title: NB13101001 Non-cancer B


title: NB13082301 Non-cancer B

status: Public on Jun 23 2021

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was 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 undetected) 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 state

value: Non-cancer B

tag: Sex

value: Male

tag: age


title: NB13073003 Non-cancer B


title: NB13080703 Non-cancer B


title: NB13073102 Non-cancer B


title: NB13081205 Non-cancer B


title: NB13080701 Non-cancer B


title: NB13071601 Non-cancer B


title: NB13072401 Non-cancer B


title: NB13070803 Non-cancer B


title: NB13070902 Non-cancer B


title: NB13062702 Non-cancer B


title: NB13072502 Non-cancer B


title: NB13072205 Non-cancer B


title: NB13071603 Non-cancer B


title: NB13071703 Non-cancer B


title: NB16022604 Non-cancer B


title: NB13070807 Non-cancer B


title: NB13062601 Non-cancer B


title: NB13081301 Non-cancer B


title: NB13062407 Non-cancer B


title: NB13062408 Non-cancer B


title: NB13070302 Non-cancer B


title: NB13062405 Non-cancer B


title: NB13061105 Non-cancer B


title: NB13061901 Non-cancer B


title: NB13061802 Non-cancer B


title: NB13052705 Non-cancer B


title: NB13060302 Non-cancer B


title: NB13060403 Non-cancer B


title: NB13052401 Non-cancer B


title: NB13061903 Non-cancer B


title: NB13060306 Non-cancer B


title: NB13052201 Non-cancer B


title: NB13040402 Non-cancer B


title: NB13052101 Non-cancer B


title: NB13040501 Non-cancer B


title: NB13040206 Non-cancer B


title: NB13041703 Non-cancer B


title: NB13042301 Non-cancer B


title: NB13041704 Non-cancer B


title: NB13031103 Non-cancer B


title: NB13031208 Non-cancer B


title: NB13040102 Non-cancer B


title: NB13032202 Non-cancer B


title: NB13032702 Non-cancer B


title: NB13040202 Non-cancer B


title: NB13032603 Non-cancer B


title: NB13021404 Non-cancer B


title: NB13040301 Non-cancer B


title: NB13030101 Non-cancer B


title: NB13030504 Non-cancer B


title: NB13020604 Non-cancer B


title: NB13012107 Non-cancer B


title: NB13012501 Non-cancer B


title: NB13050706 Non-cancer B


title: NB13051504 Non-cancer B


title: NB13020402 Non-cancer B


title: NB13030404 Non-cancer B


title: NB13022802 Non-cancer B


title: NB13031801 Non-cancer B


title: NB13040806 Non-cancer B


title: NB13042202 Non-cancer B


title: NB12122701 Non-cancer B


title: NB13011604 Non-cancer B


title: NB13011802 Non-cancer B


title: NB13011801 Non-cancer B


title: NB12122501 Non-cancer B


title: NB13012101 Non-cancer B


title: NB12122102 Non-cancer B


title: NB12122001 Non-cancer B


title: NB12121002 Non-cancer B


title: NB12120601 Non-cancer B


title: NB13010801 Non-cancer B


title: NB12112703 Non-cancer B


title: NB12120401 Non-cancer B


title: NB12112604 Non-cancer B


title: NB12111401 Non-cancer B


title: NB12110102 Non-cancer B


title: NB12120302 Non-cancer B


title: NB12111604 Non-cancer B


title: NB12112602 Non-cancer B


title: NB12112201 Non-cancer B


title: NB12112004 Non-cancer B


title: NB12112103 Non-cancer B


title: NB12102901 Non-cancer B


title: NB12111402 Non-cancer B


title: NB12102601 Non-cancer B


title: NB12102504 Non-cancer B


title: NB12102401 Non-cancer B


title: NB12101202 Non-cancer B


title: NB12101903 Non-cancer B


title: NB12092801 Non-cancer B


title: NB12100905 Non-cancer B


title: NB12100101 Non-cancer B


title: NB12091803 Non-cancer B


title: NB12100301 Non-cancer B


title: NB12100204 Non-cancer B


title: NB12100902 Non-cancer B


title: NB12100502 Non-cancer B


title: NB12083102 Non-cancer B


title: NB12081302 Non-cancer B


title: NB12082302 Non-cancer B


title: NB12082203 Non-cancer B


title: NB12072701 Non-cancer B


title: NB12071903 Non-cancer B


title: NB12072003 Non-cancer B


title: NB12062501 Non-cancer B


title: NB12081301 Non-cancer B


title: NB12070302 Non-cancer B


title: NB12060803 Non-cancer B


title: NB12072403 Non-cancer B


title: NB12061104 Non-cancer B


title: NB12061504 Non-cancer B


title: NB12060601 Non-cancer B


title: NB12080901 Non-cancer B


title: NB12071702 Non-cancer B


title: NB12062802 Non-cancer B


title: NB12060101 Non-cancer B


title: NB12060702 Non-cancer B


title: NB12062702 Non-cancer B


title: NB12052401 Non-cancer B


title: NB12062101 Non-cancer B


title: NB12051801 Non-cancer B


title: NB12052805 Non-cancer B


title: NB12051403 Non-cancer B


title: NB12050205 Non-cancer B


title: NB12052801 Non-cancer B


title: NB12051101 Non-cancer B


title: NB12042604 Non-cancer B


title: NB12042404 Non-cancer B


title: NB12040601 Non-cancer B


title: NB12040301 Non-cancer B


title: NB12040603 Non-cancer B


title: NB12022704 Non-cancer B


title: NB12031903 Non-cancer B


title: NB12022101 Non-cancer B


title: NB12051703 Non-cancer B


title: NB12022205 Non-cancer B


title: NB12040404 Non-cancer B


title: NB12053001 Non-cancer B


title: M12013002 Non-cancer B


title: NB12022104 Non-cancer B


title: NB12020701 Non-cancer B


title: M12011603 Non-cancer B


title: M12011702 Non-cancer B


title: NB12021503 Non-cancer B


title: M11122002 Non-cancer B


title: M11122601 Non-cancer B


title: M11121604 Non-cancer B


title: M11121503 Non-cancer B


title: NB12022001 Non-cancer B


title: NB12032904 Non-cancer B


title: M11121203 Non-cancer B


title: M11062403 Non-cancer B

value: Female


title: M11110403 Non-cancer B


title: M11070806 Non-cancer B


title: M11120901 Non-cancer B


title: M11120803 Non-cancer B


title: M11070102 Non-cancer B


title: M11061702 Non-cancer B


title: M11061602 Non-cancer B


title: M11061403 Non-cancer B


title: M11053001 Non-cancer B


title: M11060804 Non-cancer B


title: M11060801 Non-cancer B


title: M11051904 Non-cancer B


title: M11060802 Non-cancer B


title: M11042602 Non-cancer B


title: M11051103 Non-cancer B


title: M11060602 Non-cancer B


title: M11051301 Non-cancer B


title: M11050602 Non-cancer B


title: M11050601 Non-cancer B


title: M11053105 Non-cancer B


title: M11053102 Non-cancer B


title: M11042101 Non-cancer B


title: M11052702 Non-cancer B


title: M11042801 Non-cancer B


title: M11042004 Non-cancer B


title: M11041802 Non-cancer B


title: M11053004 Non-cancer B


title: M11041201 Non-cancer B


title: M11042002 Non-cancer B


title: M11041507 Non-cancer B


title: M11040605 Non-cancer B


title: M11040807 Non-cancer B


title: M11041401 Non-cancer B


title: M11031102 Non-cancer B


title: M11031104 Non-cancer B


title: M11040805 Non-cancer B


title: M11031601 Non-cancer B


title: M11030702 Non-cancer B


title: M11022403 Non-cancer B


title: M11021505 Non-cancer B


title: M11021703 Non-cancer B


title: M11022203 Non-cancer B


title: M11032403 Non-cancer B


title: M11032402 Non-cancer B


title: M11032401 Non-cancer B


title: M11020802 Non-cancer B


title: M11030302 Non-cancer B


title: M11030203 Non-cancer B


title: M11032304 Non-cancer B


title: M11040802 Non-cancer B


title: M11022301 Non-cancer B


title: M11020405 Non-cancer B


title: M11030903 Non-cancer B


title: M11012403 Non-cancer B


title: M11032303 Non-cancer B


title: M11012104 Non-cancer B


title: M11020401 Non-cancer B


title: M11020402 Non-cancer B


title: M11012101 Non-cancer B


title: M11021803 Non-cancer B


title: M11020404 Non-cancer B


title: M11011901 Non-cancer B


title: M11020301 Non-cancer B


title: M11010704 Non-cancer B


title: M11010705 Non-cancer B


title: M11011409 Non-cancer B


title: M11012701 Non-cancer B


title: M11020101 Non-cancer B


title: M11010503 Non-cancer B


title: M11010505 Non-cancer B


title: M10122706 Non-cancer B


title: M11020201 Non-cancer B


title: M11012103 Non-cancer B


title: M10122103 Non-cancer B


title: M11010402 Non-cancer B


title: M10122803 Non-cancer B


title: M10121602 Non-cancer B


title: M10121503 Non-cancer B


title: M10122201 Non-cancer B


title: M10122002 Non-cancer B


title: M10121304 Non-cancer B


title: M11011403 Non-cancer B


title: M11011101 Non-cancer B


title: M10121003 Non-cancer B


title: M10121302 Non-cancer B


title: M10120903 Non-cancer B


title: M11011103 Non-cancer B


title: M10121502 Non-cancer B


title: M10121303 Non-cancer B


title: M10111606 Non-cancer B


title: M10121301 Non-cancer B


title: M10120605 Non-cancer B


title: M10120602 Non-cancer B


title: M10110804 Non-cancer B


title: CHC921 Non-cancer B


title: CHC928 Non-cancer B


title: M10112206 Non-cancer B


title: M10120203 Non-cancer B


title: M10102605 Non-cancer B


title: CHC912 Non-cancer B


title: CHC849 Non-cancer B


title: CHC873 Non-cancer B


title: CHC850 Non-cancer B


title: M10112901 Non-cancer B


title: CHC786 Non-cancer B


title: CHC833 Non-cancer B


title: CHC759 Non-cancer B


title: GC1467 Gastric Cancer

value: Gastric Cancer

tag: Stage

value: IA

tag: histological subtype

value: undiff


title: GC1471 Gastric Cancer

value: IB

value: diff


title: CHC672 Non-cancer B


title: M10111101 Non-cancer B


title: GC1470 Gastric Cancer


title: GC1469 Gastric Cancer


title: GC1468 Gastric Cancer


title: GC1461 Gastric Cancer


title: GC1455 Gastric Cancer


title: GC1454 Gastric Cancer


title: GC1465 Gastric Cancer


title: GC1464 Gastric Cancer


title: GC1460 Gastric Cancer


title: GC1463 Gastric Cancer


title: GC1466 Gastric Cancer


title: GC1462 Gastric Cancer


title: GC1449 Gastric Cancer


title: GC1459 Gastric Cancer


title: GC1453 Gastric Cancer


title: GC1458 Gastric Cancer


title: GC1452 Gastric Cancer


title: GC1447 Gastric Cancer


title: GC1444 Gastric Cancer


title: GC1457 Gastric Cancer


title: GC1443 Gastric Cancer


title: GC1451 Gastric Cancer


title: GC1448 Gastric Cancer


title: GC1438 Gastric Cancer


title: GC1434 Gastric Cancer


title: GC1439 Gastric Cancer


title: GC1450 Gastric Cancer


title: GC1446 Gastric Cancer


title: GC1429 Gastric Cancer


title: GC1442 Gastric Cancer


title: GC1422 Gastric Cancer


title: GC1420 Gastric Cancer


title: GC1424 Gastric Cancer


title: GC1456 Gastric Cancer


title: GC1440 Gastric Cancer


title: GC1441 Gastric Cancer


title: GC1419 Gastric Cancer


title: GC1411 Gastric Cancer


title: GC1437 Gastric Cancer


title: GC1410 Gastric Cancer


title: GC1407 Gastric Cancer


title: GC1408 Gastric Cancer

value: IIB


title: GC1435 Gastric Cancer


title: GC1436 Gastric Cancer


title: GC1445 Gastric Cancer

value: IIA


title: GC1432 Gastric Cancer


title: GC1433 Gastric Cancer


title: GC1403 Gastric Cancer


title: GC1431 Gastric Cancer


title: GC1430 Gastric Cancer


title: GC1427 Gastric Cancer


title: GC1426 Gastric Cancer


title: GC1421 Gastric Cancer


title: GC1423 Gastric Cancer


title: GC1398 Gastric Cancer


title: GC1392 Gastric Cancer


title: GC1393 Gastric Cancer


title: GC1391 Gastric Cancer


title: GC1418 Gastric Cancer


title: GC1416 Gastric Cancer


title: GC1389 Gastric Cancer


title: GC1415 Gastric Cancer


title: GC1394 Gastric Cancer


title: GC1387 Gastric Cancer


title: GC1414 Gastric Cancer


title: GC1384 Gastric Cancer


title: GC1428 Gastric Cancer


title: GC1382 Gastric Cancer


title: GC1413 Gastric Cancer


title: GC1409 Gastric Cancer


title: GC1381 Gastric Cancer


title: GC1378 Gastric Cancer


title: GC1406 Gastric Cancer


title: GC1376 Gastric Cancer


title: GC1386 Gastric Cancer


title: GC1405 Gastric Cancer


title: GC1375 Gastric Cancer


title: GC1404 Gastric Cancer


title: GC1372 Gastric Cancer


title: GC1383 Gastric Cancer


title: GC1380 Gastric Cancer


title: GC1402 Gastric Cancer


title: GC1401 Gastric Cancer


title: GC1397 Gastric Cancer


title: GC1400 Gastric Cancer


title: GC1399 Gastric Cancer


title: GC1367 Gastric Cancer


title: GC1395 Gastric Cancer


title: GC1396 Gastric Cancer


title: GC1390 Gastric Cancer


title: GC1385 Gastric Cancer


title: GC1388 Gastric Cancer


title: GC1377 Gastric Cancer


title: GC1362 Gastric Cancer


title: GC1363 Gastric Cancer


title: GC1379 Gastric Cancer

value: special


title: GC1365 Gastric Cancer


title: GC1354 Gastric Cancer


title: GC1364 Gastric Cancer


title: GC1357 Gastric Cancer


title: GC1352 Gastric Cancer


title: GC1353 Gastric Cancer


title: GC1373 Gastric Cancer


title: GC1374 Gastric Cancer


title: GC1371 Gastric Cancer


title: GC1366 Gastric Cancer


title: GC1370 Gastric Cancer


title: GC1368 Gastric Cancer


title: GC1349 Gastric Cancer


title: GC1361 Gastric Cancer


title: GC1359 Gastric Cancer


title: GC1358 Gastric Cancer


title: GC1360 Gastric Cancer


title: GC1342 Gastric Cancer


title: GC1346 Gastric Cancer


title: GC1337 Gastric Cancer


title: GC1344 Gastric Cancer


title: GC1345 Gastric Cancer


title: GC1369 Gastric Cancer


title: GC1356 Gastric Cancer


title: GC1355 Gastric Cancer


title: GC1351 Gastric Cancer


title: GC1340 Gastric Cancer


title: GC1333 Gastric Cancer


title: GC1329 Gastric Cancer


title: GC1328 Gastric Cancer


title: GC1347 Gastric Cancer


title: GC1341 Gastric Cancer


title: GC1350 Gastric Cancer


title: GC1326 Gastric Cancer


title: GC1338 Gastric Cancer


title: GC1339 Gastric Cancer


title: GC1336 Gastric Cancer


title: GC1321 Gastric Cancer


title: GC1319 Gastric Cancer


title: GC1348 Gastric Cancer


title: GC1335 Gastric Cancer


title: GC1313 Gastric Cancer


title: GC1320 Gastric Cancer


title: GC1318 Gastric Cancer

value: II


title: GC1311 Gastric Cancer


title: GC1331 Gastric Cancer


title: GC1309 Gastric Cancer


title: GC1330 Gastric Cancer


title: GC1332 Gastric Cancer


title: GC1327 Gastric Cancer


title: GC1343 Gastric Cancer


title: GC1303 Gastric Cancer


title: GC1334 Gastric Cancer


title: GC1323 Gastric Cancer


title: GC1302 Gastric Cancer


title: GC1324 Gastric Cancer


title: GC1300 Gastric Cancer


title: GC1322 Gastric Cancer


title: GC1301 Gastric Cancer


title: GC1317 Gastric Cancer


title: GC1312 Gastric Cancer


title: GC1316 Gastric Cancer


title: GC1293 Gastric Cancer


title: GC1310 Gastric Cancer


title: GC1314 Gastric Cancer


title: GC1291 Gastric Cancer


title: GC1315 Gastric Cancer


title: GC1308 Gastric Cancer


title: GC1307 Gastric Cancer


title: GC1305 Gastric Cancer


title: GC1304 Gastric Cancer


title: GC1294 Gastric Cancer


title: GC1299 Gastric Cancer


title: GC1292 Gastric Cancer


title: GC1296 Gastric Cancer


title: GC1297 Gastric Cancer


title: GC1289 Gastric Cancer


title: GC1295 Gastric Cancer


title: GC1298 Gastric Cancer


title: GC1288 Gastric Cancer


title: GC1290 Gastric Cancer


title: GC1281 Gastric Cancer


title: GC1286 Gastric Cancer


title: GC1274 Gastric Cancer


title: GC1271 Gastric Cancer


title: GC1272 Gastric Cancer


title: GC1269 Gastric Cancer


title: GC1277 Gastric Cancer


title: GC1267 Gastric Cancer


title: GC1266 Gastric Cancer


title: GC1264 Gastric Cancer


title: GC1282 Gastric Cancer


title: GC1284 Gastric Cancer


title: GC1285 Gastric Cancer


title: GC1279 Gastric Cancer


title: GC1280 Gastric Cancer


title: GC1278 Gastric Cancer


title: GC1276 Gastric Cancer


title: GC1262 Gastric Cancer


title: GC1260 Gastric Cancer


title: GC1261 Gastric Cancer


title: GC1258 Gastric Cancer


title: GC1273 Gastric Cancer


title: GC1251 Gastric Cancer


title: GC1252 Gastric Cancer


title: GC1270 Gastric Cancer


title: GC1268 Gastric Cancer


title: GC1259 Gastric Cancer


title: GC1257 Gastric Cancer


title: GC1254 Gastric Cancer


title: GC1265 Gastric Cancer


title: GC1263 Gastric Cancer


title: GC1256 Gastric Cancer


title: GC1244 Gastric Cancer


title: GC1255 Gastric Cancer


title: GC1253 Gastric Cancer


title: GC1238 Gastric Cancer


title: GC1249 Gastric Cancer


title: GC1236 Gastric Cancer


title: GC1250 Gastric Cancer


title: GC1241 Gastric Cancer


title: GC1246 Gastric Cancer


title: GC1248 Gastric Cancer


title: GC1247 Gastric Cancer


title: GC1245 Gastric Cancer


title: GC1243 Gastric Cancer


title: GC1242 Gastric Cancer


title: GC1229 Gastric Cancer


title: GC1228 Gastric Cancer


title: GC1233 Gastric Cancer


title: GC1224 Gastric Cancer


title: GC1239 Gastric Cancer


title: GC1240 Gastric Cancer


title: GC1237 Gastric Cancer


title: GC1222 Gastric Cancer


title: GC1230 Gastric Cancer


title: GC1231 Gastric Cancer


title: GC1232 Gastric Cancer


title: GC1235 Gastric Cancer


title: GC1234 Gastric Cancer


title: GC1226 Gastric Cancer


title: GC1227 Gastric Cancer


title: GC1225 Gastric Cancer


title: GC1218 Gastric Cancer


title: GC1213 Gastric Cancer


title: GC1212 Gastric Cancer


title: GC1214 Gastric Cancer


title: GC1223 Gastric Cancer


title: GC1220 Gastric Cancer


title: GC1221 Gastric Cancer


title: GC1205 Gastric Cancer


title: GC1211 Gastric Cancer


title: GC1217 Gastric Cancer


title: GC1202 Gastric Cancer


title: GC1219 Gastric Cancer


title: GC1216 Gastric Cancer


title: GC1215 Gastric Cancer


title: GC1210 Gastric Cancer


title: GC1209 Gastric Cancer


title: GC1208 Gastric Cancer


title: GC1206 Gastric Cancer


title: GC1204 Gastric Cancer


title: GC1201 Gastric Cancer


title: GC1194 Gastric Cancer


title: GC1203 Gastric Cancer


title: GC1207 Gastric Cancer


title: GC1189 Gastric Cancer


title: GC1192 Gastric Cancer


title: GC1188 Gastric Cancer


title: GC1200 Gastric Cancer


title: GC1199 Gastric Cancer


title: GC1193 Gastric Cancer


title: GC1196 Gastric Cancer


title: GC1191 Gastric Cancer


title: GC1190 Gastric Cancer


title: GC1197 Gastric Cancer


title: GC1185 Gastric Cancer


title: GC1186 Gastric Cancer


title: GC1184 Gastric Cancer


title: GC1183 Gastric Cancer


title: GC1180 Gastric Cancer


title: GC1195 Gastric Cancer


title: GC1173 Gastric Cancer


title: GC1181 Gastric Cancer


title: GC1176 Gastric Cancer


title: GC1171 Gastric Cancer


title: GC1177 Gastric Cancer


title: GC1178 Gastric Cancer


title: GC1162 Gastric Cancer


title: GC1161 Gastric Cancer


title: GC1174 Gastric Cancer


title: GC1179 Gastric Cancer


title: GC1164 Gastric Cancer


title: GC1166 Gastric Cancer


title: GC1158 Gastric Cancer


title: GC1165 Gastric Cancer


title: GC1170 Gastric Cancer


title: GC1163 Gastric Cancer


title: GC1160 Gastric Cancer


title: GC1159 Gastric Cancer


title: GC1152 Gastric Cancer


title: GC1151 Gastric Cancer


title: GC1145 Gastric Cancer


title: GC1167 Gastric Cancer


title: GC1143 Gastric Cancer


title: GC1153 Gastric Cancer


title: GC1149 Gastric Cancer


title: GC1154 Gastric Cancer


title: GC1156 Gastric Cancer


title: GC1169 Gastric Cancer


title: GC1147 Gastric Cancer


title: GC1155 Gastric Cancer


title: GC1142 Gastric Cancer


title: GC1148 Gastric Cancer


title: GC1146 Gastric Cancer


title: GC1172 Gastric Cancer


title: GC1138 Gastric Cancer


title: GC1157 Gastric Cancer


title: GC1141 Gastric Cancer


title: GC1136 Gastric Cancer


title: GC1140 Gastric Cancer


title: GC1133 Gastric Cancer


title: GC1131 Gastric Cancer


title: GC1132 Gastric Cancer


title: GC1139 Gastric Cancer


title: GC1128 Gastric Cancer


title: GC1135 Gastric Cancer


title: GC1130 Gastric Cancer


title: GC1144 Gastric Cancer


title: GC1134 Gastric Cancer


title: GC1129 Gastric Cancer


title: GC1118 Gastric Cancer


title: GC1126 Gastric Cancer


title: GC1123 Gastric Cancer


title: GC1121 Gastric Cancer


title: GC1127 Gastric Cancer


title: GC1125 Gastric Cancer


title: GC1116 Gastric Cancer


title: GC1120 Gastric Cancer


title: GC1119 Gastric Cancer


title: GC1122 Gastric Cancer


title: GC1109 Gastric Cancer


title: GC1106 Gastric Cancer


title: GC1110 Gastric Cancer


title: GC1104 Gastric Cancer


title: GC1112 Gastric Cancer


title: GC1115 Gastric Cancer


title: GC1117 Gastric Cancer


title: GC1114 Gastric Cancer


title: GC1107 Gastric Cancer


title: GC1102 Gastric Cancer


title: GC1101 Gastric Cancer


title: GC1100 Gastric Cancer


title: GC1099 Gastric Cancer


title: GC1095 Gastric Cancer


title: GC1096 Gastric Cancer


title: GC1108 Gastric Cancer


title: GC1124 Gastric Cancer


title: GC1093 Gastric Cancer


title: GC1091 Gastric Cancer


title: GC1105 Gastric Cancer


title: GC1094 Gastric Cancer


title: GC1088 Gastric Cancer


title: GC1090 Gastric Cancer


title: GC1089 Gastric Cancer


title: GC1087 Gastric Cancer


title: GC1092 Gastric Cancer


title: GC1113 Gastric Cancer


title: GC1103 Gastric Cancer


title: GC1083 Gastric Cancer


title: GC1085 Gastric Cancer


title: GC1075 Gastric Cancer


title: GC1077 Gastric Cancer


title: GC1073 Gastric Cancer


title: GC1080 Gastric Cancer


title: GC1069 Gastric Cancer


title: GC1068 Gastric Cancer


title: GC1067 Gastric Cancer


title: GC1066 Gastric Cancer


title: GC1079 Gastric Cancer


title: GC1072 Gastric Cancer


title: GC1082 Gastric Cancer


title: GC1086 Gastric Cancer


title: GC1064 Gastric Cancer


title: GC1070 Gastric Cancer


title: GC1078 Gastric Cancer


title: GC1063 Gastric Cancer


title: GC1059 Gastric Cancer


title: GC1057 Gastric Cancer


title: GC1058 Gastric Cancer


title: GC1111 Gastric Cancer


title: GC1065 Gastric Cancer


title: GC1060 Gastric Cancer


title: GC1076 Gastric Cancer


title: GC1056 Gastric Cancer


title: GC1050 Gastric Cancer


title: GC1054 Gastric Cancer


title: GC1046 Gastric Cancer


title: GC1047 Gastric Cancer


title: GC1048 Gastric Cancer


title: GC1045 Gastric Cancer


title: GC1055 Gastric Cancer


title: GC1053 Gastric Cancer


title: GC1049 Gastric Cancer


title: GC1040 Gastric Cancer


title: GC1041 Gastric Cancer


title: GC1044 Gastric Cancer


title: GC1042 Gastric Cancer


title: GC1038 Gastric Cancer


title: GC1039 Gastric Cancer


title: GC1037 Gastric Cancer


title: GC1034 Gastric Cancer


title: GC1033 Gastric Cancer


title: GC1036 Gastric Cancer


title: GC1032 Gastric Cancer


title: GC1043 Gastric Cancer


title: GC1030 Gastric Cancer


title: GC1027 Gastric Cancer


title: GC1029 Gastric Cancer


title: GC1024 Gastric Cancer


title: GC1026 Gastric Cancer


title: GC1025 Gastric Cancer


title: GC1035 Gastric Cancer


title: GC1023 Gastric Cancer


title: GC1016 Gastric Cancer


title: GC1021 Gastric Cancer


title: GC1014 Gastric Cancer


title: GC1022 Gastric Cancer


title: GC1010 Gastric Cancer


title: GC1015 Gastric Cancer


title: GC1011 Gastric Cancer


title: GC1020 Gastric Cancer


title: GC1019 Gastric Cancer


title: GC1006 Gastric Cancer


title: GC1007 Gastric Cancer


title: GC1061 Gastric Cancer


title: GC1009 Gastric Cancer


title: GC1031 Gastric Cancer


title: GC1003 Gastric Cancer


title: GC1017 Gastric Cancer


title: GC1002 Gastric Cancer


title: GC1013 Gastric Cancer


title: GC1001 Gastric Cancer


title: GC1004 Gastric Cancer


title: GC1000 Gastric Cancer


title: GC0999 Gastric Cancer


title: GC0992 Gastric Cancer


title: GC0988 Gastric Cancer


title: GC0996 Gastric Cancer


title: GC0998 Gastric Cancer


title: GC0989 Gastric Cancer


title: GC0995 Gastric Cancer


title: GC1008 Gastric Cancer


title: GC0997 Gastric Cancer


title: GC0984 Gastric Cancer


title: GC0994 Gastric Cancer


title: GC0986 Gastric Cancer


title: GC1005 Gastric Cancer


title: GC0993 Gastric Cancer


title: GC0991 Gastric Cancer


title: GC0977 Gastric Cancer


title: GC0981 Gastric Cancer


title: GC0990 Gastric Cancer


title: GC1175 Gastric Cancer


title: GC0976 Gastric Cancer


title: GC0985 Gastric Cancer


title: GC0983 Gastric Cancer


title: GC0982 Gastric Cancer


title: GC0974 Gastric Cancer


title: GC0971 Gastric Cancer


title: GC0979 Gastric Cancer


title: GC1081 Gastric Cancer


title: GC0978 Gastric Cancer


title: GC0962 Gastric Cancer


title: GC0975 Gastric Cancer


title: GC0980 Gastric Cancer


title: GC0970 Gastric Cancer


title: GC0969 Gastric Cancer


title: GC0955 Gastric Cancer


title: GC0956 Gastric Cancer


title: GC0957 Gastric Cancer


title: GC0954 Gastric Cancer


title: GC0958 Gastric Cancer


title: GC0968 Gastric Cancer


title: GC0953 Gastric Cancer


title: GC0967 Gastric Cancer


title: GC0951 Gastric Cancer


title: GC0963 Gastric Cancer


title: GC0965 Gastric Cancer


title: GC0961 Gastric Cancer


title: GC0959 Gastric Cancer


title: GC0960 Gastric Cancer


title: GC0952 Gastric Cancer


title: GC0948 Gastric Cancer


title: GC0964 Gastric Cancer


title: GC0947 Gastric Cancer


title: GC0950 Gastric Cancer


title: GC0949 Gastric Cancer


title: GC0946 Gastric Cancer


title: GC0944 Gastric Cancer


title: GC0943 Gastric Cancer


title: GC0972 Gastric Cancer


title: GC0942 Gastric Cancer


title: GC0939 Gastric Cancer


title: GC0938 Gastric Cancer


title: GC0941 Gastric Cancer


title: GC0945 Gastric Cancer


title: GC0966 Gastric Cancer


title: GC0935 Gastric Cancer


title: GC0937 Gastric Cancer


title: GC0933 Gastric Cancer


title: GC0936 Gastric Cancer


title: GC1062 Gastric Cancer


title: GC0931 Gastric Cancer


title: GC0932 Gastric Cancer


title: GC0926 Gastric Cancer


title: GC0928 Gastric Cancer


title: GC0929 Gastric Cancer


title: GC0940 Gastric Cancer


title: GC0925 Gastric Cancer


title: GC0927 Gastric Cancer


title: GC0922 Gastric Cancer


title: GC0918 Gastric Cancer


title: GC0924 Gastric Cancer


title: GC0923 Gastric Cancer


title: GC0934 Gastric Cancer


title: GC0920 Gastric Cancer


title: GC0921 Gastric Cancer


title: GC0919 Gastric Cancer


title: GC0916 Gastric Cancer


title: GC0917 Gastric Cancer


title: GC0913 Gastric Cancer


title: GC0915 Gastric Cancer


title: GC0914 Gastric Cancer


title: GC0930 Gastric Cancer


title: GC0912 Gastric Cancer


title: GC0905 Gastric Cancer


title: GC0906 Gastric Cancer


title: GC0900 Gastric Cancer


title: GC0910 Gastric Cancer


title: GC0911 Gastric Cancer


title: GC0901 Gastric Cancer


title: GC0908 Gastric Cancer


title: GC0909 Gastric Cancer


title: GC0903 Gastric Cancer


title: GC0897 Gastric Cancer


title: GC0902 Gastric Cancer


title: GC0898 Gastric Cancer


title: GC0891 Gastric Cancer


title: GC0893 Gastric Cancer


title: GC0889 Gastric Cancer


title: GC0904 Gastric Cancer


title: GC0896 Gastric Cancer


title: GC0899 Gastric Cancer


title: GC0886 Gastric Cancer


title: GC0885 Gastric Cancer


title: GC0894 Gastric Cancer


title: GC0890 Gastric Cancer


title: GC0888 Gastric Cancer


title: GC0892 Gastric Cancer


title: GC0887 Gastric Cancer


title: GC0883 Gastric Cancer


title: GC0895 Gastric Cancer


title: GC0880 Gastric Cancer


title: GC0882 Gastric Cancer


title: GC0875 Gastric Cancer


title: GC0878 Gastric Cancer


title: GC0873 Gastric Cancer


title: GC0879 Gastric Cancer


title: GC0877 Gastric Cancer


title: GC0874 Gastric Cancer


title: GC0876 Gastric Cancer


title: GC0865 Gastric Cancer


title: GC0867 Gastric Cancer


title: GC0869 Gastric Cancer


title: GC0868 Gastric Cancer


title: GC0866 Gastric Cancer


title: GC0870 Gastric Cancer


title: GC0872 Gastric Cancer


title: GC0863 Gastric Cancer


title: GC0881 Gastric Cancer


title: GC0862 Gastric Cancer


title: GC0861 Gastric Cancer


title: GC0859 Gastric Cancer


title: GC0856 Gastric Cancer


title: GC0855 Gastric Cancer


title: GC0857 Gastric Cancer


title: GC0858 Gastric Cancer


title: GC0871 Gastric Cancer


title: GC0853 Gastric Cancer


title: GC0854 Gastric Cancer


title: GC0884 Gastric Cancer


title: GC0864 Gastric Cancer


title: GC0845 Gastric Cancer


title: GC0851 Gastric Cancer


title: GC0852 Gastric Cancer


title: GC0847 Gastric Cancer


title: GC0849 Gastric Cancer


title: GC0850 Gastric Cancer


title: GC0841 Gastric Cancer


title: GC0840 Gastric Cancer


title: GC0839 Gastric Cancer


title: GC0844 Gastric Cancer


title: GC0837 Gastric Cancer


title: GC0835 Gastric Cancer


title: GC0836 Gastric Cancer


title: GC0834 Gastric Cancer


title: GC0848 Gastric Cancer


title: GC0832 Gastric Cancer


title: GC0831 Gastric Cancer


title: GC0829 Gastric Cancer


title: GC0833 Gastric Cancer


title: GC0826 Gastric Cancer


title: GC0828 Gastric Cancer


title: GC0827 Gastric Cancer


title: GC0825 Gastric Cancer


title: GC0842 Gastric Cancer


title: GC0843 Gastric Cancer


title: GC0838 Gastric Cancer


title: GC0824 Gastric Cancer


title: GC0823 Gastric Cancer


title: GC0821 Gastric Cancer


title: GC0822 Gastric Cancer


title: GC0819 Gastric Cancer


title: GC0817 Gastric Cancer


title: GC0820 Gastric Cancer


title: GC0830 Gastric Cancer


title: GC0846 Gastric Cancer


title: GC0814 Gastric Cancer


title: GC0813 Gastric Cancer


title: GC0816 Gastric Cancer


title: GC0812 Gastric Cancer


title: GC0815 Gastric Cancer


title: GC0811 Gastric Cancer


title: GC0810 Gastric Cancer


title: GC0809 Gastric Cancer


title: GC0801 Gastric Cancer


title: GC0804 Gastric Cancer


title: GC0805 Gastric Cancer


title: GC0806 Gastric Cancer


title: GC0808 Gastric Cancer


title: GC0800 Gastric Cancer


title: GC0818 Gastric Cancer


title: GC0799 Gastric Cancer


title: GC0803 Gastric Cancer


title: GC0797 Gastric Cancer


title: GC0794 Gastric Cancer


title: GC0798 Gastric Cancer


title: GC0795 Gastric Cancer


title: GC0793 Gastric Cancer


title: GC0792 Gastric Cancer


title: GC0790 Gastric Cancer


title: GC0791 Gastric Cancer


title: GC0807 Gastric Cancer


title: GC0786 Gastric Cancer


title: GC0785 Gastric Cancer


title: GC0787 Gastric Cancer


title: GC0789 Gastric Cancer


title: GC0788 Gastric Cancer


title: GC0802 Gastric Cancer


title: GC0783 Gastric Cancer


title: GC0796 Gastric Cancer


title: GC0780 Gastric Cancer


title: GC0778 Gastric Cancer


title: GC0776 Gastric Cancer


title: GC0774 Gastric Cancer


title: GC0773 Gastric Cancer


title: GC0775 Gastric Cancer


title: GC0777 Gastric Cancer


title: GC0771 Gastric Cancer


title: GC0782 Gastric Cancer


title: GC0767 Gastric Cancer


title: GC0770 Gastric Cancer


title: GC0764 Gastric Cancer


title: GC0766 Gastric Cancer


title: GC0784 Gastric Cancer


title: GC0765 Gastric Cancer


title: GC0769 Gastric Cancer


title: GC0758 Gastric Cancer


title: GC0755 Gastric Cancer


title: GC0761 Gastric Cancer


title: GC0762 Gastric Cancer


title: GC0760 Gastric Cancer


title: GC0756 Gastric Cancer


title: GC0768 Gastric Cancer


title: GC0772 Gastric Cancer


title: GC0754 Gastric Cancer


title: GC0763 Gastric Cancer


title: GC0751 Gastric Cancer


title: GC0749 Gastric Cancer


title: GC0750 Gastric Cancer


title: GC0747 Gastric Cancer


title: GC0753 Gastric Cancer


title: GC0757 Gastric Cancer


title: GC0759 Gastric Cancer


title: GC0743 Gastric Cancer


title: GC0745 Gastric Cancer


title: GC0744 Gastric Cancer


title: GC0738 Gastric Cancer


title: GC0739 Gastric Cancer


title: GC0741 Gastric Cancer


title: GC0742 Gastric Cancer


title: GC0737 Gastric Cancer


title: GC0735 Gastric Cancer


title: GC0734 Gastric Cancer


title: GC0732 Gastric Cancer


title: GC0733 Gastric Cancer


title: GC0729 Gastric Cancer


title: GC0731 Gastric Cancer


title: GC0746 Gastric Cancer


title: GC0728 Gastric Cancer


title: GC0730 Gastric Cancer


title: GC0748 Gastric Cancer


title: GC0727 Gastric Cancer


title: GC0726 Gastric Cancer


title: GC0724 Gastric Cancer


title: GC0725 Gastric Cancer


title: GC0723 Gastric Cancer


title: GC0721 Gastric Cancer


title: GC0719 Gastric Cancer


title: GC0711 Gastric Cancer


title: GC0717 Gastric Cancer


title: GC0720 Gastric Cancer


title: GC0714 Gastric Cancer


title: GC0718 Gastric Cancer


title: GC0716 Gastric Cancer


title: GC0713 Gastric Cancer


title: GC0710 Gastric Cancer


title: GC0709 Gastric Cancer


title: GC0705 Gastric Cancer


title: GC0704 Gastric Cancer


title: GC0722 Gastric Cancer


title: GC0702 Gastric Cancer


title: GC0703 Gastric Cancer


title: GC0708 Gastric Cancer


title: GC0706 Gastric Cancer


title: GC0707 Gastric Cancer


title: GC0698 Gastric Cancer


title: GC0700 Gastric Cancer


title: GC0715 Gastric Cancer


title: GC0699 Gastric Cancer


title: GC0712 Gastric Cancer


title: GC0701 Gastric Cancer


title: GC0695 Gastric Cancer


title: GC0697 Gastric Cancer


title: GC0694 Gastric Cancer


title: GC0693 Gastric Cancer


title: GC0692 Gastric Cancer


title: GC0686 Gastric Cancer


title: GC0687 Gastric Cancer


title: GC0689 Gastric Cancer


title: GC0684 Gastric Cancer


title: GC0690 Gastric Cancer


title: GC0683 Gastric Cancer


title: GC0691 Gastric Cancer


title: GC0681 Gastric Cancer


title: GC0676 Gastric Cancer


title: GC0677 Gastric Cancer


title: GC0673 Gastric Cancer


title: GC0674 Gastric Cancer


title: GC0671 Gastric Cancer


title: GC0680 Gastric Cancer


title: GC0679 Gastric Cancer


title: GC0678 Gastric Cancer


title: GC0669 Gastric Cancer


title: GC0688 Gastric Cancer


title: GC0667 Gastric Cancer


title: GC0666 Gastric Cancer


title: GC0665 Gastric Cancer


title: GC0663 Gastric Cancer


title: GC0662 Gastric Cancer


title: GC0660 Gastric Cancer


title: GC0668 Gastric Cancer


title: GC0675 Gastric Cancer


title: GC0659 Gastric Cancer


title: GC0672 Gastric Cancer


title: GC0658 Gastric Cancer


title: GC0657 Gastric Cancer


title: GC0656 Gastric Cancer


title: GC0652 Gastric Cancer


title: GC0670 Gastric Cancer


title: GC0653 Gastric Cancer


title: GC0664 Gastric Cancer


title: GC0647 Gastric Cancer


title: GC0648 Gastric Cancer


title: GC0649 Gastric Cancer


title: GC0646 Gastric Cancer


title: GC0661 Gastric Cancer


title: GC0644 Gastric Cancer


title: GC0643 Gastric Cancer


title: GC0655 Gastric Cancer


title: GC0645 Gastric Cancer


title: GC0640 Gastric Cancer


title: GC0641 Gastric Cancer


title: GC0642 Gastric Cancer


title: GC0639 Gastric Cancer


title: GC0740 Gastric Cancer


title: GC0637 Gastric Cancer


title: GC0638 Gastric Cancer


title: GC0635 Gastric Cancer


title: GC0631 Gastric Cancer


title: GC0636 Gastric Cancer


title: GC0634 Gastric Cancer


title: GC0630 Gastric Cancer


title: GC0633 Gastric Cancer


title: GC0628 Gastric Cancer


title: GC0632 Gastric Cancer


title: GC0627 Gastric Cancer


title: GC0626 Gastric Cancer


title: GC0625 Gastric Cancer


title: GC0629 Gastric Cancer


title: GC0624 Gastric Cancer


title: GC0619 Gastric Cancer


title: GC0622 Gastric Cancer


title: GC0623 Gastric Cancer


title: GC0618 Gastric Cancer


title: GC0614 Gastric Cancer


title: GC0620 Gastric Cancer


title: GC0621 Gastric Cancer


title: GC0613 Gastric Cancer


title: GC0617 Gastric Cancer


title: GC0609 Gastric Cancer


title: GC0612 Gastric Cancer


title: GC0610 Gastric Cancer


title: GC0608 Gastric Cancer


title: GC0611 Gastric Cancer


title: GC0606 Gastric Cancer


title: GC0650 Gastric Cancer


title: GC0602 Gastric Cancer


title: GC0616 Gastric Cancer


title: GC0607 Gastric Cancer


title: GC0605 Gastric Cancer


title: GC0601 Gastric Cancer


title: GC0600 Gastric Cancer


title: GC0597 Gastric Cancer


title: GC0603 Gastric Cancer


title: GC0604 Gastric Cancer


title: GC0615 Gastric Cancer


title: GC0595 Gastric Cancer


title: GC0594 Gastric Cancer


title: GC0598 Gastric Cancer


title: GC0587 Gastric Cancer


title: GC0586 Gastric Cancer


title: GC0585 Gastric Cancer


title: GC0581 Gastric Cancer


title: GC0582 Gastric Cancer


title: GC0584 Gastric Cancer


title: GC0588 Gastric Cancer


title: GC0589 Gastric Cancer


title: GC0583 Gastric Cancer


title: GC0590 Gastric Cancer


title: GC0592 Gastric Cancer


title: GC0591 Gastric Cancer


title: GC0596 Gastric Cancer


title: GC0651 Gastric Cancer


title: GC0577 Gastric Cancer


title: GC0593 Gastric Cancer


title: GC0574 Gastric Cancer


title: GC0579 Gastric Cancer


title: GC0580 Gastric Cancer


title: GC0578 Gastric Cancer


title: GC0575 Gastric Cancer


title: GC0576 Gastric Cancer


title: GC0572 Gastric Cancer


title: GC0569 Gastric Cancer


title: GC0570 Gastric Cancer


title: GC0573 Gastric Cancer


title: GC0571 Gastric Cancer


title: GC0568 Gastric Cancer


title: GC0564 Gastric Cancer


title: GC0566 Gastric Cancer


title: GC0552 Gastric Cancer


title: GC0567 Gastric Cancer


title: GC0555 Gastric Cancer


title: GC0556 Gastric Cancer


title: GC0561 Gastric Cancer


title: GC0559 Gastric Cancer


title: GC0563 Gastric Cancer


title: GC0554 Gastric Cancer


title: GC0557 Gastric Cancer


title: GC0558 Gastric Cancer


title: GC0553 Gastric Cancer


title: GC0562 Gastric Cancer


title: GC0565 Gastric Cancer


title: GC0560 Gastric Cancer


title: GC0551 Gastric Cancer


title: GC0549 Gastric Cancer


title: GC0550 Gastric Cancer


title: GC0548 Gastric Cancer


title: GC0544 Gastric Cancer


title: GC0543 Gastric Cancer


title: GC0545 Gastric Cancer


title: GC0547 Gastric Cancer


title: 125589: Human - rat snATAC mix

type: SRA

city: Ann Arbor

first: Stephen

last: Parker

state: MI

address: 100 Washtenaw Avenue

country: USA

institute: University of Michigan

description: ***Raw data are unavailable due to patient privacy concerns***

library_source: genomic

data_processing:
Adapters were trimmed using cta (v. 0.1.2; https://github.com/ParkerLab/cta)
For single-nucleus experiments, we used a custom python script (available in https://github.com/porchard/snATACseq-NextFlow) for 10x Genomics barcode correction
Reads were mapped using BWA-MEM (-I 200,200,5000 -M; v. 0.7.15-r1140). If the sample contained only human nuclei, we used the hg19 reference genome. If the sample contained human and rat nuclei, we mapped the library twice, once to hg19 and once to rn6
For single-nucleus experiments, we filtered out nuclei corresponding to 10x barcodes with fewer than 1000 alignments in the BAM file
We used Picard MarkDuplicates to mark duplicates, and filtered to high-quality, non-duplicate autosomal read pairs using SAMtools view with flags ‘-f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30’
We anonymized the BAM files using anonymizeBAM (--strict; v. 0.4.5)
We generated single-end BED files using bedtools bamtobed
We called peaks and generated bedGraph files using macs2 callpeak -f BED --SPMR --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all
We generated the bigWig file from the bedGraph file using bedGraphToBigWig from the UCSC genome browser
Genome_build: hg19 (human) and rn6 (when rat nuclei were included in the library)
Supplementary_files_format_and_content: ATAC-seq read mapping locations, anonymized (BED files)
Supplementary_files_format_and_content: ATAC-seq signal tracks (bigWig files)
Supplementary_files_format_and_content: ATAC-seq peak calls (broadPeak files)

molecule: genomic DNA

organism:
Homo sapiens
Rattus norvegicus

source_name: Skeletal muscle

extract_protocol:
Tissue from human (49mg of pulverized human skeletal muscle) and rat (45mg of pulverized gastrocnemius samples) were used. We used the previously published ENCODE protocol (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S1.pdf) (The ENCODE Project Consortium 2012, 2012) to isolate nuclei. After isolating nuclei from each sample (species) individually, the nuclei were mixed in equal proportions. The desired concentration of nuclei was achieved by resuspending the appropriate number of nuclei in 1X diluted nuclei buffer for snATAC-seq
The nuclei were submitted to the University of Michigan Advanced Genomics core for processing on the 10x Genomics Chromium platform. 15.4K nuclei were loaded into a single well

tag: tissue

value: Skeletal muscle


title: 1846: Human - rat multiome mix (ATAC component)

extract_protocol:
Tissue from human (74mg of pulverized human skeletal muscle) and rat (79mg of pulverized gastrocnemius samples) were used in the multiome experiment. The pulverized tissues were mixed together prior to isolation. For this experiment, we developed a customized protocol based on those recommended by 10x Genomics (https://www.10xgenomics.com/resources/demonstrated-protocols/) and on the previously developed protocol (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S2.pdf)  to isolate nuclei (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S4.pdf). The desired concentration of nuclei was achieved by resuspending the appropriate number of nuclei in 1X diluted nuclei buffer.
The nuclei were submitted to the University of Michigan Advanced Genomics core for processing on the 10x Genomics Chromium platform. 16.1K nuclei were loaded into a single well.


title: 1846: Human - rat multiome mix (RNA component)

description:
***Raw data are unavailable due to patient privacy concerns***
nuclear RNA

library_source: transcriptomic

data_processing:
snRNA-seq data was processed using starSOLO (STAR v. 2.7.3a; options --soloUMIfiltering MultiGeneUMI --soloCBmatchWLtype 1MM_multi_pseudocounts --soloCellFilter None). For human-only libraries we used the GENCODE v. 19 annotation (with hg19). For human-rat mix libraries we processed the data twice, once for human and once for rat, and used the NCBI Rattus norvegicus Annotation Release 106 with rat genome rn6.
We filtered the mapped BAM file using samtools view -h -b -q 255 -F 4 -F 256 -F 2048
We anonymized the BAM files using anonymizeBAM (--strict; v. 0.4.5)
We generated single-end BED files using bedtools bamtobed
RNA-seq coverage files were generated from the anonymized BAM file using pybedtools (Dale et al., 2011) (a python wrapper around BEDTools; BedTool().genome_coverage() function, with arguments bg=True, split=True, and strand and scale set appropriately to produce both reverse and forward strand bedGraph files scaled to 1 million reads), followed by conversion of bedGraph files to bigWig files using bedGraphToBigWig (v. 4)
Genome_build: hg19 (human) and rn6 (when rat nuclei were included in the library)
Supplementary_files_format_and_content: RNA-seq read mapping locations, anonymized (BED files)
Supplementary_files_format_and_content: RNA-seq signal tracks for forward and reverse strands (bigWig files)


title: HMGB1_sCLIP_Rep1

city: Cologne

first: Yulia

last: Kargapolova

address: Robert-Koch-Straße 21

department: CMMC

country: Germany

institute: Cologne University

description: RNA-protein complex

data_processing:
Library strategy: sCLIP
demultiplexing
trimming
alignment (STAR)
peak calling (clipper)
Genome_build: hg19
Supplementary_files_format_and_content: called peaks : bed format; files for visualization with igv or ucsc browser - bw format

source_name: Human Caucasian foetal lung fibroblast (IMR90-79)

growth_protocol: IMR90-79 cells were grown in Minimum Essential Medium Eagle supplemented with 20% FBS, x1 penecilin-streptomycin and non-essential amino acids solution till reaching 90% confluency. Cells were further treated in accordance to sCLIP protocol (Kargapolova, Yulia et al. 2017).

extract_protocol:
sCLIP  was  performed  on  ~25  million  UV-crosslinked  nuclei  from  proliferating  IMR90  as  previously described (Kargapolova et al, 2017). RNA-RBP interactions were stabilized with UV crosslinking (245 nm, 150 mJ/cm2 x2 with 1min pause, on ice). The cells were lysed in lysis buffer (Tris-HCl (pH 7,6) (50mM); NaCl (250mM); EDTA (1 mM); Empigen BB (0,5%)), supplemented with protease inhibitor cocktail (Roche) and lysate was treated by TURBO DNase and RNaseT1 (1:1000) 10 min at 37 oC. Endogenous HMGB1/HMGB2 RNA-RBP complexes were immunoprecipitated with a specific primary antibody of interest (3 µg per 500 µl of protein lysate) using magnetic beads (Protein G Dynabeads (Life Technology)) for overnight and washed with 5 washes, 5 min each with lysis buffer. The second round of RNase digestion was performed on the beads for 5 min with 1:1000 diluted RNaseI (Ambion). An aliquot (1/3) of the IP beads was labelled with biotinylated ADP (Jena Bioscience) and T4 RNA-ligase (ThermoFisher) overnight. The signal from RNP complex was visualized using HRP-conjugated Streptavidin (Sigma). The rest of the IP was eluted from the beads, run on standard protein gels and transferred to the nitrocellulose membrane. The region corresponding to RNP complexes was cut and the RNA was eluted using proteinase K (ThermoFisher).
Next, the eluted RNA was polyadenylated. For the cDNA synthesis primers containing random and experimental barcodes were used. At this step the samples were pooled. The cDNA containing T7 promoter sequence was in vitro transcribed, dephosphorylated and treated with PNK, following the 3’ end adaptor ligation using T4 RNA-ligase 2 (a truncated variant, NEB, detailed below). Finally, the aRNA was reversely transcribed and PCR amplified with 10 cycles. Libraries were quality controlled by using Qubit (ThermoFisher) and Bioanalyzer (Agilent).
For the first replica nitrocellulose membrane containing HMGB1- and HMGB2-containing RNA-protein complexes was cut into 2 parts, upper (>25kDa above the expected protein) and lower (between 5kDa and 25kDa above the expected protein size). Libraries were prepared using different barcodes for each fraction, sequenced and reads were merged after mapping. For the second replica no fractionation was performed.

tag: passages

tag: cell line

tag: antibody

value: anti-HMGB1 ab 18256 (4ug)


title: GC0542 Gastric Cancer


title: LM_pt85_post_1

type: genomic

city: Montreal

first: Gerald

last: Batist

state: Québec

address: 3755 Cote Ste-Catherine

country: Canada

institute: Jewish General Hospital

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions. Briefly, 250 ng of gDNA from was first digested with Nsp I restriction endonuclease and ligated to specific adaptors that recognize the cohesive four base pair overhangs. The digested and ligated sample was then amplified by PCR using Titanium Taq Polymerase (CloneTech). Each PCR reactions were run on a 2% agarose gel (E-Gel 48-well, LifeTechnologies) with PCR Marker (Affymetrix) to ensure consistent PCR products distribution between 150 bp to 2000 bp. The PCR amplification was followed by a purification step with Purification bead. Purified PCR product was quantified by Nanodrop in order to assess the average DNA yield. PCR products were fragmented according to specific Affymetrix recommendation (Technical Note: P/N 703289 Rev1). Fragmention size distribution was confirmed by majority of distribution between 25 to 125 bp, using a 4% agarose gel (E-Gel 48-well, LifeTechnologies) with TrackIt 25 bp DNA Marker (LifeTechnologies). After labeling with biotin, the DNA target was hybridized to the CytoScan® HD array (Affymetrix) and incubated at 490C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. CytoScan array were then washed in a GeneChips® Fluidics Station 450 (Affymetrix).

scan_protocol: The Arrays were then washed in a GeneChips fluidics stations 450 (Affymetrix), and scanned on a Gene Chip Scanner 3000 (Affymetrix).

data_processing:
The raw .CEL files were processed using Nexus Copy Number TM (BioDiscovery Inc, CA, USA) using SNP-FASST2 Segmentation Algorithm in which B-allele frequency probes are assigned to a range of possible states and a combination of the BAF and Log-R states are used to make the final copy number and allelic event calls. Quadratic correction and median probes re-centering were applied as well as removal of 3% outliers. The significance threshold for segmentation was set at 5.10-7 also requiring a minimum of 20 probes per segment and a maximum probe spacing of 1000 between adjacent probes before breaking a segment. The log ratio thresholds for single copy gain and single copy loss were set at 0.1 and -0.15, respectively. The log ratio thresholds for two or more copy gain and homozygous loss were set at 0.7 and -1.1 respectively. The Homozygous Frequency Threshold was set to 0.85. The Homozygous Value Threshold was set to 0.8. Sex chromosomes were excluded from the analysis. Robust variance sample quality calculation was below 0.15 for all the samples analysed.
Detected Segment types: Gain Mosaic, LossMosaic GAin, Loss, LOH; Probe array data: Copy Number State, Log2Ratio, Weighted Log2Ratio, LOH, Allele Difference, Genotype Calls, Smooth Signal, B-allele Frequency

label: biotin

source_name: Liver Met pt85 post-treatment bx 1

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Liver metastasis biopsies were  snap frozen in liquid nitrogen or immersed in RNALater solution. Snap frozen and washed RNALater samples were embedded in optimal cutting temperature (OCT) medium.  All fresh frozen and RNA-later samples were embedded in optimal cutting temperature (OCT) medium.  Cryosections (5 μm thick) were cut and stained with hematoxylin and eosin (H&E). The percentage of normal cells, tumor cells and necrotic areas was determined by a pathologist and the threshold for suitable tumor cell area for extraction was set at ≥40% of the specimen including <20% of necrotic cells. When needed, biopsies were macro dissected to reach these thresholds.

extract_protocol: Genomic material isolation from  samples was performed using the AllPrep Universal Kit (Qiagen) according to manufacturer's instructions. Genomic DNA was quantified using Picogreen protocol (Quant-iT™ PicoGreen® dsDNA Products, Invitrogen, P-7589) and read on SpectraMAX GeminiXS Spectrophotometer and its approximating average size was assessed using a 1% agarose gel (E-Gel 48-well, LifeTechnologies) with High Range DNA Marker (Life Technologies).

treatment_protocol: Pre-treatment liver metastasis biopsies were collected at baseline prior first line therapy; Post biopsies were collected at the time of clinical resistance after first line therapy (FOLFOX or FOLFIRI with or without bevacizumab)

tag: cancer type

value: Colerectal Cancer

tag: tissue type

value: Liver metastasis

tag: chemotherapy treatment

value: FOLFOX

tag: other treatment

value: No


title: Beads_only_control_Rep1

description: RNA-protein complex

value: no antibody control


title: LM_pt135_post

source_name: Liver Met pt135 post-treatment bx


title: GC0540 Gastric Cancer

value: Female


title: GC0539 Gastric Cancer

value: Gastric Cancer


title: LM_pt90_post

source_name: Liver Met pt90 post-treatment bx


title: LM_pt76_post

source_name: Liver Met pt76 post-treatment bx


title: LM_pt80_post

source_name: Liver Met pt80 post-treatment bx

value: Bevacuzimab


title: GC0538 Gastric Cancer

value: IA


title: GC0537 Gastric Cancer

value: Male


title: GC0541 Gastric Cancer

value: diff


title: HMGB2_sCLIP_Rep1

description: RNA-protein complex

value: anti-HMGB2 ab 67282 (4ug)


title: GC0536 Gastric Cancer


title: LM_pt58_post

source_name: Liver Met pt58 post-treatment bx


title: GC0535 Gastric Cancer


title: GC0534 Gastric Cancer


title: LM_pt56_post

source_name: Liver Met pt56 post-treatment bx


title: LM_pt35_post

source_name: Liver Met pt35 post-treatment bx


title: LM_pt85_post_2

source_name: Liver Met pt85 post-treatment bx 2


title: GC0533 Gastric Cancer


title: GC0546 Gastric Cancer


title: LM_pt130_pre

source_name: Liver Met pt130 pre-treatment bx

value: Not available


title: GC0532 Gastric Cancer


title: LM_pt135_pre

source_name: Liver Met pt135 pre-treatment bx


title: GC0531 Gastric Cancer


title: LM_pt14_post

source_name: Liver Met pt14 post-treatment bx


title: GC0529 Gastric Cancer

value: undiff


title: LM_pt111_pre

source_name: Liver Met pt111 pre-treatment bx


title: GC0528 Gastric Cancer


title: LM_pt109_pre

source_name: Liver Met pt109 pre-treatment bx

value: FOLFOXIRI


title: LM_pt108_pre

source_name: Liver Met pt108 pre-treatment bx

value: FOLFIRI


title: GC0525 Gastric Cancer

source_name: Serum


title: LM_pt90_pre

source_name: Liver Met pt90 pre-treatment bx


title: GC0526 Gastric Cancer


title: LM_pt105_pre

source_name: Liver Met pt105 pre-treatment bx


title: LM_pt104_pre

source_name: Liver Met pt104 pre-treatment bx


title: LM_pt84_pre

source_name: Liver Met pt84 pre-treatment bx


title: LM_pt85_pre

source_name: Liver Met pt85 pre-treatment bx


title: GC0524 Gastric Cancer


title: GC0523 Gastric Cancer


title: GC0522 Gastric Cancer


title: GC0520 Gastric Cancer


title: GC0519 Gastric Cancer


title: GC0521 Gastric Cancer


title: LM_pt82_pre

source_name: Liver Met pt82 pre-treatment bx


title: LM_pt83_pre

source_name: Liver Met pt83 pre-treatment bx


title: GC0518 Gastric Cancer


title: LM_pt80_pre

source_name: Liver Met pt80 pre-treatment bx


title: LM_pt118_pre

source_name: Liver Met pt118 pre-treatment bx


title: GC0517 Gastric Cancer


title: LM_pt71_pre

source_name: Liver Met pt71 pre-treatment bx


title: LM_pt67_pre

source_name: Liver Met pt67 pre-treatment bx


title: GC0527 Gastric Cancer


title: GC0515 Gastric Cancer


title: GC0516 Gastric Cancer


title: GC0514 Gastric Cancer


title: GC0512 Gastric Cancer


title: GC0513 Gastric Cancer


title: LM_pt62_pre

source_name: Liver Met pt62 pre-treatment bx


title: LM_pt56_pre

source_name: Liver Met pt56 pre-treatment bx


title: LM_pt58_pre

source_name: Liver Met pt58 pre-treatment bx


title: LM_pt54_pre

source_name: Liver Met pt54 pre-treatment bx


title: LM_pt76_pre

source_name: Liver Met pt76 pre-treatment bx


title: GC0508 Gastric Cancer

source_name: Serum


title: GC0507 Gastric Cancer


title: LM_pt35_pre

source_name: Liver Met pt35 pre-treatment bx


title: LM_pt47_pre

source_name: Liver Met pt47 pre-treatment bx


title: LM_pt38_pre

source_name: Liver Met pt38 pre-treatment bx


title: GC0510 Gastric Cancer


title: LM_pt37_pre

source_name: Liver Met pt37 pre-treatment bx


title: GC0509 Gastric Cancer


title: GC0506 Gastric Cancer


title: LM_pt34_pre

source_name: Liver Met pt34 pre-treatment bx


title: LM_pt63_pre

source_name: Liver Met pt63 pre-treatment bx


title: GC0505 Gastric Cancer


title: GC0504 Gastric Cancer


title: LM_pt19_pre

source_name: Liver Met pt19 pre-treatment bx


title: GC0503 Gastric Cancer


title: LM_pt26_pre

source_name: Liver Met pt26 pre-treatment bx


title: GC0511 Gastric Cancer


title: LM_pt61_pre

source_name: Liver Met pt61 pre-treatment bx


title: GC0501 Gastric Cancer


title: GC0502 Gastric Cancer


title: LM_pt18_pre

source_name: Liver Met pt18 pre-treatment bx


title: GC0500 Gastric Cancer


title: GC0499 Gastric Cancer


title: LM_pt16_pre

source_name: Liver Met pt16 pre-treatment bx


title: GC0498 Gastric Cancer


title: LM_pt3_pre

source_name: Liver Met pt3 pre-treatment bx


title: LM_pt28_pre

source_name: Liver Met pt28 pre-treatment bx


title: GC0496 Gastric Cancer


title: GC0493 Gastric Cancer


title: GC0494 Gastric Cancer


title: GC0495 Gastric Cancer


title: NC1 [miRNA]

city: 广州

first: Runguang

last: LI

address: 广州大道北沙太南路

country: China

institute: 南方医科大学

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: sequence and expression of all miRNAs

organism: Rattus norvegicus

source_name: control group_BMSCs

growth_protocol: 12 8-week old SD rats were randomly divided into exercise group and control group (n = 6). Exercise group was treated with 8 weeks moderate treadmill running. In the first 3 days, the initial speed, slope and time were set as 10 m/min at 0° slope for 20 min, which increased up to 20 m/min at 5° slope for 60 min after 2 days’ rest. The exercise was carried out once a day, 5 days a week for 8 weeks. Finally, Femur and Tibia BMSCs were collected for sequencing.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq2000/2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

tag: strain

value: Sprague-Dawley rats

tag: group

value: control group

tag: cell type

value: Bone marrow mesenchymal stem cells (BMSCs)


title: NC2 [miRNA]


title: GC0497 Gastric Cancer


title: GC0491 Gastric Cancer


title: GC0490 Gastric Cancer


title: GC0492 Gastric Cancer


title: treadmill 2 [miRNA]

source_name: exercise group_BMSCs

value: exercise group


title: treadmill 1 [miRNA]


title: GC0487 Gastric Cancer

value: IB


title: GC0488 Gastric Cancer


title: GC0489 Gastric Cancer


title: GC0486 Gastric Cancer


title: GC0485 Gastric Cancer


title: LM_pt1_pre

source_name: Liver Met pt1 pre-treatment bx

value: Colerectal Cancer

value: Liver metastasis

value: FOLFOX


title: GC0483 Gastric Cancer

source_name: Serum

value: Gastric Cancer


title: GC0484 Gastric Cancer

value: IA


title: treadmill 3 [miRNA]


title: GC0481 Gastric Cancer

value: Male


title: GC0480 Gastric Cancer

value: diff


title: GC0479 Gastric Cancer


title: GC0478 Gastric Cancer

value: Female


title: NC3 [miRNA]


title: GC0476 Gastric Cancer


title: GC0475 Gastric Cancer


title: GC0472 Gastric Cancer


title: GC0471 Gastric Cancer


title: GC0474 Gastric Cancer


title: GC0470 Gastric Cancer


title: GC0477 Gastric Cancer


title: GC0468 Gastric Cancer


title: GC0467 Gastric Cancer


title: GC0473 Gastric Cancer


title: GC0465 Gastric Cancer


title: GC0466 Gastric Cancer


title: GC0469 Gastric Cancer


title: GC0464 Gastric Cancer


title: GC0463 Gastric Cancer


title: GC0461 Gastric Cancer


title: GC0462 Gastric Cancer


title: GC0459 Gastric Cancer


title: GC0460 Gastric Cancer


title: colonoid_P18_FLICRD1_204680150093_R01C01

city: Vancouver

first: Theodore

middle: S

last: Steiner

state: BC

address: Rm. C328 HP East, VGH

department: Medicine/Infectious Diseases

institute: University of British Columbia

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Control Software with an Illumina iScan under standard setting

data_processing: Raw staining intensities in .IDAT files were imported into R (v3.6.3), and converted into methylated and unmethylated signals using minfi (v1.30.0). Methylation data was further normalized in R using functional normalization and beta-mixture quantile dilation using using minfi and wateRmelon  (v1.28.0), respectively, and batch-corrected using ComBat in sva (v3.32.1). Probes exhibiting a detection p-value > 1x10-4 or a beadcount < 3 in at least one sample were discarded. In addition, XY, SNP probes, and cross-reactive/polymorphic probes as previously curated (Pidsley et al., 2016) were removed from all samples. Probes remaining: 773,348.

label: Cy3 and Cy5

source_name: human colonoid monolayer

label_protocol: Standard Illumina Protocol (Infinium Human MethylationEPIC BeadChip arrays)

extract_protocol: genomic DNA was extracted and purified from cultured human colonoid monolayer samples using Qiagen DNeasy Blood and Tissue kit, and bisulfite-converted using Zymo EZ DNA Methylation kit according to standard instructions

value: human colonoid monolayer

tag: passage

value: female

tag: condition

value: FliC RD1


title: colonoid_P18_USRD1_204680150093_R06C01

tag: Sex

value: US RD1


title: GC0458 Gastric Cancer

tag: disease state

tag: age


title: colonoid_P33_USRD1_REP_204680150093_R05C01


title: colonoid_P33_ALI_204680150093_R03C01

value: ALI


title: colonoid_P33_FLICRD5_204680150093_R02C01

value: FliC RD5


title: colonoid_P18_FLICRD5_204676960062_R05C01


title: GC0456 Gastric Cancer

tag: Stage

tag: histological subtype


title: colonoid_P18_ALI_204676960062_R02C01

tag: tissue


title: colonoid_P18_USRD5_REP_204680150093_R04C01

value: US RD5


title: GC0457 Gastric Cancer


title: colonoid_P33_USRD5_204676960062_R06C01


title: colonoid_P33_USRD1_204676960062_R01C01


title: GC0454 Gastric Cancer

value: undiff


title: colonoid_P18_USRD5_204676960062_R03C01


title: genomic DNA from cord blood NGT_57

city: Setagaya

first: Tomoko

last: Kawai

state: Tokyo

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

description: NGT cord blood

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner (iScan) setting

data_processing: GenomeStudio software v1.9.0

label: Cy5 and Cy3

source_name: cord blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cord blood using QIAsymphony DNA Midi Kit (96) according to standard instructions

value: NGT

tag: neonate gender

value: male

tag: gestational age (wks)

tag: birth weight (g)

tag: gestational weight gain (kg)

tag: pre-pregnancy bmi


title: genomic DNA from cord blood NGT_61

description: NGT cord blood


title: genomic DNA from cord blood NGT_48

description: NGT cord blood


title: GC0453 Gastric Cancer


title: GC0452 Gastric Cancer


title: genomic DNA from cord blood NGT_56

description: NGT cord blood


title: GC0451 Gastric Cancer


title: GC0450 Gastric Cancer


title: GC0449 Gastric Cancer


title: genomic DNA from cord blood NGT_53

description: NGT cord blood


title: genomic DNA from cord blood NGT_55

description: NGT cord blood


title: genomic DNA from cord blood NGT_54

description: NGT cord blood


title: colonoid_P33_FLICRD1_204676960062_R04C01


title: genomic DNA from cord blood NGT_52

description: NGT cord blood


title: genomic DNA from cord blood NGT_51

description: NGT cord blood


title: genomic DNA from cord blood NGT_49

description: NGT cord blood


title: genomic DNA from cord blood NGT_46

description: NGT cord blood


title: GC0448 Gastric Cancer


title: genomic DNA from cord blood NGT_58

description: NGT cord blood


title: GC0447 Gastric Cancer


title: GC0455 Gastric Cancer


title: genomic DNA from cord blood NGT_47

description: NGT cord blood


title: genomic DNA from cord blood NGT_50

description: NGT cord blood


title: genomic DNA from cord blood NGT_60

description: NGT cord blood


title: GC0446 Gastric Cancer


title: GC0443 Gastric Cancer


title: GC0444 Gastric Cancer


title: GC0442 Gastric Cancer


title: GC0445 Gastric Cancer


title: GC0440 Gastric Cancer


title: GC0441 Gastric Cancer


title: GC0439 Gastric Cancer


title: genomic DNA from cord blood NGT_59

description: NGT cord blood


title: GC0438 Gastric Cancer


title: GC0435 Gastric Cancer


title: GC0434 Gastric Cancer


title: genomic DNA from cord blood NGT_45

description: NGT cord blood


title: genomic DNA from cord blood NGT_44

description: NGT cord blood


title: GC0433 Gastric Cancer


title: genomic DNA from cord blood NGT_39

description: NGT cord blood


title: genomic DNA from cord blood NGT_43

description: NGT cord blood


title: GC0432 Gastric Cancer


title: genomic DNA from cord blood NGT_42

description: NGT cord blood


title: genomic DNA from cord blood NGT_41

description: NGT cord blood


title: GC0436 Gastric Cancer


title: GC0437 Gastric Cancer


title: GC0431 Gastric Cancer


title: genomic DNA from cord blood NGT_40

description: NGT cord blood


title: GC0430 Gastric Cancer


title: genomic DNA from cord blood NGT_35

description: NGT cord blood


title: GC0427 Gastric Cancer


title: genomic DNA from cord blood NGT_36

description: NGT cord blood


title: GC0426 Gastric Cancer


title: GC0429 Gastric Cancer


title: genomic DNA from cord blood NGT_37

description: NGT cord blood


title: GC0424 Gastric Cancer


title: genomic DNA from cord blood NGT_38

description: NGT cord blood


title: GC0423 Gastric Cancer


title: GC0425 Gastric Cancer


title: GC0422 Gastric Cancer


title: genomic DNA from cord blood NGT_24

description: NGT cord blood


title: genomic DNA from cord blood NGT_23

description: NGT cord blood


title: genomic DNA from cord blood NGT_34

description: NGT cord blood


title: genomic DNA from cord blood NGT_29

description: NGT cord blood


title: genomic DNA from cord blood NGT_33

description: NGT cord blood


title: GC0421 Gastric Cancer


title: genomic DNA from cord blood NGT_26

description: NGT cord blood


title: genomic DNA from cord blood NGT_30

description: NGT cord blood


title: genomic DNA from cord blood NGT_31

description: NGT cord blood


title: genomic DNA from cord blood NGT_32

description: NGT cord blood


title: GC0419 Gastric Cancer


title: genomic DNA from cord blood NGT_22

description: NGT cord blood


title: genomic DNA from cord blood NGT_20

description: NGT cord blood


title: genomic DNA from cord blood NGT_27

description: NGT cord blood


title: GC0417 Gastric Cancer


title: GC0418 Gastric Cancer


title: genomic DNA from cord blood NGT_28

description: NGT cord blood


title: GC0416 Gastric Cancer


title: genomic DNA from cord blood NGT_21

description: NGT cord blood


title: GC0413 Gastric Cancer


title: GC0415 Gastric Cancer


title: GC0414 Gastric Cancer


title: GC0412 Gastric Cancer


title: GC0411 Gastric Cancer


title: GC0420 Gastric Cancer


title: GC0410 Gastric Cancer


title: genomic DNA from cord blood NGT_19

description: NGT cord blood


title: genomic DNA from cord blood NGT_25

description: NGT cord blood


title: genomic DNA from cord blood NGT_18

description: NGT cord blood


title: genomic DNA from cord blood NGT_17

description: NGT cord blood


title: GC0409 Gastric Cancer


title: genomic DNA from cord blood NGT_16

description: NGT cord blood


title: GC0407 Gastric Cancer


title: genomic DNA from cord blood NGT_15

description: NGT cord blood


title: GC0406 Gastric Cancer


title: GC0408 Gastric Cancer


title: GC0405 Gastric Cancer


title: genomic DNA from cord blood NGT_13

description: NGT cord blood


title: GC0404 Gastric Cancer


title: genomic DNA from cord blood NGT_14

description: NGT cord blood


title: genomic DNA from cord blood NGT_10

description: NGT cord blood


title: GC0402 Gastric Cancer


title: genomic DNA from cord blood NGT_9

description: NGT cord blood


title: genomic DNA from cord blood NGT_7

description: NGT cord blood


title: GC0403 Gastric Cancer


title: GC0400 Gastric Cancer


title: GC0401 Gastric Cancer


title: genomic DNA from cord blood NGT_11

description: NGT cord blood


title: genomic DNA from cord blood NGT_8

description: NGT cord blood


title: GC0398 Gastric Cancer


title: GC0397 Gastric Cancer


title: genomic DNA from cord blood NGT_3

description: NGT cord blood


title: GC0396 Gastric Cancer


title: GC0395 Gastric Cancer


title: cord blood GDM_163

data_processing:
GenomeStudio software v1.9.0
The normalization method of uploaded dataset is dependent on GenomeStudio Methylation Module normalization algorithms. We performed normalization to internal controls and background subtraction.

value: GDM

tag: neonatal 1 hour plasma glucose level (mg/dl)

value: GDM cord blood


title: genomic DNA from cord blood NGT_4

description: NGT cord blood


title: genomic DNA from cord blood NGT_2

description: NGT cord blood


title: genomic DNA from cord blood NGT_12

description: NGT cord blood


title: GC0394 Gastric Cancer

value: Gastric Cancer


title: cord blood GDM_165


title: cord blood GDM_164


title: genomic DNA from cord blood NGT_5

description: NGT cord blood


title: GC0393 Gastric Cancer

value: IA


title: GC0392 Gastric Cancer

value: Male


title: GC0391 Gastric Cancer

value: diff


title: genomic DNA from cord blood NGT_1

description: NGT cord blood


title: cord blood GDM_162


title: genomic DNA from cord blood NGT_6

description: NGT cord blood


title: GC0390 Gastric Cancer


title: GC0389 Gastric Cancer


title: GC0388 Gastric Cancer

value: Female


title: GC0399 Gastric Cancer


title: GC0387 Gastric Cancer


title: cord blood GDM_159


title: GC0386 Gastric Cancer


title: cord blood GDM_160


title: GC0385 Gastric Cancer


title: cord blood GDM_157


title: cord blood GDM_156


title: cord blood GDM_161


title: GC0384 Gastric Cancer


title: GC0382 Gastric Cancer


title: GC0383 Gastric Cancer


title: GC0381 Gastric Cancer


title: GC0380 Gastric Cancer


title: GC0379 Gastric Cancer


title: cord blood GDM_149


title: cord blood GDM_154


title: cord blood GDM_153


title: GC0378 Gastric Cancer


title: GC0377 Gastric Cancer


title: cord blood GDM_150


title: GC0376 Gastric Cancer


title: cord blood GDM_146


title: cord blood GDM_148


title: GC0375 Gastric Cancer


title: cord blood GDM_147


title: cord blood GDM_145


title: cord blood GDM_142


title: GC0374 Gastric Cancer


title: GC0370 Gastric Cancer


title: cord blood GDM_141


title: GC0371 Gastric Cancer


title: cord blood GDM_140


title: cord blood GDM_143


title: cord blood GDM_138


title: cord blood GDM_155


title: cord blood GDM_137


title: cord blood GDM_158


title: GC0369 Gastric Cancer


title: cord blood GDM_151


title: GC0367 Gastric Cancer


title: cord blood GDM_134


title: cord blood GDM_144


title: GC0373 Gastric Cancer


title: GC0368 Gastric Cancer


title: GC0366 Gastric Cancer


title: cord blood GDM_135


title: GC0364 Gastric Cancer


title: GC0365 Gastric Cancer


title: cord blood GDM_132


title: GC0363 Gastric Cancer


title: cord blood GDM_128


title: cord blood GDM_152


title: cord blood GDM_129


title: GC0362 Gastric Cancer


title: GC0361 Gastric Cancer


title: GC0359 Gastric Cancer


title: GC0358 Gastric Cancer


title: cord blood GDM_130


title: GC0357 Gastric Cancer


title: GC0355 Gastric Cancer


title: GC0354 Gastric Cancer


title: GC0356 Gastric Cancer


title: cord blood GDM_131


title: cord blood GDM_126


title: GC0353 Gastric Cancer


title: GC0352 Gastric Cancer


title: GC0351 Gastric Cancer


title: cord blood GDM_125


title: GC0350 Gastric Cancer


title: cord blood GDM_124


title: cord blood GDM_123


title: GC0360 Gastric Cancer


title: GC0349 Gastric Cancer


title: GC0348 Gastric Cancer


title: cord blood GDM_136


title: cord blood GDM_139


title: GC0347 Gastric Cancer


title: GC0346 Gastric Cancer


title: cord blood GDM_120


title: cord blood GDM_112


title: GC0345 Gastric Cancer


title: cord blood GDM_118


title: cord blood GDM_119


title: cord blood GDM_113


title: cord blood GDM_122


title: cord blood GDM_127


title: cord blood GDM_133


title: GC0344 Gastric Cancer


title: cord blood GDM_117


title: cord blood GDM_116


title: GC0343 Gastric Cancer


title: cord blood GDM_121


title: GC0342 Gastric Cancer


title: cord blood GDM_110


title: cord blood GDM_108


title: cord blood GDM_109


title: GC0341 Gastric Cancer


title: GC0340 Gastric Cancer


title: cord blood GDM_114


title: GC0338 Gastric Cancer


title: GC0336 Gastric Cancer


title: GC0339 Gastric Cancer


title: GC0337 Gastric Cancer


title: GC0335 Gastric Cancer


title: cord blood GDM_115


title: cord blood GDM_111


title: GC0333 Gastric Cancer


title: GC0332 Gastric Cancer


title: cord blood GDM_107


title: GC0330 Gastric Cancer


title: cord blood GDM_106


title: GC0331 Gastric Cancer


title: GC0334 Gastric Cancer


title: cord blood GDM_102


title: GC0329 Gastric Cancer


title: GC0327 Gastric Cancer


title: cord blood GDM_104


title: cord blood GDM_105


title: GC0326 Gastric Cancer


title: GC0325 Gastric Cancer


title: cord blood GDM_101


title: cord blood GDM_100


title: GC0324 Gastric Cancer


title: cord blood GDM_103


title: cord blood GDM_99


title: cord blood GDM_98


title: GC0328 Gastric Cancer


title: GC0323 Gastric Cancer


title: GC0322 Gastric Cancer


title: GC0321 Gastric Cancer


title: cord blood GDM_88


title: cord blood GDM_97


title: GC0320 Gastric Cancer


title: GC0319 Gastric Cancer


title: GC0318 Gastric Cancer


title: cord blood GDM_92


title: cord blood GDM_94


title: cord blood GDM_87


title: GC0317 Gastric Cancer


title: cord blood GDM_96


title: cord blood GDM_90


title: GC0316 Gastric Cancer


title: cord blood GDM_91


title: cord blood GDM_89


title: GC0315 Gastric Cancer


title: GC0314 Gastric Cancer


title: cord blood GDM_85


title: GC0313 Gastric Cancer


title: GC0312 Gastric Cancer


title: cord blood GDM_86


title: cord blood GDM_95


title: cord blood GDM_84


title: GC0309 Gastric Cancer


title: cord blood GDM_83


title: cord blood GDM_82


title: GC0308 Gastric Cancer


title: cord blood GDM_93


title: GC0307 Gastric Cancer


title: cord blood GDM_81


title: GC0306 Gastric Cancer


title: cord blood GDM_76


title: GC0310 Gastric Cancer


title: GC0305 Gastric Cancer


title: GC0304 Gastric Cancer


title: GC0303 Gastric Cancer


title: GC0311 Gastric Cancer


title: GC0302 Gastric Cancer


title: cord blood GDM_80


title: GC0301 Gastric Cancer


title: cord blood GDM_78


title: cord blood GDM_75


title: cord blood GDM_73


title: cord blood GDM_74


title: cord blood GDM_79


title: GC0299 Gastric Cancer


title: cord blood GDM_77


title: GC0298 Gastric Cancer


title: GC0297 Gastric Cancer


title: cord blood GDM_70


title: GC0296 Gastric Cancer


title: cord blood GDM_71


title: cord blood GDM_72


title: cord blood GDM_69


title: GC0292 Gastric Cancer


title: GC0291 Gastric Cancer


title: cord blood GDM_65


title: GC0290 Gastric Cancer


title: cord blood GDM_68


title: GC0294 Gastric Cancer


title: GC0289 Gastric Cancer


title: GC0288 Gastric Cancer


title: cord blood GDM_60


title: cord blood GDM_66


title: GC0286 Gastric Cancer


title: GC0295 Gastric Cancer


title: cord blood GDM_62


title: GC0285 Gastric Cancer


title: cord blood GDM_63


title: cord blood GDM_67


title: GC0283 Gastric Cancer


title: GC0284 Gastric Cancer


title: GC0282 Gastric Cancer


title: cord blood GDM_58


title: GC0281 Gastric Cancer


title: cord blood GDM_61


title: cord blood GDM_56


title: cord blood GDM_57


title: GC0279 Gastric Cancer


title: cord blood GDM_64


title: GC0278 Gastric Cancer


title: cord blood GDM_54


title: GC0277 Gastric Cancer


title: GC0276 Gastric Cancer


title: GC0280 Gastric Cancer


title: GC0275 Gastric Cancer


title: GC0274 Gastric Cancer


title: cord blood GDM_51


title: cord blood GDM_55


title: cord blood GDM_48


title: cord blood GDM_52


title: GC0273 Gastric Cancer


title: cord blood GDM_59


title: cord blood GDM_53


title: GC0271 Gastric Cancer

value: IB


title: cord blood GDM_50


title: GC0270 Gastric Cancer


title: GC0269 Gastric Cancer


title: cord blood GDM_45


title: cord blood GDM_44


title: GC0267 Gastric Cancer


title: cord blood GDM_47


title: GC0268 Gastric Cancer


title: cord blood GDM_46


title: GC0272 Gastric Cancer


title: GC0266 Gastric Cancer


title: cord blood GDM_40

value: female


title: cord blood GDM_43


title: GC0265 Gastric Cancer


title: GC0264 Gastric Cancer


title: cord blood GDM_49


title: GC0263 Gastric Cancer


title: cord blood GDM_42


title: cord blood GDM_41


title: cord blood GDM_38


title: GC0260 Gastric Cancer


title: GC0262 Gastric Cancer


title: cord blood GDM_39


title: cord blood GDM_37


title: GC0257 Gastric Cancer


title: GC0259 Gastric Cancer


title: GC0256 Gastric Cancer


title: cord blood GDM_31


title: cord blood GDM_35


title: cord blood GDM_34


title: cord blood GDM_36


title: GC0255 Gastric Cancer


title: cord blood GDM_30


title: GC0254 Gastric Cancer


title: GC0258 Gastric Cancer


title: GC0252 Gastric Cancer


title: GC0253 Gastric Cancer


title: cord blood GDM_33


title: GC0251 Gastric Cancer

value: II


title: GC0250 Gastric Cancer


title: cord blood GDM_28


title: cord blood GDM_26


title: cord blood GDM_29


title: GC0248 Gastric Cancer


title: GC0249 Gastric Cancer


title: GC0247 Gastric Cancer


title: cord blood GDM_25


title: cord blood GDM_21


title: cord blood GDM_20


title: cord blood GDM_23


title: GC0245 Gastric Cancer


title: cord blood GDM_32


title: GC0242 Gastric Cancer


title: cord blood GDM_24


title: GC0241 Gastric Cancer


title: cord blood GDM_19


title: Liver_Highω3diet_fish8

city: St. John's

first: Xi

last: Xue

state: NL

address: 1 Marine Lab Road

department: Department of Ocean Sciences

institute: Memorial University of Newfoundland

hyb_protocol: Equal quantities (825 ng) of each labeled aRNA (refer to label protocol) from one experimental sample and the common reference were pooled, fragmented following the manufacturer's instructions and co-hybridized to a cGRASP-designed Agilent 44K salmonid oligonucleotide microarray (GEO accession # GPL11299) as per the manufacturer’s instructions (Agilent, Mississauga, ON). The arrays were hybridized at 65°C for 17 h with 10 rpm rotation in an Agilent hybridization oven. The array slides were washed immediately following hybridization as per the manufacturer's instructions.

scan_protocol: Each microarray was scanned at 5 µm resolution and 90% of laser power using a ScanArray Gx Plus scanner and ScanArray Express software (v4.0; Perkin Elmer, Woodbridge, ON) with photomultiplier tube (PMT) set to balance fluorescence signal between channels.

data_processing: Signal intensity data was extracted from tiff images using Imagene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (median background + 2 * SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene.

organism: Salmo salar

source_name: Liver tissue, High ω3 diet, individual fish

label_protocol: Eight individual fish from each experimental diet groups were used in the microarray analysis using a common reference design. An equal quantity of each DNase I-treated, column-purified liver total RNA sample involved in the microarray experiment was pooled to make a common reference for the microarray hybridizations. Anti-sense amplified RNA (aRNA) was in vitro transcribed from 1 µg of each experimental RNA or reference pooled RNA using Ambion's Amino Allyl MessageAmp II aRNA Amplification kit (Life Technologies), following the manufacturers' instructions. The quantity and quality of aRNA were assessed using UV spectrophotometry and agarose gel electrophoresis. Twenty µg of aRNA was precipitated overnight following standard molecular biology procedures and re-suspended in coupling buffer; the resulting solution was used in a labeling reaction following the manufacturer's protocol. Resulting aRNA was labeled with either Cy3 (for the common reference) or Cy5 (for the experimental individuals) fluor (GE HealthCare, Mississauga, ON) through a dye-coupling reaction, following the manufacturer's instructions. The labeling efficiency was measured using the microarray function of the NanoDrop spectrophotometer.

growth_protocol: Atlantic salmon post-smolts (average weight 203 g) were randomly distributed among 8 tanks (500 L) with flow-through seawater  (~11°C, dissolved oxygen ≥ 10 mg L-1), and all fish were kept on a photoperiod of 24 hours light. Quadruplicate tanks of fish were fed each experimental diet overnight, using automatic feeders. At the end of trial, 5 fish from each tank were euthanized with 400 mg L-1 of tricaine-methane-sulfonate (TMS; Syndel Laboratories, Vancouver, BC) after 24 h of fasting. Body weight and fork length of fish were measured and recorded. Liver tissues (50-100 mg sample-1) were rapidly dissected from fish, placed in RNase-free 1.5 mL tubes, flash-frozen in liquid nitrogen, and stored at -80°C until RNA extractions were performed.

extract_protocol: Liver samples were homogenized in 1 ml of TRIzol reagent (Invitrogen/Life Technologies, Burlington, ON) with stainless steel beads (5 mm; QIAGEN, Mississauga, ON) using a TissueLyser (QIAGEN), frozen on dry ice and stored at -80°C. Frozen homogenates were slowly thawed on wet ice and the TRIzol total RNA extractions were then completed following the manufacturer’s instructions. Due to low 260/230 ratios (i.e. ranging from 0.7 to 1.7) following TRIzol extraction, all RNA samples were re-extracted using the phenol-chloroform phase separation method. Briefly, to separate the TRIzol-extracted RNA from organic materials, an equal volume of acid phenol:chloroform:isoamyl alcohol (125:24:1) (pH 4.5) (AM9720; Ambion/Life Technologies) was added to the samples, vortexed for 30 sec and centrifuged at 16,100 x g at 4°C for 20 min. The RNA was then recovered from the aqueous layer from the previous step by precipitation with 0.1 volumes of 3 M sodium acetate (pH 5.5) (Ambion/Life Technologies) and 2.5 volumes of anhydrous ethyl alcohol (Commercial Alcohols Inc., Brampton, ON) at -80°C for 1 h, followed by centrifugation at 16,100 x g at 4°C for 30 min. To wash the resulting RNA pellet, 1 ml of 75% ethanol was added and centrifuged at 16,100 x g at 4°C for 20 min. The ethanol was removed, and the RNA pellet was air-dried at room temperature for 10 min and resuspended in nuclease-free water (Invitrogen/Life Technologies). Total RNA of each sample was then treated with DNase I (QIAGEN) to degrade residual genomic DNA, and all samples were purified from salts, proteins and nucleotides using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s protocols.

value: Liver

tag: life stage

value: Juvenile

source_name: pool of RNAs from liver tissues invovled in the microarray experiment (i.e. High ω6, High ω3)


title: cord blood GDM_27


title: Liver_Highω3diet_fish7


title: cord blood GDM_13


title: GC0244 Gastric Cancer


title: cord blood GDM_22


title: GC0239 Gastric Cancer


title: Liver_Highω3diet_fish6


title: GC0240 Gastric Cancer


title: cord blood GDM_15


title: cord blood GDM_18


title: cord blood GDM_17


title: GC0246 Gastric Cancer


title: GC0238 Gastric Cancer


title: GC0236 Gastric Cancer


title: GC0237 Gastric Cancer


title: GC0234 Gastric Cancer


title: Liver_Highω3diet_fish1


title: Liver_Highω3diet_fish3


title: GC0233 Gastric Cancer


title: Liver_Highω3diet_fish2


title: Liver_Highω3diet_fish4


title: cord blood GDM_12


title: cord blood GDM_16


title: GC0232 Gastric Cancer


title: GC0231 Gastric Cancer


title: GC0230 Gastric Cancer


title: Liver_Highω6diet_fish7

source_name: Liver tissue, High ω6 diet, individual fish


title: GC0229 Gastric Cancer


title: Liver_Highω6diet_fish8


title: GC0228 Gastric Cancer


title: Liver_Highω3diet_fish5


title: Liver_Highω6diet_fish5


title: cord blood GDM_6


title: cord blood GDM_10


title: cord blood GDM_11


title: Liver_Highω6diet_fish6


title: Liver_Highω6diet_fish4


title: cord blood GDM_9


title: cord blood GDM_4


title: GC0222 Gastric Cancer


title: GC0223 Gastric Cancer


title: cord blood GDM_7


title: GC0227 Gastric Cancer


title: GC0221 Gastric Cancer


title: MCF-7 cells, KD 2

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

description:
SAMPLE 5
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The probe intensities were normalized by quantile algorithm based on the intensity distribution among all slides.

label_protocol: Biotinylated cRNA were prepared with IlluminaTM TotalPrepTM RNA Amplification Kit (Ambion).

extract_protocol: Total RNA was extracted using NucleoZOL reagent (Machery-Nagel, Düren, Germany) according to the manufacturer’s protocol.

treatment_protocol: MCF-7 cells were transfected with 100 nM siRNA against MTORT1 for 48 hours.

tag: cell line

tag: transfection

value: siRNA against MTORT1


title: GC0220 Gastric Cancer


title: GC0224 Gastric Cancer


title: GC0219 Gastric Cancer


title: cord blood GDM_3


title: cord blood GDM_8


title: Liver_Highω6diet_fish2


title: FemaleValMetRep5

city: Pittsburgh

first: Cristi

middle: Lara

last: Galindo

state: Pennsylvania

address: 200 Lothrop Avenue

institute: University of Pittsburgh

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, filtered for low abindance (<80) reads, and then mapped to mm10 whole genome using STAR v3.5.1a
Reads were annotated to Ensembl Transcript Release 100 and then quantile normalized
Normalized counts were batch corrected and then analyzed for differential expression using Partek GSA
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes quantile normalized and logged (base 2) adjusted counts

organism: Mus musculus

source_name: whole heart

extract_protocol:
Whole hearts were excised, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transgene

value: hBDNF

tag: hbdnf genotype

value: Val/Met

value: whole heart

value: 8 weeks


title: FemaleValMetRep6


title: MCF-7 cells, C 3

description:
SAMPLE 3
replicate 3

value: Negative control siRNA


title: MCF-7 cells, C 1

description:
SAMPLE 1
replicate 1


title: FemaleValRep6

value: Val/Val


title: MCF-7 cells, C 2

description:
SAMPLE 2
replicate 2


title: FemaleValRep5


title: GC0216 Gastric Cancer

value: Gastric Cancer

tag: Sex


title: FemaleValRep4


title: GC0217 Gastric Cancer

tag: disease state

value: IA


title: cord blood GDM_2

value: GDM

value: GDM cord blood


title: GC0226 Gastric Cancer

value: Female

tag: age

value: undiff


title: GC0213 Gastric Cancer

tag: Stage


title: FemaleMetRep5

value: Met/Met


title: GC0214 Gastric Cancer

value: Male

value: IB

tag: histological subtype


title: GC0212 Gastric Cancer

value: diff


title: cord blood GDM_1

value: female

tag: tissue


title: Liver_Highω6diet_fish3

value: Liver

value: Juvenile


title: GC0211 Gastric Cancer


title: FemaleValRep3

value: hBDNF

value: whole heart


title: FemaleMetRep4

value: 8 weeks


title: cord blood GDM_5

tag: neonate gender


title: FemaleMetRep6


title: MaleValMetRep5

value: Val/Met


title: MaleValMetRep6


title: GC0210 Gastric Cancer

value: Gastric Cancer


title: MaleValRep5

value: Val/Val


title: GC0209 Gastric Cancer

value: IA


title: MaleMetRep4


title: GC0208 Gastric Cancer


title: MaleValMetRep4


title: GC0207 Gastric Cancer


title: MaleValRep4


title: FemaleMetRep3


title: MaleValRep3


title: GC0204 Gastric Cancer


title: GC0206 Gastric Cancer


title: GC0202 Gastric Cancer


title: GC0203 Gastric Cancer


title: GC0201 Gastric Cancer


title: FemaleMetRep2


title: FemaleMetRep1


title: Liver_Highω6diet_fish1


title: cord blood GDM_14

value: GDM

tag: gestational age (wks)

value: GDM cord blood


title: FemaleValMetRep2

value: Female


title: GC0205 Gastric Cancer

value: undiff


title: FemaleValMetRep1


title: GC0195 Gastric Cancer

value: Male


title: GC0225 Gastric Cancer


title: GC0196 Gastric Cancer


title: FemaleValRep1


title: MaleMetRep3

value: Met/Met


title: GC0200 Gastric Cancer


title: GC0197 Gastric Cancer


title: GC0199 Gastric Cancer


title: MaleMetRep2


title: MaleMetRep1


title: MaleValMetRep3


title: MaleValMetRep2


title: MaleValRep2


title: MaleValRep1


title: GC0192 Gastric Cancer


title: GC0194 Gastric Cancer

value: diff


title: GC0190 Gastric Cancer


title: GC0189 Gastric Cancer

value: IB


title: GC0188 Gastric Cancer


title: GC0193 Gastric Cancer


title: FemaleValRep2


title: GC0191 Gastric Cancer


title: MCF-7 cells, KD 3

description:
SAMPLE 6
replicate 3

value: siRNA against MTORT1


title: 63_40_rna-hg19: Human snRNA 40k nuclei

source_name: Skeletal muscle

extract_protocol:
Two pieces of tissue (weighing 85.3 mg and 85.8 mg) were cut from one human skeletal muscle sample and two tissue pieces (weighing 95.9 mg and 92.6 mg) were cut from a second human skeletal muscle sample (quadriceps femoris muscle group). Each of the samples was cut on dry ice using a frozen scalpel to prevent thawing. The samples were pulverized using a CP02 cryoPREP automated dry pulverizer (Covaris 500001). We developed a customized nuclei isolation protocol (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S2.pdf) derived from the previously published ENCODE protocol (The ENCODE Project Consortium 2012, 2012). All four pulverized tissue pieces were mixed and redistributed to perform four different nuclei isolations. The desired concentration of nuclei was achieved by resuspending the appropriate number of nuclei in RNA nuclei buffer (1% BSA in PBS containing  0.2U/uL of RNAse inhibitor).
The nuclei were submitted to the University of Michigan Advanced Genomics core for processing on the 10x Genomics Chromium platform (v. 3.1 chemistry for snRNA-seq). Nuclei were loaded at 40K nuclei/well.

value: Skeletal muscle


title: GC0187 Gastric Cancer

value: special


title: 133157-hg19: Human snRNA no FANS rep 2

extract_protocol:
Three separate pieces of tissue were cut from a single human skeletal muscle sample (weighing 60mg, 50mg and 50mg; quadriceps femoris muscle group). Nuclei were isolated using a modified version of the ENCODE protocol (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S1.pdf) (The ENCODE Project Consortium 2012, 2012), customized from Step 5 onwards to accommodate FANS (Fluorescence assisted nuclei sorting). In step 5, the nuclei were resuspended in 700 µL of Sort buffer (1% BSA, 1mM EDTA in PBS) and filtered through a 30 µm filter. Three different nuclei isolations were performed and the nuclei suspended in sort buffer were mixed, pooled together and divided into two groups, one with FANS and one without FANS. FANS nuclei were sorted according to the previously published FANS protocol using DRAQ7 (Preissl et al. 2018). DRAQ7 (0.3mM from Cell Signaling Technology) was added to the FANS nuclei suspension, at 100 fold dilution to get a final concentration of 3 μM. Nuclei were gently mixed and incubated for 10 minutes on ice. Nuclei were analyzed in the presence of DRAQ7 and sorted for high DRAQ7 positive signal using Beckman Coulter’s Astrios MoFlo. We followed the gating strategy outlined in the FANS protocol (Preissl et al, 2018). The sorted nuclei were collected in a recovery buffer (5% BSA in PBS). The nuclei with and without FANS were spun at 1000g for 15 min at 4°C. The nuclei were resuspended in 100 µL of 1X diluted nuclei buffer and counted in the Countess II FL Automated Cell Counter. The appropriate amount of nuclei were split for snRNA-seq and spun down at 500g for 10 min at 4°C and resuspended in RNA nuclei buffer (1%BSA+PBS in 0.2U RNAse inhibitor).
The nuclei were submitted to the Universiy of Michigan Advanced Genomics core for processing on the 10x Genomics Chromium platform (v. 3.1 chemistry for snRNA-seq). Nuclei were loaded at 15.4K nuclei/well.


title: 133156-hg19: Human snRNA FANS rep 1


title: GC0186 Gastric Cancer


title: 63_20_rna-hg19: Human snRNA 20k nuclei

extract_protocol:
Two pieces of tissue (weighing 85.3 mg and 85.8 mg) were cut from one human skeletal muscle sample and two tissue pieces (weighing 95.9 mg and 92.6 mg) were cut from a second human skeletal muscle sample (quadriceps femoris muscle group). Each of the samples was cut on dry ice using a frozen scalpel to prevent thawing. The samples were pulverized using a CP02 cryoPREP automated dry pulverizer (Covaris 500001). We developed a customized nuclei isolation protocol (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S2.pdf) derived from the previously published ENCODE protocol (The ENCODE Project Consortium 2012, 2012). All four pulverized tissue pieces were mixed and redistributed to perform four different nuclei isolations. The desired concentration of nuclei was achieved by resuspending the appropriate number of nuclei in RNA nuclei buffer (1% BSA in PBS containing  0.2U/uL of RNAse inhibitor).
The nuclei were submitted to the University of Michigan Advanced Genomics core for processing on the 10x Genomics Chromium platform (v. 3.1 chemistry for snRNA-seq). Nuclei were loaded at 20K nuclei/well.


title: 133158-hg19: Human snRNA FANS rep 2


title: 133155-hg19: Human snRNA no FANS rep 1


title: GC0182 Gastric Cancer


title: MaleValMetRep1

value: hBDNF

value: whole heart


title: HSM2.bulk.rep2.hg19: Human bulk ATAC, sample HSM2 rep 2

extract_protocol:
2 tissue pieces weighing 99.4 mg and 80.7 mg were cut from one human skeletal muscle sample (HSM1) and 2 pieces weighing 67.6 mg and 103.5 mg were cut from a second human skeletal muscle sample (HSM2). Each of the samples was cut on dry ice using frozen scalpel to prevent thawing. The samples were pulverized using a CP02 cryoPREP automated dry pulverizer (Covaris 500001). For bulk ATAC-seq we followed the nuclei isolation protocol outlined in https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S2.pdf, except in the final step the nuclei were resuspended in 250 μL of 1% BSA in PBS.
The nuclei were counted in  Countess II FL Automated Cell Counter, and the appropriate volume of the suspension for 50K nuclei was spun down and used for the downstream transposition reaction (a modified version of the ENCODE protocol; https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S3.pdf) (The ENCODE Project Consortium 2012, 2012)


title: GC0181 Gastric Cancer


title: GC0180 Gastric Cancer


title: GC0183 Gastric Cancer


title: HSM2.bulk.rep1.hg19: Human bulk ATAC, sample HSM2 rep 1


title: 63_20-hg19: Human snATAC 20k nuclei

extract_protocol:
Two pieces of tissue (weighing 85.3 mg and 85.8 mg) were cut from one human skeletal muscle sample and two tissue pieces (weighing 95.9 mg and 92.6 mg) were cut from a second human skeletal muscle sample (quadriceps femoris muscle group). Each of the samples was cut on dry ice using a frozen scalpel to prevent thawing. The samples were pulverized using a CP02 cryoPREP automated dry pulverizer (Covaris 500001). We developed a customized nuclei isolation protocol (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S2.pdf) derived from the previously published ENCODE protocol (The ENCODE Project Consortium 2012, 2012). All four pulverized tissue pieces were mixed and redistributed to perform four different nuclei isolations. The desired concentration of nuclei was achieved by resuspending the appropriate number of nuclei in 1X diluted nuclei buffer.
The nuclei were submitted to the University of Michigan Advanced Genomics core for processing on the 10x Genomics Chromium platform. Nuclei were loaded at 20K nuclei/well.


title: GC0178 Gastric Cancer


title: 63_40-hg19: Human snATAC 40k nuclei

extract_protocol:
Two pieces of tissue (weighing 85.3 mg and 85.8 mg) were cut from one human skeletal muscle sample and two tissue pieces (weighing 95.9 mg and 92.6 mg) were cut from a second human skeletal muscle sample (quadriceps femoris muscle group). Each of the samples was cut on dry ice using a frozen scalpel to prevent thawing. The samples were pulverized using a CP02 cryoPREP automated dry pulverizer (Covaris 500001). We developed a customized nuclei isolation protocol (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S2.pdf) derived from the previously published ENCODE protocol (The ENCODE Project Consortium 2012, 2012). All four pulverized tissue pieces were mixed and redistributed to perform four different nuclei isolations. The desired concentration of nuclei was achieved by resuspending the appropriate number of nuclei in 1X diluted nuclei buffer.
The nuclei were submitted to the University of Michigan Advanced Genomics core for processing on the 10x Genomics Chromium platform. Nuclei were loaded at 40K nuclei/well.


title: GC0177 Gastric Cancer

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