BC0181]

description: miRNA


title: Breast Cancer [BC1286]

description: miRNA


title: Breast Cancer [BC1203]

description: miRNA


title: Breast Cancer [BC1187]

description: miRNA


title: Breast Cancer [BC1001]

description: miRNA


title: Breast Cancer [BC1593]

description: miRNA


title: Breast Cancer [BC1008]

description: miRNA


title: Breast Cancer [BC0085]

description: miRNA


title: Breast Cancer [BC1017]

description: miRNA


title: Breast Cancer [BC1522]

description: miRNA


title: Breast Cancer [BC0140]

description: miRNA


title: Breast Cancer [BC0583]

description: miRNA


title: Breast Cancer [BC1181]

description: miRNA


title: Breast Cancer [BC1080]

description: miRNA


title: Breast Cancer [BC0285]

description: miRNA


title: Breast Cancer [BC1557]

description: miRNA


title: Breast Cancer [BC1594]

description: miRNA


title: Breast Cancer [BC1034]

description: miRNA


title: Breast Cancer [BC1559]

description: miRNA


title: Breast Cancer [BC1534]

description: miRNA


title: Breast Cancer [BC0415]

description: miRNA


title: Breast Cancer [BC0223]

description: miRNA


title: Breast Cancer [BC1541]

description: miRNA


title: Breast Cancer [BC1230]

description: miRNA


title: Breast Cancer [BC0043]

description: miRNA


title: Breast Cancer [BC1492]

description: miRNA


title: Breast Cancer [BC0936]

description: miRNA


title: Breast Cancer [BC1140]

description: miRNA


title: Breast Cancer [BC1290]

description: miRNA


title: Breast Cancer [BC0848]

description: miRNA


title: Breast Cancer [BC0449]

description: miRNA


title: Breast Cancer [BC0802]

description: miRNA


title: Breast Cancer [BC0934]

description: miRNA


title: Breast Cancer [BC0980]

description: miRNA


title: Breast Cancer [BC0443]

description: miRNA


title: Breast Cancer [BC0831]

description: miRNA


title: Breast Cancer [BC0928]

description: miRNA


title: Breast Cancer [BC1159]

description: miRNA


title: Breast Cancer [BC0075]

description: miRNA


title: Breast Cancer [BC1304]

description: miRNA


title: Breast Cancer [BC0609]

description: miRNA


title: Breast Cancer [BC1139]

description: miRNA


title: Breast Cancer [BC1011]

description: miRNA


title: Breast Cancer [BC1066]

description: miRNA


title: Breast Cancer [BC0308]

description: miRNA


title: Breast Cancer [BC1223]

description: miRNA


title: Breast Cancer [BC1129]

description: miRNA


title: Breast Cancer [BC0857]

description: miRNA


title: Breast Cancer [BC0426]

description: miRNA


title: Breast Cancer [BC0367]

description: miRNA


title: Breast Cancer [BC1145]

description: miRNA


title: Breast Cancer [BC0976]

description: miRNA


title: Breast Cancer [BC0507]

description: miRNA


title: Breast Cancer [BC0926]

description: miRNA


title: Breast Cancer [BC1134]

description: miRNA


title: Breast Cancer [BC0418]

description: miRNA


title: Breast Cancer [BC1056]

description: miRNA


title: Breast Cancer [BC0655]

description: miRNA


title: Breast Cancer [BC1364]

description: miRNA


title: Breast Cancer [BC0332]

description: miRNA


title: Breast Cancer [BC1346]

description: miRNA


title: Breast Cancer [BC1398]

description: miRNA


title: Breast Cancer [BC0576]

description: miRNA


title: Breast Cancer [BC0927]

description: miRNA


title: Breast Cancer [BC0467]

description: miRNA


title: Breast Cancer [BC0138]

description: miRNA


title: Breast Cancer [BC1326]

description: miRNA


title: Breast Cancer [BC1050]

description: miRNA


title: Breast Cancer [BC1023]

description: miRNA


title: Breast Cancer [BC1338]

description: miRNA


title: Breast Cancer [BC0122]

description: miRNA


title: Breast Cancer [BC1207]

description: miRNA


title: Breast Cancer [BC0541]

description: miRNA


title: Breast Cancer [BC1075]

description: miRNA


title: Breast Cancer [BC0442]

description: miRNA


title: Breast Cancer [BC1521]

description: miRNA


title: Breast Cancer [BC0989]

description: miRNA


title: Breast Cancer [BC1410]

description: miRNA


title: Breast Cancer [BC1108]

description: miRNA


title: Breast Cancer [BC0594]

description: miRNA


title: Breast Cancer [BC0209]

description: miRNA


title: Breast Cancer [BC1329]

description: miRNA


title: Breast Cancer [BC0982]

description: miRNA


title: Breast Cancer [BC0384]

description: miRNA


title: Breast Cancer [BC0437]

description: miRNA


title: Breast Cancer [BC0440]

description: miRNA


title: Breast Cancer [BC1047]

description: miRNA


title: Breast Cancer [BC1192]

description: miRNA


title: Breast Cancer [BC0408]

description: miRNA


title: Breast Cancer [BC0328]

description: miRNA


title: Breast Cancer [BC1000]

description: miRNA


title: Breast Cancer [BC1076]

description: miRNA


title: Breast Cancer [BC0218]

description: miRNA


title: Breast Cancer [BC1012]

description: miRNA


title: Breast Cancer [BC0343]

description: miRNA


title: Breast Cancer [BC0435]

description: miRNA


title: Breast Cancer [BC1194]

description: miRNA


title: Breast Cancer [BC1024]

description: miRNA


title: Breast Cancer [BC0957]

description: miRNA


title: Breast Cancer [BC0581]

description: miRNA


title: Breast Cancer [BC1318]

description: miRNA


title: Breast Cancer [BC0045]

description: miRNA


title: Breast Cancer [BC1255]

description: miRNA


title: Breast Cancer [BC1237]

description: miRNA


title: Breast Cancer [BC0918]

description: miRNA


title: Breast Cancer [BC0872]

description: miRNA


title: Breast Cancer [BC0621]

description: miRNA


title: Breast Cancer [BC0157]

description: miRNA


title: Breast Cancer [BC1021]

description: miRNA


title: Breast Cancer [BC0630]

description: miRNA


title: Breast Cancer [BC0522]

description: miRNA


title: Breast Cancer [BC1425]

description: miRNA


title: Breast Cancer [BC0433]

description: miRNA


title: Breast Cancer [BC0056]

description: miRNA


title: Breast Cancer [BC1038]

description: miRNA


title: Breast Cancer [BC1258]

description: miRNA


title: Breast Cancer [BC0811]

description: miRNA


title: Breast Cancer [BC1399]

description: miRNA


title: Breast Cancer [BC1467]

description: miRNA


title: Breast Cancer [BC0180]

description: miRNA


title: Breast Cancer [BC1352]

description: miRNA


title: Breast Cancer [BC0913]

description: miRNA


title: Breast Cancer [BC1039]

description: miRNA


title: Breast Cancer [BC0448]

description: miRNA


title: Breast Cancer [BC0635]

description: miRNA


title: Breast Cancer [BC0454]

description: miRNA


title: Breast Cancer [BC0858]

description: miRNA


title: Breast Cancer [BC1371]

description: miRNA


title: Breast Cancer [BC1409]

description: miRNA


title: Breast Cancer [BC1090]

description: miRNA


title: Breast Cancer [BC0047]

description: miRNA


title: Breast Cancer [BC0712]

description: miRNA


title: Breast Cancer [BC1416]

description: miRNA


title: Breast Cancer [BC0225]

description: miRNA


title: Breast Cancer [BC1199]

description: miRNA


title: Breast Cancer [BC1205]

description: miRNA


title: Breast Cancer [BC1141]

description: miRNA


title: Breast Cancer [BC1307]

description: miRNA


title: Breast Cancer [BC0164]

description: miRNA


title: Breast Cancer [BC1156]

description: miRNA


title: Breast Cancer [BC0118]

description: miRNA


title: Breast Cancer [BC0187]

description: miRNA


title: Breast Cancer [BC0216]

description: miRNA


title: Breast Cancer [BC1033]

description: miRNA


title: Breast Cancer [BC0450]

description: miRNA


title: Breast Cancer [BC0824]

description: miRNA


title: Breast Cancer [BC0586]

description: miRNA


title: Breast Cancer [BC0132]

description: miRNA


title: Breast Cancer [BC1361]

description: miRNA


title: Breast Cancer [BC1552]

description: miRNA


title: Breast Cancer [BC0611]

description: miRNA


title: Breast Cancer [BC1031]

description: miRNA


title: Breast Cancer [BC0163]

description: miRNA


title: Breast Cancer [BC1272]

description: miRNA


title: Breast Cancer [BC1019]

description: miRNA


title: Breast Cancer [BC1264]

description: miRNA


title: Breast Cancer [BC1059]

description: miRNA


title: Breast Cancer [BC0841]

description: miRNA


title: Breast Cancer [BC0632]

description: miRNA


title: Breast Cancer [BC0629]

description: miRNA


title: Breast Cancer [BC0924]

description: miRNA


title: Breast Cancer [BC0360]

description: miRNA


title: Breast Cancer [BC1239]

description: miRNA


title: Breast Cancer [BC0882]

description: miRNA


title: Breast Cancer [BC1377]

description: miRNA


title: Breast Cancer [BC0553]

description: miRNA


title: Breast Cancer [BC1158]

description: miRNA


title: Breast Cancer [BC0205]

description: miRNA


title: Breast Cancer [BC1225]

description: miRNA


title: Breast Cancer [BC0404]

description: miRNA


title: Breast Cancer [BC0893]

description: miRNA


title: Breast Cancer [BC0627]

description: miRNA


title: Breast Cancer [BC0854]

description: miRNA


title: Breast Cancer [BC0568]

description: miRNA


title: Breast Cancer [BC0212]

description: miRNA


title: Breast Cancer [BC0080]

description: miRNA


title: Breast Cancer [BC1268]

description: miRNA


title: Breast Cancer [BC0290]

description: miRNA


title: Breast Cancer [BC1279]

description: miRNA


title: Breast Cancer [BC1124]

description: miRNA


title: Breast Cancer [BC1396]

description: miRNA


title: Breast Cancer [BC1046]

description: miRNA


title: Breast Cancer [BC1135]

description: miRNA


title: Breast Cancer [BC1133]

description: miRNA


title: Breast Cancer [BC1119]

description: miRNA


title: Breast Cancer [BC1259]

description: miRNA


title: Breast Cancer [BC1051]

description: miRNA


title: Breast Cancer [BC0233]

description: miRNA


title: Breast Cancer [BC1153]

description: miRNA


title: Breast Cancer [BC1027]

description: miRNA


title: Breast Cancer [BC1114]

description: miRNA


title: Breast Cancer [BC1266]

description: miRNA


title: Breast Cancer [BC0995]

description: miRNA


title: Breast Cancer [BC1102]

description: miRNA


title: Breast Cancer [BC1043]

description: miRNA


title: Breast Cancer [BC0879]

description: miRNA


title: Breast Cancer [BC1055]

description: miRNA


title: Breast Cancer [BC0385]

description: miRNA


title: Breast Cancer [BC0999]

description: miRNA


title: Breast Cancer [BC0915]

description: miRNA


title: Breast Cancer [BC1116]

description: miRNA


title: Breast Cancer [BC0139]

description: miRNA


title: Breast Cancer [BC1009]

description: miRNA


title: Breast Cancer [BC0322]

description: miRNA


title: Breast Cancer [BC0806]

description: miRNA


title: Breast Cancer [BC0684]

description: miRNA


title: Breast Cancer [BC0134]

description: miRNA


title: Breast Cancer [BC0605]

description: miRNA


title: Breast Cancer [BC1362]

description: miRNA


title: Breast Cancer [BC0838]

description: miRNA


title: Breast Cancer [BC0023]

description: miRNA


title: Breast Cancer [BC0420]

description: miRNA


title: Breast Cancer [BC0554]

description: miRNA


title: Breast Cancer [BC0073]

description: miRNA


title: Breast Cancer [BC0405]

description: miRNA


title: Breast Cancer [BC0210]

description: miRNA


title: Breast Cancer [BC0436]

description: miRNA


title: Breast Cancer [BC1193]

description: miRNA


title: Breast Cancer [BC1350]

description: miRNA


title: Breast Cancer [BC0079]

description: miRNA


title: Breast Cancer [BC1330]

description: miRNA


title: Breast Cancer [BC1040]

description: miRNA


title: Breast Cancer [BC1281]

description: miRNA


title: Breast Cancer [BC0992]

description: miRNA


title: Breast Cancer [BC1375]

description: miRNA


title: Breast Cancer [BC0588]

description: miRNA


title: Breast Cancer [BC0994]

description: miRNA


title: Breast Cancer [BC0203]

description: miRNA


title: Breast Cancer [BC0889]

description: miRNA


title: Breast Cancer [BC0036]

description: miRNA


title: Breast Cancer [BC0984]

description: miRNA


title: Breast Cancer [BC1169]

description: miRNA


title: Breast Cancer [BC0974]

description: miRNA


title: Breast Cancer [BC1184]

description: miRNA


title: Breast Cancer [BC1002]

description: miRNA


title: Breast Cancer [BC1086]

description: miRNA


title: Breast Cancer [BC0215]

description: miRNA


title: Breast Cancer [BC0294]

description: miRNA


title: Breast Cancer [BC0403]

description: miRNA


title: Breast Cancer [BC0943]

description: miRNA


title: Breast Cancer [BC0190]

description: miRNA


title: Breast Cancer [BC0539]

description: miRNA


title: Breast Cancer [BC0853]

description: miRNA


title: Breast Cancer [BC0660]

description: miRNA


title: Breast Cancer [BC0517]

description: miRNA


title: Breast Cancer [BC0998]

description: miRNA


title: Breast Cancer [BC1208]

description: miRNA


title: Breast Cancer [BC1189]

description: miRNA


title: Breast Cancer [BC1057]

description: miRNA


title: Breast Cancer [BC1271]

description: miRNA


title: Breast Cancer [BC0124]

description: miRNA


title: Breast Cancer [BC0914]

description: miRNA


title: Breast Cancer [BC0985]

description: miRNA


title: Breast Cancer [BC1137]

description: miRNA


title: Breast Cancer [BC1293]

description: miRNA


title: Breast Cancer [BC1317]

description: miRNA


title: Breast Cancer [BC1200]

description: miRNA


title: Breast Cancer [BC1120]

description: miRNA


title: Breast Cancer [BC0947]

description: miRNA


title: Breast Cancer [BC1143]

description: miRNA


title: Breast Cancer [BC0540]

description: miRNA


title: Breast Cancer [BC1217]

description: miRNA


title: Breast Cancer [BC0432]

description: miRNA


title: Breast Cancer [BC1242]

description: miRNA


title: Breast Cancer [BC0411]

description: miRNA


title: Breast Cancer [BC0022]

description: miRNA


title: Breast Cancer [BC1157]

description: miRNA


title: Breast Cancer [BC0491]

description: miRNA


title: Breast Cancer [BC1219]

description: miRNA


title: Breast Cancer [BC1229]

description: miRNA


title: Breast Cancer [BC1308]

description: miRNA


title: Breast Cancer [BC0498]

description: miRNA


title: Breast Cancer [BC0439]

description: miRNA


title: Breast Cancer [BC0937]

description: miRNA


title: Breast Cancer [BC1390]

description: miRNA


title: Breast Cancer [BC0470]

description: miRNA


title: Breast Cancer [BC0840]

description: miRNA


title: Breast Cancer [BC0537]

description: miRNA


title: Breast Cancer [BC0189]

description: miRNA


title: Breast Cancer [BC0548]

description: miRNA


title: Breast Cancer [BC0547]

description: miRNA


title: Breast Cancer [BC1401]

description: miRNA


title: Breast Cancer [BC0535]

description: miRNA


title: Breast Cancer [BC1074]

description: miRNA


title: Breast Cancer [BC1109]

description: miRNA


title: Breast Cancer [BC1548]

description: miRNA


title: Breast Cancer [BC1343]

description: miRNA


title: Breast Cancer [BC1356]

description: miRNA


title: Breast Cancer [BC1176]

description: miRNA


title: Breast Cancer [BC1196]

description: miRNA


title: Breast Cancer [BC1036]

description: miRNA


title: Breast Cancer [BC1150]

description: miRNA


title: Breast Cancer [BC1295]

description: miRNA


title: Breast Cancer [BC0573]

description: miRNA


title: Breast Cancer [BC1262]

description: miRNA


title: Breast Cancer [BC0136]

description: miRNA


title: Breast Cancer [BC0946]

description: miRNA


title: Breast Cancer [BC1016]

description: miRNA


title: Breast Cancer [BC1287]

description: miRNA


title: Breast Cancer [BC0175]

description: miRNA


title: Breast Cancer [BC0099]

description: miRNA


title: Breast Cancer [BC0169]

description: miRNA


title: Breast Cancer [BC1030]

description: miRNA


title: Breast Cancer [BC1340]

description: miRNA


title: Breast Cancer [BC0046]

description: miRNA


title: Breast Cancer [BC0822]

description: miRNA


title: Breast Cancer [BC1082]

description: miRNA


title: Breast Cancer [BC1328]

description: miRNA


title: Breast Cancer [BC0224]

description: miRNA


title: Breast Cancer [BC1520]

description: miRNA


title: Breast Cancer [BC1058]

description: miRNA


title: Breast Cancer [BC1324]

description: miRNA


title: Breast Cancer [BC0971]

description: miRNA


title: Breast Cancer [BC0863]

description: miRNA


title: Breast Cancer [BC0172]

description: miRNA


title: Breast Cancer [BC0558]

description: miRNA


title: Breast Cancer [BC0634]

description: miRNA


title: Breast Cancer [BC0917]

description: miRNA


title: Breast Cancer [BC0453]

description: miRNA


title: Breast Cancer [BC1320]

description: miRNA


title: Breast Cancer [BC1226]

description: miRNA


title: Breast Cancer [BC0191]

description: miRNA


title: Breast Cancer [BC1165]

description: miRNA


title: Breast Cancer [BC1064]

description: miRNA


title: Breast Cancer [BC0430]

description: miRNA


title: Breast Cancer [BC1427]

description: miRNA


title: Breast Cancer [BC1380]

description: miRNA


title: Breast Cancer [BC0159]

description: miRNA


title: Breast Cancer [BC1422]

description: miRNA


title: Breast Cancer [BC0451]

description: miRNA


title: Breast Cancer [BC0981]

description: miRNA


title: Breast Cancer [BC0866]

description: miRNA


title: Breast Cancer [BC1060]

description: miRNA


title: Breast Cancer [BC1370]

description: miRNA


title: Breast Cancer [BC1228]

description: miRNA


title: Breast Cancer [BC0058]

description: miRNA


title: Breast Cancer [BC0531]

description: miRNA


title: Breast Cancer [BC1214]

description: miRNA


title: Breast Cancer [BC1568]

description: miRNA


title: Breast Cancer [BC0919]

description: miRNA


title: Breast Cancer [BC0556]

description: miRNA


title: Breast Cancer [BC0503]

description: miRNA


title: Breast Cancer [BC0261]

description: miRNA


title: Breast Cancer [BC1221]

description: miRNA


title: Breast Cancer [BC0898]

description: miRNA


title: Breast Cancer [BC1163]

description: miRNA


title: Breast Cancer [BC1162]

description: miRNA


title: Breast Cancer [BC0127]

description: miRNA


title: Breast Cancer [BC0876]

description: miRNA


title: Breast Cancer [BC0116]

description: miRNA


title: Breast Cancer [BC0338]

description: miRNA


title: Breast Cancer [BC0090]

description: miRNA


title: Breast Cancer [BC0204]

description: miRNA


title: Breast Cancer [BC1107]

description: miRNA


title: Breast Cancer [BC0078]

description: miRNA


title: Breast Cancer [BC1315]

description: miRNA


title: Breast Cancer [BC1005]

description: miRNA


title: Breast Cancer [BC0048]

description: miRNA


title: Breast Cancer [BC0463]

description: miRNA


title: Breast Cancer [BC1463]

description: miRNA


title: Breast Cancer [BC1444]

description: miRNA


title: Breast Cancer [BC1485]

description: miRNA


title: Breast Cancer [BC0330]

description: miRNA


title: Breast Cancer [BC0734]

description: miRNA


title: Breast Cancer [BC0780]

description: miRNA


title: Breast Cancer [BC1288]

description: miRNA


title: Breast Cancer [BC0757]

description: miRNA


title: Breast Cancer [BC0044]

description: miRNA


title: Breast Cancer [BC0422]

description: miRNA


title: Breast Cancer [BC0008]

description: miRNA


title: Breast Cancer [BC1502]

description: miRNA


title: Breast Cancer [BC0106]

description: miRNA


title: Breast Cancer [BC0730]

description: miRNA


title: Breast Cancer [BC0603]

description: miRNA


title: Breast Cancer [BC0873]

description: miRNA


title: Breast Cancer [BC1475]

description: miRNA


title: Breast Cancer [BC1332]

description: miRNA


title: Breast Cancer [BC1325]

description: miRNA


title: Breast Cancer [BC0486]

description: miRNA


title: Breast Cancer [BC0978]

description: miRNA


title: Breast Cancer [BC0783]

description: miRNA


title: Breast Cancer [BC1505]

description: miRNA


title: Breast Cancer [BC0813]

description: miRNA


title: Breast Cancer [BC1243]

description: miRNA


title: Breast Cancer [BC0728]

description: miRNA


title: Breast Cancer [BC0323]

description: miRNA


title: Breast Cancer [BC1105]

description: miRNA


title: Breast Cancer [BC0795]

description: miRNA


title: Breast Cancer [BC0278]

description: miRNA


title: Breast Cancer [BC0038]

description: miRNA


title: Breast Cancer [BC0789]

description: miRNA


title: Breast Cancer [BC1327]

description: miRNA


title: Breast Cancer [BC1440]

description: miRNA


title: Breast Cancer [BC1104]

description: miRNA


title: Breast Cancer [BC1584]

description: miRNA


title: Breast Cancer [BC1302]

description: miRNA


title: Breast Cancer [BC1452]

description: miRNA


title: Breast Cancer [BC0733]

description: miRNA


title: Breast Cancer [BC1282]

description: miRNA


title: Breast Cancer [BC1441]

description: miRNA


title: Breast Cancer [BC0829]

description: miRNA


title: Breast Cancer [BC1495]

description: miRNA


title: Breast Cancer [BC0739]

description: miRNA


title: Breast Cancer [BC1312]

description: miRNA


title: Breast Cancer [BC1065]

description: miRNA


title: Breast Cancer [BC0776]

description: miRNA


title: Breast Cancer [BC0986]

description: miRNA


title: Breast Cancer [BC1437]

description: miRNA


title: Breast Cancer [BC0759]

description: miRNA


title: Breast Cancer [BC1215]

description: miRNA


title: Breast Cancer [BC1473]

description: miRNA


title: Breast Cancer [BC0723]

description: miRNA


title: Breast Cancer [BC1231]

description: miRNA


title: Breast Cancer [BC0731]

description: miRNA


title: Breast Cancer [BC0718]

description: miRNA


title: Breast Cancer [BC1061]

description: miRNA


title: Breast Cancer [BC1032]

description: miRNA


title: Breast Cancer [BC1454]

description: miRNA


title: Breast Cancer [BC1254]

description: miRNA


title: Breast Cancer [BC0775]

description: miRNA


title: Breast Cancer [BC1103]

description: miRNA


title: Breast Cancer [BC0747]

description: miRNA


title: Breast Cancer [BC0196]

description: miRNA


title: Breast Cancer [BC1334]

description: miRNA


title: Breast Cancer [BC0961]

description: miRNA


title: Breast Cancer [BC0014]

description: miRNA


title: Breast Cancer [BC0736]

description: miRNA


title: Breast Cancer [BC0758]

description: miRNA


title: Breast Cancer [BC1471]

description: miRNA


title: Breast Cancer [BC1365]

description: miRNA


title: Breast Cancer [BC1432]

description: miRNA


title: Breast Cancer [BC0748]

description: miRNA


title: Breast Cancer [BC1617]

description: miRNA


title: Breast Cancer [BC0877]

description: miRNA


title: Breast Cancer [BC1151]

description: miRNA


title: Breast Cancer [BC0766]

description: miRNA


title: Breast Cancer [BC1478]

description: miRNA


title: Breast Cancer [BC1322]

description: miRNA


title: Breast Cancer [BC1489]

description: miRNA


title: Breast Cancer [BC1311]

description: miRNA


title: Breast Cancer [BC1213]

description: miRNA


title: Breast Cancer [BC1382]

description: miRNA


title: Breast Cancer [BC1483]

description: miRNA


title: Breast Cancer [BC0904]

description: miRNA


title: Breast Cancer [BC1477]

description: miRNA


title: Breast Cancer [BC0768]

description: miRNA


title: Breast Cancer [BC1406]

description: miRNA


title: Breast Cancer [BC1423]

description: miRNA


title: Breast Cancer [BC1449]

description: miRNA


title: Breast Cancer [BC1171]

description: miRNA


title: Breast Cancer [BC1436]

description: miRNA


title: Breast Cancer [BC1234]

description: miRNA


title: Breast Cancer [BC1331]

description: miRNA


title: Breast Cancer [BC0732]

description: miRNA


title: Breast Cancer [BC0902]

description: miRNA


title: Breast Cancer [BC0939]

description: miRNA


title: Breast Cancer [BC0729]

description: miRNA


title: Breast Cancer [BC1450]

description: miRNA


title: Breast Cancer [BC1333]

description: miRNA


title: Breast Cancer [BC0790]

description: miRNA


title: Breast Cancer [BC1447]

description: miRNA


title: Breast Cancer [BC1029]

description: miRNA


title: Breast Cancer [BC0012]

description: miRNA


title: Breast Cancer [BC1301]

description: miRNA


title: Breast Cancer [BC1439]

description: miRNA


title: Breast Cancer [BC1298]

description: miRNA


title: Breast Cancer [BC1418]

description: miRNA


title: Breast Cancer [BC1545]

description: miRNA


title: Breast Cancer [BC0264]

description: miRNA


title: Breast Cancer [BC0779]

description: miRNA


title: Breast Cancer [BC0798]

description: miRNA


title: Breast Cancer [BC1306]

description: miRNA


title: Breast Cancer [BC1042]

description: miRNA


title: Breast Cancer [BC1275]

description: miRNA


title: Breast Cancer [BC1285]

description: miRNA


title: Breast Cancer [BC1251]

description: miRNA


title: Breast Cancer [BC1555]

description: miRNA


title: Breast Cancer [BC1620]

description: miRNA


title: Breast Cancer [BC0773]

description: miRNA


title: Breast Cancer [BC1195]

description: miRNA


title: Breast Cancer [BC1408]

description: miRNA


title: Breast Cancer [BC0812]

description: miRNA


title: Breast Cancer [BC1291]

description: miRNA


title: Breast Cancer [BC0738]

description: miRNA


title: Breast Cancer [BC0721]

description: miRNA


title: Breast Cancer [BC0083]

description: miRNA


title: Breast Cancer [BC0160]

description: miRNA


title: Breast Cancer [BC1415]

description: miRNA


title: Breast Cancer [BC1099]

description: miRNA


title: Breast Cancer [BC0805]

description: miRNA


title: Breast Cancer [BC0062]

description: miRNA


title: Breast Cancer [BC1442]

description: miRNA


title: Breast Cancer [BC0929]

description: miRNA


title: Breast Cancer [BC1619]

description: miRNA


title: Breast Cancer [BC0147]

description: miRNA


title: Breast Cancer [BC0987]

description: miRNA


title: Breast Cancer [BC0681]

description: miRNA


title: Breast Cancer [BC0226]

description: miRNA


title: Breast Cancer [BC1606]

description: miRNA


title: Breast Cancer [BC0017]

description: miRNA


title: Breast Cancer [BC0004]

description: miRNA


title: Breast Cancer [BC0996]

description: miRNA


title: Breast Cancer [BC0674]

description: miRNA


title: Breast Cancer [BC1260]

description: miRNA


title: Breast Cancer [BC0750]

description: miRNA


title: Breast Cancer [BC0452]

description: miRNA


title: Breast Cancer [BC0019]

description: miRNA


title: Breast Cancer [BC1554]

description: miRNA


title: Breast Cancer [BC0081]

description: miRNA


title: Breast Cancer [BC0241]

description: miRNA


title: Breast Cancer [BC0754]

description: miRNA


title: Breast Cancer [BC0818]

description: miRNA


title: Breast Cancer [BC0855]

description: miRNA


title: Breast Cancer [BC0751]

description: miRNA


title: Breast Cancer [BC0991]

description: miRNA


title: Breast Cancer [BC1536]

description: miRNA


title: Breast Cancer [BC0376]

description: miRNA


title: Breast Cancer [BC0357]

description: miRNA


title: Breast Cancer [BC1602]

description: miRNA


title: Breast Cancer [BC0807]

description: miRNA


title: Breast Cancer [BC0878]

description: miRNA


title: Breast Cancer [BC0860]

description: miRNA


title: Breast Cancer [BC0361]

description: miRNA


title: Breast Cancer [BC0832]

description: miRNA


title: Breast Cancer [BC0280]

description: miRNA


title: Breast Cancer [BC0011]

description: miRNA


title: Breast Cancer [BC1565]

description: miRNA


title: Breast Cancer [BC0815]

description: miRNA


title: Breast Cancer [BC1007]

description: miRNA


title: Breast Cancer [BC1404]

description: miRNA


title: Breast Cancer [BC1161]

description: miRNA


title: Breast Cancer [BC0015]

description: miRNA


title: Breast Cancer [BC1518]

description: miRNA


title: Breast Cancer [BC1607]

description: miRNA


title: Breast Cancer [BC1174]

description: miRNA


title: Breast Cancer [BC0792]

description: miRNA


title: Breast Cancer [BC1092]

description: miRNA


title: Breast Cancer [BC1586]

description: miRNA


title: Breast Cancer [BC1389]

description: miRNA


title: Breast Cancer [BC0814]

description: miRNA


title: Breast Cancer [BC0842]

description: miRNA


title: Breast Cancer [BC0112]

description: miRNA


title: Breast Cancer [BC0686]

description: miRNA


title: Breast Cancer [BC0042]

description: miRNA


title: Breast Cancer [BC1113]

description: miRNA


title: Breast Cancer [BC0344]

description: miRNA


title: Breast Cancer [BC0168]

description: miRNA


title: Breast Cancer [BC0763]

description: miRNA


title: Breast Cancer [BC0383]

description: miRNA


title: Breast Cancer [BC0569]

description: miRNA


title: Breast Cancer [BC0456]

description: miRNA


title: Breast Cancer [BC1426]

description: miRNA


title: Breast Cancer [BC0823]

description: miRNA


title: Breast Cancer [BC1526]

description: miRNA


title: Breast Cancer [BC0875]

description: miRNA


title: Breast Cancer [BC1130]

description: miRNA


title: Breast Cancer [BC1598]

description: miRNA


title: Breast Cancer [BC0843]

description: miRNA


title: Breast Cancer [BC0549]

description: miRNA


title: Breast Cancer [BC1533]

description: miRNA


title: Breast Cancer [BC0956]

description: miRNA


title: Breast Cancer [BC0077]

description: miRNA


title: Breast Cancer [BC0794]

description: miRNA


title: Breast Cancer [BC1532]

description: miRNA


title: Breast Cancer [BC0111]

description: miRNA


title: Breast Cancer [BC1383]

description: miRNA


title: Breast Cancer [BC1069]

description: miRNA


title: Breast Cancer [BC0828]

description: miRNA


title: Breast Cancer [BC0281]

description: miRNA


title: Breast Cancer [BC1608]

description: miRNA


title: Breast Cancer [BC0005]

description: miRNA


title: Breast Cancer [BC1567]

description: miRNA


title: Breast Cancer [BC1553]

description: miRNA


title: Breast Cancer [BC0237]

description: miRNA


title: Breast Cancer [BC1414]

description: miRNA


title: Breast Cancer [BC0691]

description: miRNA


title: Breast Cancer [BC0151]

description: miRNA


title: Breast Cancer [BC0959]

description: miRNA


title: Breast Cancer [BC0499]

description: miRNA


title: Breast Cancer [BC1385]

description: miRNA


title: Breast Cancer [BC1511]

description: miRNA


title: Breast Cancer [BC1592]

description: miRNA


title: Breast Cancer [BC1280]

description: miRNA


title: Breast Cancer [BC0764]

description: miRNA


title: Breast Cancer [BC0041]

description: miRNA


title: Breast Cancer [BC0892]

description: miRNA


title: Breast Cancer [BC0896]

description: miRNA


title: Breast Cancer [BC0265]

description: miRNA


title: Breast Cancer [BC0682]

description: miRNA


title: Breast Cancer [BC0908]

description: miRNA


title: Breast Cancer [BC1095]

description: miRNA


title: Breast Cancer [BC0661]

description: miRNA


title: Breast Cancer [BC0346]

description: miRNA


title: Breast Cancer [BC0932]

description: miRNA


title: Breast Cancer [BC1575]

description: miRNA


title: Breast Cancer [BC1531]

description: miRNA


title: Breast Cancer [BC0052]

description: miRNA


title: Breast Cancer [BC1025]

description: miRNA


title: Breast Cancer [BC1106]

description: miRNA


title: Breast Cancer [BC1429]

description: miRNA


title: Breast Cancer [BC1249]

description: miRNA


title: Breast Cancer [BC0665]

description: miRNA


title: Breast Cancer [BC0772]

description: miRNA


title: Breast Cancer [BC0026]

description: miRNA


title: Breast Cancer [BC0698]

description: miRNA


title: Breast Cancer [BC0113]

description: miRNA


title: Breast Cancer [BC1506]

description: miRNA


title: Breast Cancer [BC0034]

description: miRNA


title: Breast Cancer [BC1595]

description: miRNA


title: Breast Cancer [BC0821]

description: miRNA


title: Breast Cancer [BC1542]

description: miRNA


title: Breast Cancer [BC0201]

description: miRNA


title: Breast Cancer [BC1519]

description: miRNA


title: Breast Cancer [BC1010]

description: miRNA


title: Breast Cancer [BC1468]

description: miRNA


title: Breast Cancer [BC1126]

description: miRNA


title: Breast Cancer [BC1098]

description: miRNA


title: Breast Cancer [BC0688]

description: miRNA


title: Breast Cancer [BC0830]

description: miRNA


title: Breast Cancer [BC0677]

description: miRNA


title: Breast Cancer [BC0441]

description: miRNA


title: Breast Cancer [BC1515]

description: miRNA


title: Breast Cancer [BC0909]

description: miRNA


title: Breast Cancer [BC0267]

description: miRNA


title: Breast Cancer [BC0719]

description: miRNA


title: Breast Cancer [BC1583]

description: miRNA


title: Breast Cancer [BC0964]

description: miRNA


title: Breast Cancer [BC1421]

description: miRNA


title: Breast Cancer [BC0809]

description: miRNA


title: Breast Cancer [BC1419]

description: miRNA


title: Breast Cancer [BC1097]

description: miRNA


title: Breast Cancer [BC0365]

description: miRNA


title: Breast Cancer [BC1572]

description: miRNA


title: Breast Cancer [BC0213]

description: miRNA


title: Breast Cancer [BC0884]

description: miRNA


title: Breast Cancer [BC0292]

description: miRNA


title: Breast Cancer [BC0478]

description: miRNA


title: Breast Cancer [BC0601]

description: miRNA


title: Breast Cancer [BC0638]

description: miRNA


title: Breast Cancer [BC1132]

description: miRNA


title: Breast Cancer [BC0636]

description: miRNA


title: Breast Cancer [BC0625]

description: miRNA


title: Breast Cancer [BC1402]

description: miRNA


title: Breast Cancer [BC0598]

description: miRNA


title: Breast Cancer [BC0480]

description: miRNA


title: Breast Cancer [BC0533]

description: miRNA


title: Breast Cancer [BC0955]

description: miRNA


title: Breast Cancer [BC0354]

description: miRNA


title: Breast Cancer [BC0874]

description: miRNA


title: Breast Cancer [BC0153]

description: miRNA


title: Breast Cancer [BC0298]

description: miRNA


title: Breast Cancer [BC0313]

description: miRNA


title: Breast Cancer [BC1170]

description: miRNA


title: Breast Cancer [BC0515]

description: miRNA


title: Breast Cancer [BC0167]

description: miRNA


title: Breast Cancer [BC0311]

description: miRNA


title: Breast Cancer [BC0459]

description: miRNA


title: Breast Cancer [BC0481]

description: miRNA


title: Breast Cancer [BC1292]

description: miRNA


title: Breast Cancer [BC0219]

description: miRNA


title: Breast Cancer [BC0820]

description: miRNA


title: Breast Cancer [BC1497]

description: miRNA


title: Breast Cancer [BC1015]

description: miRNA


title: Breast Cancer [BC1235]

description: miRNA


title: Breast Cancer [BC0953]

description: miRNA


title: Breast Cancer [BC0286]

description: miRNA


title: Breast Cancer [BC0826]

description: miRNA


title: Breast Cancer [BC1186]

description: miRNA


title: Breast Cancer [BC0495]

description: miRNA


title: Breast Cancer [BC1579]

description: miRNA


title: Breast Cancer [BC0087]

description: miRNA


title: Breast Cancer [BC0149]

description: miRNA


title: Breast Cancer [BC0331]

description: miRNA


title: Breast Cancer [BC1601]

description: miRNA


title: Breast Cancer [BC0485]

description: miRNA


title: Breast Cancer [BC1622]

description: miRNA


title: Breast Cancer [BC1148]

description: miRNA


title: Breast Cancer [BC1182]

description: miRNA


title: Breast Cancer [BC0246]

description: miRNA


title: Breast Cancer [BC1101]

description: miRNA


title: Breast Cancer [BC1118]

description: miRNA


title: Breast Cancer [BC1397]

description: miRNA


title: Breast Cancer [BC0193]

description: miRNA


title: Breast Cancer [BC0326]

description: miRNA


title: Breast Cancer [BC1112]

description: miRNA


title: Breast Cancer [BC1117]

description: miRNA


title: Breast Cancer [BC0329]

description: miRNA


title: Breast Cancer [BC1093]

description: miRNA


title: Breast Cancer [BC1612]

description: miRNA


title: Breast Cancer [BC0197]

description: miRNA


title: Breast Cancer [BC0353]

description: miRNA


title: Breast Cancer [BC0027]

description: miRNA


title: Breast Cancer [BC0152]

description: miRNA


title: Breast Cancer [BC0431]

description: miRNA


title: Breast Cancer [BC1022]

description: miRNA


title: Breast Cancer [BC1144]

description: miRNA


title: Breast Cancer [BC1297]

description: miRNA


title: Breast Cancer [BC0633]

description: miRNA


title: Breast Cancer [BC0179]

description: miRNA


title: Breast Cancer [BC1517]

description: miRNA


title: Breast Cancer [BC0244]

description: miRNA


title: Breast Cancer [BC0009]

description: miRNA


title: Breast Cancer [BC0716]

description: miRNA


title: Breast Cancer [BC0970]

description: miRNA


title: Breast Cancer [BC0472]

description: miRNA


title: Breast Cancer [BC0006]

description: miRNA


title: Breast Cancer [BC1319]

description: miRNA


title: Breast Cancer [BC1256]

description: miRNA


title: Breast Cancer [BC1369]

description: miRNA


title: Breast Cancer [BC1321]

description: miRNA


title: Breast Cancer [BC0862]

description: miRNA


title: Breast Cancer [BC0770]

description: miRNA


title: Breast Cancer [BC0327]

description: miRNA


title: Breast Cancer [BC1248]

description: miRNA


title: Breast Cancer [BC1407]

description: miRNA


title: Breast Cancer [BC1363]

description: miRNA


title: Breast Cancer [BC1138]

description: miRNA


title: Breast Cancer [BC0752]

description: miRNA


title: Breast Cancer [BC1115]

description: miRNA


title: Breast Cancer [BC1600]

description: miRNA


title: Breast Cancer [BC0067]

description: miRNA


title: Breast Cancer [BC1577]

description: miRNA


title: Breast Cancer [BC0911]

description: miRNA


title: Breast Cancer [BC0057]

description: miRNA


title: Breast Cancer [BC0262]

description: miRNA


title: Breast Cancer [BC1596]

description: miRNA


title: Breast Cancer [BC1544]

description: miRNA


title: Breast Cancer [BC0277]

description: miRNA


title: Breast Cancer [BC0696]

description: miRNA


title: Breast Cancer [BC0816]

description: miRNA


title: Breast Cancer [BC0010]

description: miRNA


title: Breast Cancer [BC1516]

description: miRNA


title: Breast Cancer [BC0899]

description: miRNA


title: Breast Cancer [BC0379]

description: miRNA


title: Breast Cancer [BC0269]

description: miRNA


title: Breast Cancer [BC0363]

description: miRNA


title: Breast Cancer [BC0368]

description: miRNA


title: Breast Cancer [BC1537]

description: miRNA


title: Breast Cancer [BC0659]

description: miRNA


title: Breast Cancer [BC1508]

description: miRNA


title: Breast Cancer [BC0663]

description: miRNA


title: Breast Cancer [BC1241]

description: miRNA


title: Breast Cancer [BC0836]

description: miRNA


title: Breast Cancer [BC0369]

description: miRNA


title: Breast Cancer [BC0410]

description: miRNA


title: Breast Cancer [BC0144]

description: miRNA


title: Breast Cancer [BC0965]

description: miRNA


title: Breast Cancer [BC0378]

description: miRNA


title: Breast Cancer [BC0171]

description: miRNA


title: Breast Cancer [BC0774]

description: miRNA


title: Breast Cancer [BC0016]

description: miRNA


title: Breast Cancer [BC1136]

description: miRNA


title: Breast Cancer [BC1216]

description: miRNA


title: Breast Cancer [BC0644]

description: miRNA


title: Breast Cancer [BC0266]

description: miRNA


title: Breast Cancer [BC0293]

description: miRNA


title: Breast Cancer [BC0429]

description: miRNA


title: Breast Cancer [BC0287]

description: miRNA


title: Breast Cancer [BC0561]

description: miRNA


title: Breast Cancer [BC0658]

description: miRNA


title: Breast Cancer [BC1172]

description: miRNA


title: Breast Cancer [BC0551]

description: miRNA


title: Breast Cancer [BC1006]

description: miRNA


title: Breast Cancer [BC0283]

description: miRNA


title: Breast Cancer [BC1540]

description: miRNA


title: Breast Cancer [BC0623]

description: miRNA


title: Breast Cancer [BC1591]

description: miRNA


title: Breast Cancer [BC1556]

description: miRNA


title: Breast Cancer [BC0567]

description: miRNA


title: Breast Cancer [BC0560]

description: miRNA


title: Breast Cancer [BC0231]

description: miRNA


title: Breast Cancer [BC1049]

description: miRNA


title: Breast Cancer [BC0319]

description: miRNA


title: Breast Cancer [BC0643]

description: miRNA


title: Breast Cancer [BC0631]

description: miRNA


title: Breast Cancer [BC0975]

description: miRNA


title: Breast Cancer [BC0125]

description: miRNA


title: Breast Cancer [BC0316]

description: miRNA


title: Breast Cancer [BC0664]

description: miRNA


title: Breast Cancer [BC0593]

description: miRNA


title: Breast Cancer [BC0288]

description: miRNA


title: Breast Cancer [BC0604]

description: miRNA


title: Breast Cancer [BC0550]

description: miRNA


title: Breast Cancer [BC0084]

description: miRNA


title: Breast Cancer [BC0258]

description: miRNA


title: Breast Cancer [BC1212]

description: miRNA


title: Breast Cancer [BC1603]

description: miRNA


title: Breast Cancer [BC0173]

description: miRNA


title: Breast Cancer [BC0291]

description: miRNA


title: Breast Cancer [BC0260]

description: miRNA


title: Breast Cancer [BC0641]

description: miRNA


title: Breast Cancer [BC1459]

description: miRNA


title: Breast Cancer [BC0133]

description: miRNA


title: Breast Cancer [BC0591]

description: miRNA


title: Breast Cancer [BC1391]

description: miRNA


title: Breast Cancer [BC0473]

description: miRNA


title: Breast Cancer [BC0618]

description: miRNA


title: Breast Cancer [BC0095]

description: miRNA


title: Breast Cancer [BC0107]

description: miRNA


title: Breast Cancer [BC0092]

description: miRNA


title: Breast Cancer [BC1342]

description: miRNA


title: Breast Cancer [BC0407]

description: miRNA


title: Breast Cancer [BC0235]

description: miRNA


title: Breast Cancer [BC0207]

description: miRNA


title: Breast Cancer [BC0562]

description: miRNA


title: Breast Cancer [BC0509]

description: miRNA


title: Breast Cancer [BC0114]

description: miRNA


title: Breast Cancer [BC1472]

description: miRNA


title: Breast Cancer [BC0727]

description: miRNA


title: Breast Cancer [BC1341]

description: miRNA


title: Breast Cancer [BC1480]

description: miRNA


title: Breast Cancer [BC1431]

description: miRNA


title: Breast Cancer [BC1491]

description: miRNA


title: Breast Cancer [BC0130]

description: miRNA


title: Breast Cancer [BC0796]

description: miRNA


title: Breast Cancer [BC0835]

description: miRNA


title: Breast Cancer [BC0695]

description: miRNA


title: Breast Cancer [BC1395]

description: miRNA


title: Breast Cancer [BC0007]

description: miRNA


title: Breast Cancer [BC1581]

description: miRNA


title: Breast Cancer [BC0702]

description: miRNA


title: Breast Cancer [BC0055]

description: miRNA


title: Breast Cancer [BC1618]

description: miRNA


title: Breast Cancer [BC0793]

description: miRNA


title: Breast Cancer [BC1507]

description: miRNA


title: Breast Cancer [BC1560]

description: miRNA


title: Breast Cancer [BC0377]

description: miRNA


title: Breast Cancer [BC1611]

description: miRNA


title: Breast Cancer [BC0373]

description: miRNA


title: Breast Cancer [BC0652]

description: miRNA


title: Breast Cancer [BC1609]

description: miRNA


title: Breast Cancer [BC0672]

description: miRNA


title: Breast Cancer [BC1566]

description: miRNA


title: Breast Cancer [BC1549]

description: miRNA


title: Breast Cancer [BC1538]

description: miRNA


title: WT_D1_5_m1

type: SRA

city: Cambridge

first: Brian

last: Ferguson

address: Tennis Court Road

department: Department of Pathology

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic

data_processing:
Raw reads were quality and adapter trimmed using trimgalore!, reads were mapped to the mouse genome GRCm38 version 95 of the Ensembl genome using STAR aligner, reads were counted into genes using HTSeq and differentially gene expression was performed using the R package edgeR, applying gc content and length correction to the data model.
Normalised CPM, normalised using the TMM method from edgeR. Note that this is not the  the matrix used for comparisons as we process each comparisons by only normalising and filtering the data for the groups involved in the comparisons.
Assembly: GRCm38 version 95
Supplementary files format and content: tab-delimited text files for each Sample

organism: Mus musculus

source_name: Spleen

extract_protocol:
At 1.5 or 6.5 days post innoculation NK cells were isolated by FACS using NK1.1, CD45 and CD3 staining. Half a million viable NK cells (CD45+CD3-NK1.1+ cells) were lysed directly and RNA extracted using Rneasy mini plus kit (Qiagen)
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio) was used to generate cDNAs and quality was assessed using an Agilent 2100 bioanalyser. The Nextera XT DNA Library Prep Kit (Illumina) was used to generate libraries from 125 pg of input cDNA

treatment_protocol: Mice were injected intradermally with 10^3 plaque-forming units of sucrose purified, wild type vaccinia virus strain Western Reserve in PBS in the ear pinnae

value: Spleen

tag: cell line

value: Natural killer (NK) cells

tag: strain

tag: genotype

value: WT

tag: treatment

value: Vaccinia virus infected

tag: time

value: Day 1.5


title: WT_D1_5_m4


title: WT_D1_5_m2


title: WT_D1_5_m3


title: WT_D6_5_m2

value: Day 6.5


title: WT_D6_5_m3


title: Breast Cancer [BC0705]

description: miRNA


title: WT_D6_5_m4


title: Breast Cancer [BC0063]

description: miRNA


title: WT_D6_5_m1


title: M_D6_5_m4

value: Mock infected


title: M_D6_5_m3


title: M_D6_5_m2


title: M_D6_5_m1


title: Breast Cancer [BC0033]

description: miRNA

value: Breast Cancer


title: M_D1_5_m2


title: M_D1_5_m3


title: M_D1_5_m4


title: HhipCKO Control_2

city: San Francisco

first: Tien

last: Peng

state: CA

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

country: USA

institute: University of California San Francisco

data_processing:
FASTQC for  quality control, Cuadapt and Sickle for triming adaptors
reads were aligned and mapped using STAR
DESeq was use to call differential gene expression, in Rstudio
Assembly: UCSC Mouse (GRCm38/mm10)

source_name: Lung mesenchyme

extract_protocol: The RNA was extracted by QIAGEN RNeasy Mini Kits from the cultured cells, and the amount and quality of extracted RNA was measured by RNA 6000 Pico Kit (Agilent). The Bulk RNA-seq was done in GENEWIZ.

treatment_protocol: mice were Tamoxifen injected

value: Adult


title: HhipCKO Control_3


title: Ad-COMBO

city: Tampa

first: Amer

last: Beg

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads from scRNA-seq were processed using Cell Ranger (v3.0, 10X Genomics). Cell barcodes and UMIs associated with the aligned reads were subjected to correction and filtering. Filtered gene-barcodes matrices containing only barcodes with UMI counts passing threshold for cell detection were imported to Seurat v4.0 for downstream analysis.
Barcodes with fewer than 200 genes expressed, or more than 10% UMIs originated from mitochondrial genes, were excluded filtered out; genes expressed in fewer than 3 barcodes were also excluded.
Assembly: mm10
Supplementary files format and content: csv files include the number of UMIs associated with a gene (row) and a cell (column) measured from single-cell RNA-seq

source_name: mouse tumor

growth_protocol: 5*e5 B16-F10 cells were inoculated s.c. and grew in C57BL/6 mice for 12 days.

extract_protocol:
Mice with were cardiac-perfused with PBS containing 10 U/ml heparin to clear peripheral blood, and single cell suspensions were prepared by incubating minced tumor in 1 mg/ml collagenase A and 50 U/ml DNase I at 37oC for 20 min with agitation, followed by passing through a 70μm cell strainer and lysis of red blood cells for 2 min at room temperature. Each scRNA-seq sample was pooled from 3 different similarly treated tumors, CD11c+ MHC-II+ sorted cells were washed twice with 1X PBS (calcium and magnesium-free) containing 0.04% weight/volume BSA and resuspended in the same buffer following the cell preparation guide from 10x Genomics. The cell viability and counts were obtained by AO/PI dual fluorescent staining and visualization on the Nexcelom Cellometer K2 (Nexcelom Bioscience LLC, Lawrence, MA). Cells were then loaded onto the 10X Genomics Chromium Single Cell Controller at a concentration of 1,000 cells/µl in order to encapsulate up to 10,000 cells per sample.
The scRNA-Seq libraries were prepared following the protocol provided by the 10X genomics. The cDNA libraries were completed in a single bulk reaction using the 10X Genomics Chromium NextGEM Single Cell 3’ v 2 chemistry Kit.  50,000 sequencing reads per cell for scRNA-seq were generated on the Illumina NextSeq 500 instrument.
10X genomics Chromium  3' Single Cell RNA-seq

treatment_protocol: On D12, mice were subjected to an intratumoral injection with NULL, ISF35 or/ and mIFNB adenoviruses (Advs).

tag: strin

value: mouse tumor

tag: cell type

value: DC

value: ISF35 and mIFNB Adv treated B16F10 tumor


title: HhipCKO Control_1


title: HhipCKO_1


title: M_D1_5_m1


title: Ad-mIFNB

description: 10x Genomics

value: mIFNB Adv treated B16F10 tumor


title: HhipCKO_2


title: HhipCKO_3


title: HhipCKO_4


title: HhipCKO Control_4


title: MG1655 invitro E phase RNA_biol rep 2

city: STILLWATER

first: Tyrrell

last: Conway

state: OKLAHOMA

address: 307 Life sciences east, OKLAHOMA STATE UNIVERSITY

department: Microbiology and Molecular Genetics

institute: Oklahoma state university

description: RNA-Seq of exponential phase Escherichia coli grown in vitro in MOPS minimal media

data_processing:
Sequencing reads were mapped to the reference genome (accession number:U00096.3) using bowtie2
SAM files were converted to BAM format and sorted and indexed them using SAMtools
The BAM files were then converted to base count (WIG) files
Using in-house script, normalized WIG files were generated by using a simple global normalization approach in which the count at each base location was multiplied by 1 billion and divided that value by the sum of base counts at all base locations in the file
Assembly: U00096.3
Supplementary files format and content: normWIG

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli grown invitro culture

growth_protocol: Wild type E. coli MG1655 StrR cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C and agitation at 200 rpm. Culture samples were harvested during logarithmic phase (OD600=0.4-0.6). 5 ml of cultures were harvested into RNA-protect reagent (Qiagen) at 1:2 dilution and cells then were pelleted by centrifugation at 5000rpm for 10 minutes. Cell pellets were stored at -80°C until RNA extraction. To extract RNA from colonized Wild type E. coli MG1655 StrR , wild type strain was fed to CD-1 male mice and allowed it to colonize for 9 days. The mice were then euthanized, cecum was taken out and cecal mucus was extracted and immediately homogenized in 500 µl Hanks salt solution (Thermoscientific), 500 µl PCA and 210 µl 20% SDS . The tubes were kept on ice until further processing for RNA extraction.

extract_protocol:
All in-vitro RNA samples were extracted using the Qiagen RNeasy Mini Kit, following manufacturer’s protocol. For in vivo samples, RNA samples were extracted using phenol chloroform extraction method. DNase treatment was done using DNAse I enzyme (Invitrogen, Cat no. AM2238). The samples were quantified using the Agilent Bioanalyzer (Agilent, Catalog no. G2939BA).
Approximately 100 ng of total RNA from each sample were processed at University of Bern for ribo-depletion with the Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina, Catalog no. 20037135). RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep kit. Libraries were sequenced on a NovaSeq™ 6000 system, using 1×100 bp single-end read length.

value: E. coli grown invitro culture


title: Ad-Null

description: 10x Genomics

value: NULL Adv treated B16F10 tumor


title: MG1655 mice RNA_biol rep 3

description: RNA-Seq of colonized Escherichia coli extracted from mouse cecal mucus

source_name: mouse mucus from the cecum

value: mouse mucus from the cecum


title: 15-RNA-AK356-sema3c-high2, tech rep 2, biol rep 2

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building, 415 Curie Boulevard

department: Department of Bioengineering

institute: University of Pennsylvania

description: Alignment reference genome hg38

data_processing:
RNA sequencing reads were aligned to the human genome (hg38) with STAR v2.5.5a and map reads were counted using HTSeq v0.6.1 to generate a count matrix.
From the counts matrix, transcript per million (tpm) and other normalized values were calculated for each gene using publicly available scripts at: github.com/arjunrajlaboratory/RajLabSeqTools.
Differential gene expression was performed using DESeq2 in R4.1.0.
Assembly: hg38
Supplementary files format and content: Tab-delimited file displaying gene ensebl ID and gene counts

growth_protocol: FS4 and 1205Lu cells were mantained in DMEM with glutamax and 10% serum at 37°C and 5% CO2. Melanoma cells (WM1552C, WM1862, WM35, WM115, WM1366, WM278, WM39, WM793, WM1799) were mantained in Tu media ( 80% MCDB 153, 10% Leibovitz’s L-15, 2.4mM CaCl2) supplemented with 2% serum and cultured at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using phenol-chloroform extraction followed by clean-up using the RNAeasy Micro kit (Qiagen 74004).
For transwell assays, library preparation was performed using NEBnext single-cell/low input RNA library prep kit (E6420L, NEB). For NKX2.2 CRISPR experiments, library preparation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L) integrated with NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB E7770L).
RNA-seq; NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB E7600S) was used for assigning indices to all samples prior to pooling. Pooled samples were run using an Illumina NextSeq 550 75 cycle high-output kit (Illumina 20024906). Samples were processed as single end reads (75:8:8).

treatment_protocol: Cells were transduced with lentivirus to generate a Cas9 only cell line and CRISPR knockout cell lines.

value: Melanoma cells

value: sema3c high


title: 16-RNA-AK359-8hr-invading, biol rep 3

description: Alignment reference genome hg38

value: fast invaders


title: 14-RNA-AK356-sema3c-high1, tech rep 1, biol rep 2

description: Alignment reference genome hg38


title: 11-RNA-AK359-sema3c-low, biol rep 3

description: Alignment reference genome hg38

value: sema3c low


title: 12-RNA-AK357-sema3c-high, biol rep 3

description: Alignment reference genome hg38


title: 13-RNA-AK356-parental-control, biol rep 2

description: Alignment reference genome hg38

value: parental


title: MG1655 invitro E phase RNA_biol rep 1


title: 17-RNA-AK359-sema3c-high, biol rep 3

description: Alignment reference genome hg38


title: Ad-MEM40

description: 10x Genomics

value: ISF35 Adv treated B16F10 tumor


title: 10-RNA-AK359-non-invading, biol rep 3

description: Alignment reference genome hg38

value: non invading


title: 8-RNA-AK359-parental-control, biol rep 3

description: Alignment reference genome hg38


title: MG1655 mice RNA_biol rep 2


title: 9-RNA-AK359-16hr-invading, biol rep 3

description: Alignment reference genome hg38

value: slow invading


title: MULTIseq_pool

city: Ottawa

first: Jing

last: Wang

state: Ontario

address: 501 Smyth Rd

department: Regenerative Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: 10x Genomics library of a MULTI-seq pool of cells from the cerebral cortex of control (n=2) and methylmercury-treated (0.2ppm; n=2) mice

data_processing:
Raw sequencing reads were processed using CellRanger v4.0.0. The GRCh38 build of the mouse genome was used for both. Except for explicitly setting --expect-cells=25000, default parameters were used for all samples.
Sample demultiplexing was performed using the deMULTIplex R package v1.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: Cell metadata table: Various metadata (sample ID, cluster, etc) for each cell contained in the UMI count matrix. UMI count matrix: Matrix containing UMI counts for all cells passing quality control filters. Anndata object: h5 file of Anndata objects for control and MeHg-treated mice

extract_protocol:
On E15 the embryos were collected and the dorsal cerebral cortices were collected after removal of meninges from the brains of the embryos
cDNA synthesis and library construction was performed using the 10x Genomics Single Cell 3' Reagent Kit v3
3' scRNA-seq

treatment_protocol: Pregnant mice were treated with 0ppm, or 0.2ppm MeHg via drinking water starting from E0 to E13.5. Six embryos from 2 pregnant mice for each treatment (0ppm or 0.2ppm MeHg) were dissected

value: brain; cerebral cortex

value: CD1 mice

value: Embryonic day 15


title: Spleen, 12hC

city: Oslo

first: Yohan

last: Lefol

state: Oslo

address: Sognsvannsveien 20 Rikshospitalet

department: Institute of Clinical Medicine

country: Norway

institute: University of Oslo

data_processing:
The raw sequencing data was aligned to the mouse genome (GCF 000001635.23 GRCm38.p3) using STAR-aligner, chimSegmentMin was set to 30, outFilterMultimapNmax to 20, alignSJoverhangMin to 8, alignSJDBoverhangmin to 1, outFilterMismatchNmax to 10, outFilterMismatchNoverLmax to 0.04, alignIntronMin to 20, and alignIntronMax to 1000000.
Genes were then counted using htseq-count with the following GFF file: GCF 000001635.23 GRCm38.p3 genomic.gff along with the following parameters: stranded (-s) is set to no, idattr (-i) is set to gene, and type (-t) is set to exon.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

extract_protocol:
The RNA for small RNA and mRNA-seq were isolated from the same tube of cells. The TruSeq protocols (small RNA and poly-A) were used for both sequencing experiments
Illumina Poly-A mRNA-seq

value: Spleen

value: 720 minutes


title: Spleen, 6hC

value: 360 minutes


title: Spleen, 24hC

value: 1440 minutes


title: Spleen, 48hC

value: 2880 minutes


title: 7-RNA-AK356-sema3c-low2, tech rep 2, biol rep 2

description: Alignment reference genome hg38


title: VEH+LPS, replicate 1, scRNAseq

city: Columbia

first: Bryan

last: Holloman

state: SC

address: 6311 Garners Ferry Rd

institute: University of South Carolina

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, feature counting and aggregation were made using the Cell Ranger software v3.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Freshly dissected lungs were pooled in 5 ml of FACS buffer-1X PBS, 1% Fetal Bovine Serum (FBS), and 2mM EDTA, homogenized into a single cell suspension, and filtered with 40uM strainer. Next, the single-cell suspension was centrifuged at 1300 rpm for 10 min at 4°C, and the supernatant was discarded. The cells were resuspended in 1mL of RBC lysis buffer and placed on ice for 5 minutes, and the single-cell suspension was then treated with 5 ml of FACS buffer and centrifuged at 1300 rpm for 5 min at 4°C. After discarding the supernatant, cells were washed and centrifuged twice more. The cell pellet was resuspended in 1xPBS with 0.04% w/v BSA buffer and filtered.
Using the manufacturer's protocol exclusively for gene expression, the single-cell RNA-seq libraries were generated from the samples using the Chromium v2 single-cell 5′ VDJ RNA-seq reagent kit [10x Genomics], 3000 target cells per sample (Vehicle, LPS+Veh, LPS+I3C) were loaded into separate lanes onto the 10x Genomics Chromium Controller to generate the gel bead-in-emulsion (GEM) that has polyA mRNA. Samples were collected and placed on the thermocycler. Now samples are cDNA that contain R1, 10x barcode, unique molecular identifier (UMI) and template switch oligo. Amplified cDNA was cleaned up with Silane DynaBeads. Cleaned cDNA was enzymatically fragmented and the correct size selected utilizing SPRIselect breads from [Beckman Coulter]. The optimized amplicon then ligated with R2 primer sequence, and indexed with both the P5 and P7 primers.

value: Immune Cells

value: Lung

value: 8-12 weeks old


title: Spleen, 3hC

value: 180 minutes


title: MG1655 mice RNA_biol rep 1

value: mouse mucus from the cecum


title: Naive, replicate 1, scRNAseq

description: 10x Genomics


title: 5-RNA-AK357-sema3c-low, biol rep 1

description: Alignment reference genome hg38

value: Melanoma cells

value: sema3c low


title: Spleen, 0hC

value: 0 minutes


title: 4-RNA-AK357-non-invading, biol rep 1

description: Alignment reference genome hg38

value: non invading


title: Spleen, 1hC

value: 60 minutes


title: Spleen, 48hT

value: LPS, IL4, TGFb


title: Spleen, 2hC

value: 120 minutes


title: thymus2

city: Minneapolis

first: Ryan

last: Martinez

state: MN

address: 2101 6th St SE

department: Laboratory Medicine and Pathology

institute: University of Minnesota

data_processing:
Raw reads were summarized with FastQC, and trimmed with Trimmomatic. Trimmed reads were aligned to the mm10 reference genome with HISAT2. Duplicate reads based on alignment position were marked with SAMTools. Alignments with duplicates marked were summarized with RNASeQC to quantify the proportion of positional duplicates, identify risosomal alignments, and quantify the proportion of "on-target" reads. Processed alignments were filtered of reads that have a mapping quality of less than 60, and sorted by query name rather than position.
Cleaned and name-sorted alignments were processed with the featureCounts tool from the subread package. Fragments were counted in a strand-specific manner.
Raw counts were imported into the edgeR package in R. Genes that are shorter than 200bp were pruned from the counts matrix before differential expression testing. The differential expression testing was peformed with a quasi-likelihood test in edgeR between all pairwise combinations of groups.
Assembly: mm10
Supplementary files format and content: Text files that contain normalized relative expression matrix and raw read counts matrix

source_name: Thymus

extract_protocol:
Thymi were harvested and digested in Collagenase D for 30 min, while peyer's patch cells did not undergo collagenase treatment. Single cell suspensions of both cell types were stained with antibody and sorted using a FACS ARIA II. RNA from sorted cells was isolated using the Qiagen Rneasy Micro kit per the manufacturer’s instructions.
RNA libraries were generated using Clontech Stranded Total RNA Pico Mammalian v2 and sequenced  on a NextSeq instruemnt (Illuminia)

value: Thymus

value: Thymi:B cells

value: Collagenase


title: thymus3


title: thymus1


title: 2-RNA-AK357-8hr-invading, biol rep 1

description: Alignment reference genome hg38

value: fast invading


title: pp3

source_name: Peyer's Patch

value: Peyer's Patch

value: Peyer's Patch:B cells


title: 6-RNA-AK356-sema3c-low1, tech rep 1, biol rep 2

description: Alignment reference genome hg38


title: Spleen, 24hT

value: Spleen

value: 1440 minutes


title: 1-RNA-AK357-parental-control, biol rep 1

description: Alignment reference genome hg38

value: parental


title: I3C+LPS, replicate 2, scRNAseq

description: 10x Genomics

value: Immune Cells

value: Lung

value: 8-12 weeks old


title: pp2


title: Spleen, 6hT

value: 360 minutes


title: Spleen, 2hT


title: Spleen, 15mC

value: 15 minutes


title: Spleen, 3hT

value: 180 minutes


title: Spleen, 30mC

value: 30 minutes


title: pp1


title: 45-AK167-Parent3, tech rep 3, biol rep 3

description: Alignment reference genome hg38

value: Melanoma cells


title: 3-RNA-AK357-16hr-invading, biol rep 1

description: Alignment reference genome hg38

value: slow invading


title: Spleen, 30mT

value: LPS, IL4, TGFb


title: Spleen, 1hT

value: 60 minutes


title: Spleen, 15mT


title: HepG2 RRM2B cells, Cisplatin treated Rep 1

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Raw fastq files were assessed by FastQC (v0.11.5).
The adapters and low-quality sequence were trimmed by cutadapt (v-1.13).
The gene expression quantification analysis was performed by RSEM (v-1.3.0) based on the reference genome hg38 (GRCh38) with gene annotation from GENCODE (release 28).
The raw counts of reads mapped to each gene were extracted and used for subsequent analysis.
Assembly: hg38
Supplementary files format and content: out.tab files containg read counts for each sample

source_name: Liver

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HepG2 cells were treated with 3.125uM Cisplatin for 72 hours prior to RNA extraction

value: Liver

value: Hepatocyte

value: RRM2B Overexpression

value: Cisplatin 3.125 uM


title: HepG2 RRM2B cells, Cisplatin treated Rep 2


title: 44-AK167-Parent2, tech rep 2, biol rep 3

description: Alignment reference genome hg38


title: 43-AK167-Parent1, tech rep 1, biol rep 3

description: Alignment reference genome hg38


title: Spleen, 0hT

value: Spleen

value: 0 minutes


title: HepG2 RRM2B cells, untreated Rep 2

value: Untreated


title: 42-AK167-8hB3, tech rep 3, biol rep 3

description: Alignment reference genome hg38

value: invading, 8 hours


title: E14.5 Fetal Liver HSC [E14F-16]

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

data_processing:
The quality of all sequenced samples was analyzed using FastQC. The low quality of raw reads are trimmed by Trimmomatic-0.36.
Reads were mapped to the Mm10. Mapping and transcript assembly were performed with STAR using default parameters. Read counts are obtained by Htseq-count.
Genome_build: Mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

source_name: Mouse embryo fetal liver HSC

extract_protocol:
Each cell was single cell sorted into 96 well plate (1 cell/well) and RNA was extracted and converted into cDNA using SAMRT-Seq Single cell kit (Takara)
Following cDNA synthesis, DNA library preparation kit (Illumina) was used to prepare library
120pg of cDNA was simultaneously fragmented and tagged with adapter sequences by transposome. The product was then amplified using 12 cycles of PCR and purified.

tag: surface markers


title: E14.5 Fetal Liver HSC [E14F-15]


title: Spleen, 12hT

value: 720 minutes


title: 41-AK167-8hB2, tech rep 2, biol rep 3

description: Alignment reference genome hg38


title: E14.5 Fetal Liver HSC [E14F-14]


title: HepG2 RRM2B cells, untreated Rep 1


title: E14.5 Fetal Liver HSC [E14F-13]


title: E14.5 Fetal Liver HSC [E14F-12]


title: E14.5 Fetal Liver HSC [E14F-11]


title: 39-AK167-24hB3, tech rep 3, biol rep 3

description: Alignment reference genome hg38

value: invading, 24 hours


title: E14.5 Fetal Liver HSC [E14F-09]


title: HepG2 RRM2 cells, Cisplatin treated Rep 2

value: RRM2 Overexpression


title: 38-AK167-24hB2, tech rep 2, biol rep 3

description: Alignment reference genome hg38


title: E14.5 Fetal Liver HSC [E14F-10]


title: HepG2 RRM2 cells, untreated Rep 2


title: HepG2 RRM2 cells, Cisplatin treated Rep 1


title: E14.5 Fetal Liver HSC [E14F-08]


title: HepG2 RRM2 cells, untreated Rep 1


title: 36-AK167-24hT3, tech rep 3, biol rep 3

description: Alignment reference genome hg38

value: non invading, 24 hours


title: E14.5 Fetal Liver HSC [E14F-07]


title: 37-AK167-24hB1, tech rep 1, biol rep 3

description: Alignment reference genome hg38


title: E14.5 Fetal Liver HSC [E14F-05]


title: E14.5 Fetal Liver HSC [E14F-03]


title: HepG2 RTD cells, Cisplatin treated Rep 2

value: RTD Overexpression


title: 35-AK167-24hT2, tech rep 2, biol rep 3

description: Alignment reference genome hg38

value: Melanoma cells


title: 40-AK167-8hB1, tech rep 1, biol rep 3

description: Alignment reference genome hg38


title: HepG2 RTD cells, Cisplatin treated Rep 1


title: E14.5 Fetal Liver HSC [E14F-02]


title: 34-AK167-24hT1, tech rep 1, biol rep 3

description: Alignment reference genome hg38


title: E12.5 Fetal Liver HSC [E12F-16]


title: 33-AK167-8hT3, tech rep 3, biol rep 3

description: Alignment reference genome hg38

value: non invading, 8 hours


title: E14.5 Fetal Liver HSC [E14F-01]


title: HepG2 RTD cells, untreated Rep 2


title: E12.5 Fetal Liver HSC [E12F-14]


title: E12.5 Fetal Liver HSC [E12F-13]


title: 32-AK167-8hT2, tech rep 2, biol rep 3

description: Alignment reference genome hg38


title: HepG2 RTD cells, untreated Rep 1


title: E14.5 Fetal Liver HSC [E14F-06]


title: HepG2 SF10 cells, Cisplatin treated Rep 2

value: RRM2B KO


title: E12.5 Fetal Liver HSC [E12F-12]


title: E12.5 Fetal Liver HSC [E12F-10]


title: HepG2 SF10 cells, Cisplatin treated Rep 1


title: 31-AK167-8hT1, tech rep 1, biol rep 3

description: Alignment reference genome hg38


title: E12.5 Fetal Liver HSC [E12F-08]


title: E12.5 Fetal Liver HSC [E12F-09]


title: E14.5 Fetal Liver HSC [E14F-04]


title: 30-AK171-Parent3, tech rep 3, biol rep 2

description: Alignment reference genome hg38

value: parental


title: HepG2 SF10 cells, untreated Rep 2

value: Liver


title: E12.5 Fetal Liver HSC [E12F-07]


title: E12.5 Fetal Liver HSC [E12F-15]


title: 29-AK171-Parent2, tech rep 2, biol rep 2

description: Alignment reference genome hg38


title: HepG2 SF10 cells, untreated Rep 1

value: Hepatocyte


title: 28-AK171-Parent1, tech rep 1, biol rep 2

description: Alignment reference genome hg38


title: E12.5 Fetal Liver HSC [E12F-05]


title: E12.5 Fetal Liver HSC [E12F-04]


title: E12.5 Fetal Liver HSC [E12F-03]


title: HepG2 IC4 cells, Cisplatin treated Rep 2


title: 27-AK171-8hB3, tech rep 3, biol rep 2

description: Alignment reference genome hg38


title: HepG2 IC4 cells, Cisplatin treated Rep 1


title: E12.5 Fetal Liver HSC [E12F-02]


title: E12.5 Fetal Liver HSC [E12F-11]


title: E12.5 Fetal Liver HSC [E12F-01]


title: 26-AK171-8hB2, tech rep 2, biol rep 2

description: Alignment reference genome hg38


title: E11.5 Yolk Sac pre-HSC [E11Y-15]

source_name: Mouse embryo YS pre-HSC


title: 25-AK171-8hB1, tech rep 1, biol rep 2

description: Alignment reference genome hg38


title: E11.5 Yolk Sac pre-HSC [E11Y-14]


title: E11.5 Yolk Sac pre-HSC [E11Y-16]


title: HepG2 IC4 cells, untreated Rep 1


title: HepG2 IC4 cells, untreated Rep 2


title: Breast Cancer [BC1585]

description: miRNA

value: Breast Cancer

value: Serum

value: Female

value: TNM Classification 8th edition):T1

value: No


title: 24-AK171-24hB3, tech rep 3, biol rep 2

description: Alignment reference genome hg38


title: E11.5 Yolk Sac pre-HSC [E11Y-12]


title: 23-AK171-24hB2, tech rep 2, biol rep 2

description: Alignment reference genome hg38


title: E11.5 Yolk Sac pre-HSC [E11Y-11]


title: HepG2 cells, Cisplatin treated Rep 2

value: WT

value: Cisplatin 3.125 uM


title: E11.5 Yolk Sac pre-HSC [E11Y-10]


title: E11.5 Yolk Sac pre-HSC [E11Y-09]


title: HepG2 cells, Cisplatin treated Rep 1


title: E11.5 Yolk Sac pre-HSC [E11Y-07]


title: E12.5 Fetal Liver HSC [E12F-06]


title: 20-AK171-24hT2, tech rep 2, biol rep 2

description: Alignment reference genome hg38


title: E11.5 Yolk Sac pre-HSC [E11Y-08]


title: 21-AK171-24hT3, tech rep 3, biol rep 2

description: Alignment reference genome hg38


title: E11.5 Yolk Sac pre-HSC [E11Y-05]


title: E11.5 Yolk Sac pre-HSC [E11Y-04]


title: M_Healthy_3_L5

city: Genève

first: Nicolas

last: Hulo

address: 1 rue Michel Servet

country: Switzerland

institute: Université de Genève

data_processing:
Sequenced reads were mapped to the Homo sapiens UCSC hg38 genome with the STAR program (version 2.5.2a) , and the count table containing the number of mapped reads per gene was produced with featureCounts (version 1.6.0).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (csv format)

source_name: airway epithelia

extract_protocol:
human airway epithlia from healthy versus asthmatic donors have been infected or not with rhinoviruses. Infected and non-infected tissues were lysed in 800l of trizol (Ambion, 5596018) and RNA was extracted according to manufacturer’s instruction.
The TruSeq Stranded total RNA kit with Ribo-Zero Gold was used for the library preparation with 150 ng of total RNA as input.
The 18 libraries were pooled at equimolarity and loaded at 8.5 pM for clustering on a single-read Illumina Flow cell. All 100-base sequencing was performed using the TruSeq SBS HS v3 chemistry on an Illumina HiSeq 2500 sequencer

tag: disease state

value: Healthy

value: airway epithelia

value: differentiated primary cells

value: epitheial

value: wt


title: E11.5 Yolk Sac pre-HSC [E11Y-03]


title: HepG2 cells, untreated Rep 1

value: Untreated


title: 19-AK171-24hT1, tech rep 1, biol rep 2

description: Alignment reference genome hg38

value: Melanoma cells

value: non invading, 24 hours


title: E11.5 Yolk Sac pre-HSC [E11Y-13]


title: E11.5 Yolk Sac pre-HSC [E11Y-01]


title: M_Healthy_3_L3


title: 18-AK171-8hT3, tech rep 3, biol rep 2

description: Alignment reference genome hg38

value: non invading, 8 hours


title: E11.5 AGM pre-HSC  [E11A-48]

source_name: Mouse embryo AGM region pre-HSC


title: M_Healthy_3_L2


title: E11.5 Yolk Sac pre-HSC [E11Y-02]


title: 22-AK171-24hB1, tech rep 1, biol rep 2

description: Alignment reference genome hg38

value: invading, 24 hours


title: 17-AK171-8hT2, tech rep 2, biol rep 2

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-45]


title: 16-AK171-8hT1, tech rep 1, biol rep 2

description: Alignment reference genome hg38


title: HepG2 cells, untreated Rep 2

value: Liver

value: Hepatocyte


title: E11.5 AGM pre-HSC  [E11A-46]


title: E11.5 Yolk Sac pre-HSC [E11Y-06]


title: M_Healthy_2_L3


title: M_Healthy_2_L5


title: 15-AK173-Parent3, tech rep 3, biol rep 1

description: Alignment reference genome hg38

value: parental


title: M_Healthy_2_L2


title: 14-AK173-Parent2, tech rep 2, biol rep 1

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-41]


title: E11.5 AGM pre-HSC  [E11A-40]


title: M_Healthy_1_L5


title: 13-AK173-Parent1, tech rep 1, biol rep 1

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-39]


title: E11.5 AGM pre-HSC  [E11A-38]


title: E11.5 AGM pre-HSC  [E11A-36]


title: E11.5 AGM pre-HSC  [E11A-37]


title: E11.5 AGM pre-HSC  [E11A-47]


title: E11.5 AGM pre-HSC  [E11A-44]


title: E11.5 AGM pre-HSC  [E11A-35]


title: 11-AK173-8hB2, tech rep 2, biol rep 1

description: Alignment reference genome hg38

value: invading, 8 hours


title: E11.5 AGM pre-HSC  [E11A-34]


title: 10-AK173-8hB1, tech rep 1, biol rep 1

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-33]


title: E11.5 AGM pre-HSC  [E11A-32]


title: M_Asthma_3_L3

value: Asthma


title: E11.5 AGM pre-HSC  [E11A-42]


title: M_Healthy_1_L2


title: E11.5 AGM pre-HSC  [E11A-30]


title: E11.5 AGM pre-HSC  [E11A-31]


title: M_Asthma_3_L2


title: 09-AK173-24hB3, tech rep 3, biol rep 1

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-43]


title: E11.5 AGM pre-HSC  [E11A-29]


title: M_Asthma_3_L5


title: E11.5 AGM pre-HSC  [E11A-28]


title: E11.5 AGM pre-HSC  [E11A-27]


title: M_Healthy_1_L3


title: 12-AK173-8hB3, tech rep 3, biol rep 1

description: Alignment reference genome hg38


title: M_Asthma_2_L3


title: E11.5 AGM pre-HSC  [E11A-26]


title: E11.5 AGM pre-HSC  [E11A-25]


title: 06-AK173-24hT3, tech rep 3, biol rep 1

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-24]


title: M_Asthma_2_L2


title: E11.5 AGM pre-HSC  [E11A-23]


title: M_Asthma_1_L5


title: E11.5 AGM pre-HSC  [E11A-22]


title: 05-AK173-24hT2, tech rep 2, biol rep 1

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-21]


title: 04-AK173-24hT1, tech rep 1, biol rep 1

description: Alignment reference genome hg38


title: 08-AK173-24hB2, tech rep 2, biol rep 1

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-19]


title: M_Asthma_1_L3


title: 03-AK173-8hT3, tech rep 3, biol rep 1

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-16]


title: C15_Healthy_3_L5

value: Rhinovirus C15 infection


title: 02-AK173-8hT2, tech rep 2, biol rep 1

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-20]


title: M_Asthma_1_L2


title: E11.5 AGM pre-HSC  [E11A-18]


title: E11.5 AGM pre-HSC  [E11A-15]


title: 07-AK173-24hB1, tech rep 1, biol rep 1

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-14]


title: M_Asthma_2_L5


title: E11.5 AGM pre-HSC  [E11A-13]


title: 01-AK173-8hT1, tech rep 1, biol rep 1

description: Alignment reference genome hg38


title: 33-AK473-noninvading, biol rep 3

description: Alignment reference genome hg38

value: noninvading


title: C15_Healthy_3_L3

value: Healthy


title: C15_Healthy_3_L2

value: airway epithelia


title: E11.5 AGM pre-HSC  [E11A-11]


title: 32-AK473-slow invading, 16 hours, biol rep 3

description: Alignment reference genome hg38

value: invading, 16 hours


title: E11.5 AGM pre-HSC  [E11A-10]


title: E11.5 AGM pre-HSC  [E11A-12]


title: E11.5 AGM pre-HSC  [E11A-09]


title: C15_Healthy_2_L5

value: differentiated primary cells

value: epitheial


title: E11.5 AGM pre-HSC  [E11A-17]


title: C15_Healthy_2_L3

value: wt


title: 31-AK473-fast invading, 8 hours, biol rep 3

description: Alignment reference genome hg38

value: Melanoma cells


title: E11.5 AGM pre-HSC  [E11A-08]


title: E11.5 AGM pre-HSC  [E11A-06]


title: 29-AK473-sc2, tech rep 2, biol rep 3

description: Alignment reference genome hg38

value: AAVS control


title: C15_Healthy_2_L2


title: E11.5 AGM pre-HSC  [E11A-04]


title: C15_Healthy_1_L5


title: E11.5 AGM pre-HSC  [E11A-02]


title: C15_Healthy_1_L3


title: 28-AK473-sc1, tech rep 1, biol rep 3

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-01]


title: 4-2, 37C

city: Worcester

first: Amy

middle: K

last: Walker

state: Massachusetts

address: Suite 137, Biotech 2, 373 Plantation St

department: Program in Molecular Medicine

institute: UMass Chan Medical School

data_processing:
RNA for deep sequencing was purified by Qiagen RNAeasy. Duplicate samples were sent for library construction and sequencing at BGI (China)
Raw sequencing reads were processed using an in-house RNA-Seq data processing software Dolphin at University of Massachusetts Medical School
The raw read pairs were first aligned to C. elegans reference genome with ws245 annotation. The RSEM method was used to quantify the expression levels of genes
Deseq was used to produce differentially expressed gene sets with more than a 2-fold difference in gene expression, with replicates being within 0.05 in a Students T test and a False Discovery Rate (FDR) under 0.01.
Statistics were calculated with DeBrowser
Assembly: ce11 with ws254 notations
Supplementary files format and content: abundance measurements

organism: Caenorhabditis elegans

source_name: C. elegans N2 ; sams-4 RNAi

extract_protocol:
Young adult C. elegans were lysed in 0.5% SDS, 5% b-ME, 10 mM EDTA, 10 mM Tris-HCl pH 7.4, 0.5 mg/ml Proteinase K, then RNA was purified with Tri-Reagent (Sigma)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C. elegans (N2) were cultured using standard laboratory conditions on E. coli OP50.  Adults were bleached onto RNAi plates and allowed to develop to the L4 to young adult at 15C. The adults were then subjected to heat shock at 37C for hours and collected for RNA isolation and library prep

value: whole body

tag: temperature

value: sams-4 RNAi


title: 4-3, 37C

growth_protocol: C. elegans (N2) were cultured using standard laboratory conditions on E. coli OP50.  Adults were bleached onto RNAi plates and allowed to develop to the L4 to young adult at 15C


title: 26-AK473-16, tech rep 3, biol rep 3

description: Alignment reference genome hg38

value: NKX2.2 knockdown


title: C15_Healthy_1_L2


title: 27-AK473-cas9, biol rep 3

description: Alignment reference genome hg38

value: parental, cas9 only


title: 4-1, 37C


title: EV3, 37C

source_name: C. elegans N2 ; control RNAi

value: control RNAi


title: EV1, 37C


title: C15_Asthma_3_L5


title: C15_Asthma_3_L3


title: EV2, 37C


title: 25-AK473-14, tech rep 2, biol rep 3

description: Alignment reference genome hg38


title: E11.5 AGM pre-HSC  [E11A-07]


title: 30-AK473-sc3, tech rep 3, biol rep 3

description: Alignment reference genome hg38


title: 24-AK473-13, tech rep 1, biol rep 3

description: Alignment reference genome hg38


title: sams-4.3, 15C


title: sams-4.2, 15C


title: C15_Asthma_3_L2


title: sams-4.1, 15C


title: E11.5 AGM pre-HSC  [E11A-05]


title: 23-AK473-parental, biol rep 3

description: Alignment reference genome hg38

value: parental


title: E11.5 AGM pre-HSC  [E11A-03]


title: EV3b, 15C


title: EV2b, 15C


title: C15_Asthma_2_L5

value: Asthma


title: 22-AK471-noninvading, biol rep 2

description: Alignment reference genome hg38


title: C15_Asthma_2_L3

value: Rhinovirus C15 infection


title: 21-AK471-slow invading, 16 hours, biol rep 2

description: Alignment reference genome hg38


title: EV1b, 15C


title: C15_Asthma_2_L2


title: 20-AK471-fast invading, 8 hours, biol rep 2

description: Alignment reference genome hg38

value: invading, 8 hours


title: C15_Asthma_1_L5


title: 19-AK471-sc3, tech rep 3, biol rep 2

description: Alignment reference genome hg38


title: C15_Asthma_1_L2


title: 18-AK471-sc2, tech rep 2, biol rep 2

description: Alignment reference genome hg38


title: C15_Asthma_1_L3


title: 17-AK471-sc1, tech rep 1, biol rep 2

description: Alignment reference genome hg38


title: 16-AK471-cas9, biol rep 2

description: Alignment reference genome hg38


title: B48_Healthy_3_L3

value: Healthy

value: Rhinovirus B48 infection


title: B48_Healthy_3_L5

value: airway epithelia


title: B48_Healthy_3_L2

value: differentiated primary cells


title: 15-AK471-16, tech rep 3, biol rep 2

description: Alignment reference genome hg38


title: sam4-hs-1

library_source: genomic

data_processing:
Paired end reads from each sample were aligned to the C. elegans genome (ce11 with ws245 annotations) using Bowtie2 (Langmead et al., 2009)with the parameters -N 1 and -X 2000.
Duplicate reads were removed using Picard (http://broadinstitute.github.io/picard/) and the reads with low quality scores (MAPQ < 10) were removed.
HOMER software suite was used to process the remaining mapped reads (Heinz et al., 2010). The “makeUCSCfile” command was used for generating genome browser tracks, the “findPeaks” command was used for calling H3K4me3 peaks and the “annotatePeaks” command was used for making aggregation plots.
Differential peak calling was accomplished using ChipPeakAnno (Zhu et al., 2010).  TSS plots were generated using HOMER (Heinz et al., 2010)
Assembly: ce11 with ws254 notations
Supplementary files format and content: peak text files
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: nuclei

extract_protocol:
Young adult C. elegans were lysed in nuclear purification buffer using tissue homogenizer and histone-DNA-antibody complexes were isolated using activated pA-Tn5
CUT&Tag libraries were prepared for sequencing using established protocols

treatment_protocol: C. elegans (N2) were cultured using standard laboratory conditions on E. coli OP50.  Adults were bleached onto RNAi plates and allowed to develop to the L4 to young adult at 15C. The adults were then subjected to heat shock at 37C for hours and collected for CUT&Tag library prep

tag: chip antibody

value: H3K4me3 Cell signalling


title: sam1-hs-2

tag: tissue

value: sams-1 RNAi


title: EV-hs-1


title: sam1-hs-1


title: sam4-hs-2


title: EV-hs-2


title: 14-AK471-14, tech rep 2, biol rep 2

description: Alignment reference genome hg38

value: Melanoma cells


title: sam4-cn-2


title: B48_Healthy_2_L5

value: epitheial

value: wt


title: 13-AK471-13, tech rep 1, biol rep 2

description: Alignment reference genome hg38


title: sam1-cn-2

value: whole body


title: B48_Healthy_2_L3


title: sam1-cn-1


title: EV-cn-2


title: B48_Healthy_2_L2


title: EV-cn-1


title: 12-AK471-parental, biol rep 2

description: Alignment reference genome hg38


title: 11-AK469-noninvading, biol rep 1

description: Alignment reference genome hg38

value: noninvading


title: 7-AK469-sc2, tech rep 2, biol rep 1

description: Alignment reference genome hg38

value: AAVS control


title: 9-AK469-fast invading, 8 hours, biol rep 1

description: Alignment reference genome hg38


title: sam4-cn-1

value: sams-4 RNAi


title: 8-AK469-sc3, tech rep 3, biol rep 1

description: Alignment reference genome hg38


title: 10-AK469-slow invading, 16 hours, biol rep 1

description: Alignment reference genome hg38

value: invading, 16 hours


title: B48_Healthy_1_L2


title: B48_Healthy_1_L3


title: B48_Asthma_3_L3

value: Asthma


title: B48_Asthma_3_L2


title: B48_Asthma_3_L5


title: 6-AK469-sc1, tech rep 1, biol rep 1

description: Alignment reference genome hg38


title: 5-AK469-cas9, biol rep 1

description: Alignment reference genome hg38

value: parental, cas9 only


title: B48_Asthma_2_L5


title: 3-AK469-14, tech rep 2, biol rep 1

description: Alignment reference genome hg38

value: NKX2.2 knockdown


title: B48_Asthma_2_L2


title: 2-AK469-13, tech rep 1, biol rep 1

description: Alignment reference genome hg38


title: IPS_G15_L

city: Pamplona

first: Juan Roberto

last: Rodriguez-Madoz

state: Navarra

address: PIO XII 55

department: Cell Therapy Program

country: Spain

institute: Foundation For Applied Medical Research

description: Gene expression data from iPSC derived from Adipose Derived Stem Cell (ADSC_G15)

hyb_protocol: Labelled cDNA was purified with RNeasy MinElute Cleanup Kit Cat.# 74204 (Izasa/Qiagen). Labeled cDNA was hybridized to SurePrint G3 Human GE 8x60 Agilent® Microarray chip (ID: G4858A-028004).using Gene Expression Hybridization Kit Cat. # 5188-5242).

scan_protocol: Agilent Technologies Scanner G2505C US82003505

data_processing: Data were normalized with Bioconductor software using quantiles

source_name: iPSC derived from Adipose Derived Stem Cell ADSC_G15

label_protocol: For future sample normalization, RNA was treated with One-Color RNA Spike-In Kit cat. # 5188-5282 (Agilent). 200ng of RNA were used for cDNA preparation with Low Input Quick Amp Labeling Kit, one-color Cat. # 5190-2305, Agilent®. Sample labelling with dye3 (cy3) fluorofor was made with previous cited kit. Labelled cDNA was purified with RNeasy MinElute Cleanup Kit Cat.# 74204 (Izasa/Qiagen).

growth_protocol: Human iPSCs were grown on MEFs in standard human ESC media (DMEM-KO, 20% KOSR, 2mM L-Glutamine, 1% P/S, 0.1mM NEAA, 0.1mM b-mercaptoethanol, 5ng/ml bFGF). ADSCs were culture on alpha-MEM supplemented with 10% FBS, 1% P/S and 1ng/ml bFGF.

extract_protocol: Trizol

treatment_protocol: iPSC  were culture under standard culture conditions in irradiated MEFs

value: Adipose tissue

value: Induced pluripotent stem cells

tag: disease

value: Normal

tag: gender

value: Male


title: IPS_G15_D


title: IPS_G15_A0


title: B48_Healthy_1_L5

value: Healthy

value: airway epithelia

value: differentiated primary cells

value: Rhinovirus B48 infection


title: ADSC_G10

description: Gene expression data from Adipose Derived Stem Cell

source_name: Adipose Derived Stem Cell

value: Adipose Derived Stem Cell


title: ADSC_G15


title: ADSC_G17


title: B48_Asthma_1_L5

value: epitheial

value: wt


title: IPS_G15_AE


title: IPS_G15_AI


title: 1-AK469-parental, biol rep 1

description: Alignment reference genome hg38

value: Melanoma cells

value: parental


title: 4-AK469-16, tech rep 3, biol rep1

description: Alignment reference genome hg38


title: B48_Asthma_1_L2


title: B48_Asthma_2_L3


title: 20_ATAC_AK358_sema3c_low, biol rep 3

description: Alignment reference genome hg38

data_processing:
ATAC reads were aligned to the human genome (hg38) assembly using bowtie2 v2.3.4.1, filtered out low-quality alignments with samtools v1.1, removed duplicate read pairs with picard 1.96, and generated artificial single-ended text-based alignment files containing inferred Tn5 insertion points with custom python scripts and bedtools v2.25.0.
Peaks from ATAC sequencing were called using MACS2 2.1.1.20160309 with the command, “macs2 callpeak --nomodel --nolambda --keep-dup all --call-summits -B --SPMR --format BED -q 0.05 --shift 75 --extsize 150”.
Assembly: hg38
Supplementary files format and content: Data provided as wiggle files and tab-delimited files of ATAC-seq peaks.

growth_protocol: FS4 and 1205Lu cells were mantained in DMEM with glutamax and 10% serum at 37°C and 5% CO2.

extract_protocol:
Nuclei from early-, late-, and non-invaders were extracted from 50,000 lysed cells and collected in lo-bind tubes. DNA tagmentation was performed using the Illumina Tagment DNA Enzyme TDE1 (20034197).
Libraries were prepared using custom primer indices follwed by double-sided bead purification using Agencourt AM Pure XP magnetic beads (A63880).
Libraries were tested for average fragment length using Agilent High Sensitvity DNA Kit (5067-4626) and the concentration was tested using Qubit™ dsDNA HS kit (#Q32851, Invitrogen).
ATAC-seq; Samples were run as paired-end using 150-cycle NextSeq 500/550 High Output Kit v2.5.

treatment_protocol: Early-, late-, and non-invading cells were collected for analysis.


title: 19_ATAC_AK358_sema3c_high, biol rep 3

description: Alignment reference genome hg38


title: systemic sclerosis 3

city: Bao Tou

first: Tiantian

last: Ding

address: No 41, Linyin Road, Kundulun district, Baotou

country: China

institute: The First Affiliated Hospital of Baotou Medical College

data_processing:
remove adapter sequences and low-quality reads from raw data used Seqtk (Version: 1.3-r106)
Use HISAT2 software to perform genome mapping analysis
Differential expression analysis was performed using the edgeR R package (1.10.1)
Assembly: GRCh38
Supplementary files format and content: Supplementary_files_format_and_content: mRNA_gene_expression.xls
Supplementary files format and content: Supplementary_files_format_and_content: lncRNA_expression_anno.xls
Supplementary files format and content: Supplementary_files_format_and_content: circRNA_expression.xls

source_name: plasma

extract_protocol:
Plasma exosomes and exosomal RNA of 6 systemic sclerosis patients and 6 health people were purified by exoRNeasy Serum/Plasma Maxi Kit per the manufacturer’s instruction
RNA libraries for RNA-seq were prepared using SMARTER RNA-Seq Library Prep Kit following manufacturer's protocols.

value: plasma

value: exosome


title: systemic sclerosis 6


title: Healthy control 5


title: Healthy control 2


title: systemic sclerosis 5


title: Healthy control 6


title: Healthy control 3


title: 15_ATAC_AK358_parental_control, biol rep 3

description: Alignment reference genome hg38


title: systemic sclerosis 4


title: Healthy control 1


title: Healthy control 4


title: systemic sclerosis 1


title: systemic sclerosis 2


title: 17_ATAC_AK358_16hr_invading, biol rep 3

description: Alignment reference genome hg38

value: invading, 16 hours


title: B48_Asthma_1_L3

value: Asthma


title: A549 cell, only radiation therapy group

city: Busan

first: Jaewan

last: Jeon

address: 875, Haeun-daero, Haeundae-gu, Busan, Republic of Korea

country: South Korea

institute: Jaewan Jeon

description: radiation

data_processing:
Low-quality raw reads were removed from the sequencer.
Sequence reads were trimmed for adaptor sequence using Cutadapt.
Trimmed sequence reads were mapped to GRCh38 using bowtie2 v2.3.4.1.
Read count extraction was performed using featureCounts v1.6.0 and then FPKM values were calculated based on the read counts.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lung cancer

extract_protocol:
RNA was extracted using QIAzol® Lysis Reagent (Cat. No. 79306), RNeasy® Mini Kit (Cat. No. 74106), Tungsten Carbide Beads  (Cat. No. 69997). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

value: lung cancer

value: adenocarcinomic human alveolar basal epithelial cells

value: only radiation therapy


title: 18_ATAC_AK358_non_invading, biol rep 3

description: Alignment reference genome hg38

value: non invading


title: A549 cell, only aerobic exercise group

description: exercise

value: only aerobic exercise


title: 14_ATAC_AK357_sema3c_low2, tech rep 2, biol rep 2

description: Alignment reference genome hg38


title: A549 cell, control

description: con

value: Control


title: A549 cell, Combination of aerobic exercise and radiation therapy group

description: ex-ra

value: Combined aerobic exercise and radiation therapy


title: 13_ATAC_AK357_sema3c_high2, tech rep 2, biol rep 2

description: Alignment reference genome hg38


title: 12_ATAC_AK357_sema3c_low1, tecg rep 1, biol rep 2

description: Alignment reference genome hg38