title: Blood, Non-smoker_1730


title: Blood, Smoker_1729

status: Public on Apr 10 2020

type: genomic

city: Hangzhou

first: Yi

last: Xu

state: Zhejiang

address: No. 17, Dazhi Road, old Zhejiang, Shangcheng District

department: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases

country: China

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48 °C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: All samples were genotyped using the Infinium Human Exome-12 v1.1 BeadChip (Illumina, Inc., San Diego, CA, USA) according to the manufacturer’s protocol.

data_processing:
After genotyping, we performed the following quality control analyses on all genotyped SNPs. First, among 242 901 genotyped variants, we excluded all insertions and deletions to ensure that all base pair positions were unique and referred to the same variant. Second, any SNP with a call rate of <95% was excluded. Third, we removed those SNPs that were not in Hardy–Weinberg equilibrium at a p value of < 1.0 × 10−6. Finally, we used a 5% minor allele frequency (MAF) as a threshold to define rare and common variants, and any SNP with an MAF of <0.05 was excluded from the analysis.
[value definition]  Genotype: AA,AB,BB,or NC (no call)

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: The concentration of each DNA sample was first measured using the QuantiT™ dsDNA assay kit (Life Technologies, Carlsbad, CA) and then 50 DNA samples were pooled in equimolar amounts, as suggested by the manufacturers.

extract_protocol: Genomic DNA was extracted from EDTA-treated peripheral venous blood of each subject using the Qiagen DNA purification kit. All DNA samples were treated with RNase A to remove potential contaminating RNA, and DNA quality and the concentration of each sample was determined by the A260/A280 absorbance ratio.

tag: ethnicity

value: African-American

tag: age

tag: gender

value: Male

tag: cpd

tag: hsi

tag: ftnd

value: Smoker

tag: tissue

value: Blood


title: Blood, Non-smoker_1725

value: Non-smoker


title: Blood, Smoker_1723


title: Blood, Smoker_1727

value: Female


title: Blood, Smoker_1722


title: Blood, Smoker_1726


title: Blood, Non-smoker_1721


title: Blood, Smoker_1719


title: Blood, Smoker_1720


title: Blood, Non-smoker_1718


title: Blood, Smoker_1716


title: Blood, Smoker_1717


title: Blood, Non-smoker_1715


title: Blood, Smoker_1713


title: Blood, Smoker_1714


title: Blood, Non-smoker_1712


title: Blood, Smoker_1710


title: Blood, Smoker_1711


title: Blood, Smoker_1709


title: Blood, Smoker_1708


title: Blood, Smoker_1705


title: Blood, Smoker_1701


title: Blood, Smoker_1702


title: Blood, Smoker_1707


title: Blood, Smoker_1706


title: Blood, Smoker_1704


title: Blood, Smoker_1700


title: Blood, Smoker_1698


title: Blood, Smoker_1697


title: Blood, Smoker_1699


title: Blood, Non-smoker_1696


title: Blood, Smoker_1695


title: Blood, Smoker_1692


title: Blood, Smoker_1691


title: Blood, Smoker_1689


title: Blood, Smoker_1694


title: Blood, Smoker_1703


title: Blood, Smoker_1693


title: Blood, Non-smoker_1688


title: Blood, Smoker_1685


title: Blood, Smoker_1687


title: Blood, Smoker_1686


title: Blood, Smoker_1684


title: Blood, Smoker_1680


title: Blood, Smoker_1679


title: Blood, Smoker_1683


title: Blood, Smoker_1681


title: Blood, Smoker_1676


title: Blood, Smoker_1677


title: Blood, Smoker_1678


title: Blood, Smoker_1674


title: Blood, Smoker_1690


title: Blood, Non-smoker_1670


title: Blood, Smoker_1668


title: Blood, Non-smoker_1669


title: Blood, Non-smoker_1673


title: Blood, Non-smoker_1672


title: Blood, Smoker_1667


title: Blood, Non-smoker_1664


title: Blood, Smoker_1671


title: Blood, Non-smoker_1665


title: Blood, Smoker_1663


title: Blood, Non-smoker_1666


title: Blood, Smoker_1682


title: Blood, Smoker_1661


title: Blood, Smoker_1660


title: Blood, Smoker_1662


title: Blood, Non-smoker_1675


title: Blood, Smoker_1656


title: Blood, Smoker_1657


title: Blood, Non-smoker_1658


title: Blood, Non-smoker_1659


title: Blood, Non-smoker_1655


title: Blood, Non-smoker_1652


title: Blood, Smoker_1653


title: Blood, Non-smoker_1651


title: Blood, Smoker_1650


title: Blood, Non-smoker_1649


title: Blood, Non-smoker_1648


title: Blood, Smoker_1645


title: Blood, Smoker_1641


title: Blood, Non-smoker_1639


title: Blood, Smoker_1644


title: Blood, Non-smoker_1642


title: Blood, Smoker_1640


title: Blood, Smoker_1643


title: Blood, Non-smoker_1638


title: Blood, Non-smoker_1637


title: Blood, Non-smoker_1634


title: Blood, Smoker_1636


title: Blood, Smoker_1635


title: Blood, Non-smoker_1654


title: Blood, Non-smoker_1633


title: Blood, Non-smoker_1632


title: Blood, Non-smoker_1631


title: Blood, Non-smoker_1628


title: Blood, Smoker_1627


title: Blood, Smoker_1626


title: Blood, Non-smoker_1625


title: Blood, Smoker_1630


title: Blood, Non-smoker_1646


title: Blood, Non-smoker_1647


title: Blood, Non-smoker_1624


title: Blood, Smoker_1622


title: Blood, Non-smoker_1623


title: Blood, Non-smoker_1621


title: Blood, Non-smoker_1618


title: Blood, Non-smoker_1620


title: Blood, Smoker_1617


title: Blood, Smoker_1615


title: Blood, Non-smoker_1613


title: Blood, Smoker_1616


title: Blood, Smoker_1614


title: Blood, Smoker_1629


title: Blood, Smoker_1609


title: Blood, Smoker_1610


title: Blood, Smoker_1608


title: Blood, Non-smoker_1606


title: Blood, Non-smoker_1612


title: Blood, Non-smoker_1607


title: Blood, Non-smoker_1728


title: Blood, Non-smoker_1605


title: Blood, Non-smoker_1603


title: Blood, Smoker_1604


title: Blood, Non-smoker_1601


title: Blood, Non-smoker_1599


title: Blood, Non-smoker_1602


title: Blood, Non-smoker_1600


title: Blood, Non-smoker_1598


title: Blood, Smoker_1619


title: Blood, Smoker_1597


title: Blood, Non-smoker_1595


title: Blood, Smoker_1596


title: Blood, Non-smoker_1611


title: Blood, Non-smoker_1593


title: Blood, Smoker_1588


title: Blood, Smoker_1589


title: Blood, Non-smoker_1590


title: Blood, Non-smoker_1591


title: Blood, Non-smoker_1586


title: Blood, Smoker_1592


title: Blood, Smoker_1584


title: Blood, Smoker_1587


title: Blood, Non-smoker_1581


title: Blood, Smoker_1585


title: Blood, Non-smoker_1582


title: Blood, Non-smoker_1583


title: Blood, Non-smoker_1579


title: Blood, Non-smoker_1578


title: Blood, Non-smoker_1576


title: Blood, Non-smoker_1575


title: Blood, Smoker_1574


title: Blood, Non-smoker_1572


title: Blood, Non-smoker_1594


title: Blood, Smoker_1573


title: Blood, Smoker_1571


title: Blood, Smoker_1570


title: Blood, Smoker_1567


title: Blood, Smoker_1568


title: Blood, Smoker_1565


title: Blood, Non-smoker_1566


title: Blood, Smoker_1564


title: Blood, Smoker_1562


title: Blood, Smoker_1563


title: Blood, Smoker_1561


title: Blood, Smoker_1560


title: Blood, Smoker_1724


title: Blood, Non-smoker_1558


title: Blood, Non-smoker_1580


title: Blood, Smoker_1559


title: Blood, Smoker_1556


title: Blood, Non-smoker_1577


title: Blood, Smoker_1551


title: Blood, Non-smoker_1554


title: Blood, Smoker_1553


title: Blood, Smoker_1552


title: Blood, Non-smoker_1550


title: Blood, Smoker_1548


title: Blood, Non-smoker_1549


title: Blood, Smoker_1547


title: Blood, Non-smoker_1545


title: Blood, Non-smoker_1569


title: Blood, Non-smoker_1736


title: Blood, Non-smoker_1546


title: Blood, Non-smoker_1544


title: Blood, Non-smoker_1542


title: Blood, Non-smoker_1543


title: Blood, Smoker_1537


title: Blood, Non-smoker_1555


title: Blood, Smoker_1539


title: Blood, Smoker_1535


title: Blood, Non-smoker_1536


title: Blood, Smoker_1534


title: Blood, Non-smoker_1557


title: Blood, Non-smoker_1533


title: Blood, Non-smoker_1529


title: Blood, Smoker_1532


title: Blood, Smoker_1531


title: Blood, Non-smoker_1525


title: Blood, Non-smoker_1518


title: Blood, Smoker_1524


title: Blood, Non-smoker_1519


title: Blood, Non-smoker_1517


title: Blood, Non-smoker_1520


title: Blood, Smoker_1523


title: Blood, Smoker_1522


title: Blood, Non-smoker_1521


title: Blood, Smoker_1541


title: Blood, Non-smoker_1538


title: Blood, Non-smoker_1540


title: Blood, Non-smoker_1514


title: Blood, Smoker_1515


title: Blood, Non-smoker_1513


title: Blood, Non-smoker_1530


title: Blood, Smoker_1527


title: Blood, Smoker_1528


title: Blood, Non-smoker_1526


title: Blood, Smoker_1512


title: Blood, Non-smoker_1509


title: Blood, Smoker_1508


title: Blood, Non-smoker_1507


title: Blood, Non-smoker_1506


title: Blood, Smoker_1505


title: Blood, Smoker_1504


title: Blood, Non-smoker_1516


title: Blood, Non-smoker_1503


title: Blood, Non-smoker_1502


title: Blood, Smoker_1499


title: Blood, Smoker_1500


title: Blood, Non-smoker_1501


title: Blood, Smoker_1492


title: Blood, Non-smoker_1495


title: Blood, Smoker_1494


title: Blood, Smoker_1511


title: Blood, Smoker_1498


title: Blood, Non-smoker_1493


title: Blood, Smoker_1510


title: Blood, Smoker_1491


title: Blood, Non-smoker_1497


title: Blood, Non-smoker_1490


title: Blood, Smoker_1488


title: Blood, Smoker_1486


title: Blood, Smoker_1487


title: Blood, Smoker_1484


title: Blood, Smoker_1482


title: Blood, Smoker_1483


title: Blood, Non-smoker_1489


title: Blood, Non-smoker_1485


title: Blood, Smoker_1481


title: Blood, Smoker_1480


title: Blood, Non-smoker_1479


title: Blood, Smoker_1477


title: Blood, Non-smoker_1496


title: Blood, Smoker_1478


title: Blood, Smoker_1474


title: Blood, Smoker_1476


title: Blood, Non-smoker_1472


title: Blood, Smoker_1473


title: Blood, Non-smoker_1475


title: Blood, Non-smoker_1471


title: Blood, Smoker_1470


title: Blood, Non-smoker_1469


title: Blood, Smoker_1466


title: Blood, Non-smoker_1468


title: Blood, Smoker_1464


title: Blood, Non-smoker_1465


title: Blood, Smoker_1467


title: Blood, Smoker_1460


title: Blood, Smoker_1463


title: Blood, Smoker_1453


title: Blood, Smoker_1451


title: Blood, Smoker_1456


title: Blood, Smoker_1454


title: Blood, Non-smoker_1462


title: Blood, Smoker_1450


title: Blood, Non-smoker_1459


title: Blood, Non-smoker_1461


title: Blood, Smoker_1458


title: Blood, Smoker_1455


title: Blood, Non-smoker_1452


title: Blood, Smoker_1448


title: Blood, Smoker_1445


title: Blood, Smoker_1447


title: Blood, Smoker_1449


title: Blood, Smoker_1443


title: Blood, Smoker_1442


title: Blood, Non-smoker_1444


title: Blood, Smoker_1441


title: Blood, Smoker_1440


title: Blood, Non-smoker_1437


title: Blood, Smoker_1438


title: Blood, Smoker_1436


title: Blood, Non-smoker_1435


title: Blood, Non-smoker_1434


title: Blood, Smoker_1433


title: Blood, Smoker_1430


title: Blood, Non-smoker_1429


title: Blood, Non-smoker_1427


title: Blood, Smoker_1432


title: Blood, Smoker_1431


title: Blood, Smoker_1446


title: Blood, Smoker_1428


title: Blood, Smoker_1425


title: Blood, Smoker_1426


title: Blood, Non-smoker_1421


title: Blood, Smoker_1422


title: Blood, Non-smoker_1424


title: Blood, Smoker_1417


title: Blood, Non-smoker_1420


title: Blood, Smoker_1418


title: Blood, Smoker_1423


title: Blood, Smoker_1414


title: Blood, Smoker_1415


title: Blood, Non-smoker_1419


title: Blood, Non-smoker_1439


title: Blood, Non-smoker_1413


title: Blood, Smoker_1416


title: Blood, Smoker_1411


title: Blood, Non-smoker_1412


title: Blood, Non-smoker_1410


title: Blood, Smoker_1409


title: Blood, Non-smoker_1408


title: Blood, Non-smoker_1407


title: Blood, Smoker_1406


title: Blood, Non-smoker_1457


title: Blood, Smoker_1405


title: Blood, Non-smoker_1402


title: Blood, Non-smoker_1400


title: Blood, Non-smoker_1403


title: Blood, Non-smoker_1404


title: Blood, Non-smoker_1401


title: Blood, Smoker_1399


title: Blood, Non-smoker_1398


title: Blood, Smoker_1392


title: Blood, Smoker_1393


title: Blood, Non-smoker_1394


title: Blood, Non-smoker_1395


title: Blood, Non-smoker_1390


title: Blood, Non-smoker_1396


title: Blood, Non-smoker_1397


title: Blood, Non-smoker_1389


title: Blood, Smoker_1391


title: Blood, Smoker_1388


title: Blood, Non-smoker_1387


title: Blood, Non-smoker_1385


title: Blood, Smoker_1384


title: Blood, Non-smoker_1382


title: Blood, Non-smoker_1386


title: Blood, Smoker_1383


title: Blood, Non-smoker_1380


title: Blood, Non-smoker_1381


title: Blood, Smoker_1379


title: Blood, Non-smoker_1378


title: Blood, Smoker_1376


title: Blood, Non-smoker_1374


title: Blood, Smoker_1375


title: Blood, Non-smoker_1371


title: Blood, Non-smoker_1372


title: Blood, Smoker_1373


title: Blood, Non-smoker_1370


title: Blood, Smoker_1364


title: Blood, Smoker_1366


title: Blood, Smoker_1361


title: Blood, Non-smoker_1363


title: Blood, Non-smoker_1360


title: Blood, Smoker_1359


title: Blood, Non-smoker_1367


title: Blood, Smoker_1365


title: Blood, Smoker_1356


title: Blood, Smoker_1357


title: Blood, Smoker_1353


title: Blood, Non-smoker_1362


title: Blood, Non-smoker_1368


title: Blood, Non-smoker_1355


title: Blood, Smoker_1377


title: Blood, Non-smoker_1352


title: Blood, Smoker_1350


title: Blood, Non-smoker_1351


title: Blood, Non-smoker_1354


title: Blood, Non-smoker_1348


title: Blood, Smoker_1349


title: Blood, Non-smoker_1347


title: Blood, Non-smoker_1369


title: Blood, Non-smoker_1346


title: Blood, Non-smoker_1343


title: Blood, Non-smoker_1342


title: Blood, Non-smoker_1345


title: Blood, Non-smoker_1341


title: Blood, Non-smoker_1340


title: Blood, Non-smoker_1358


title: Blood, Smoker_1338


title: Blood, Non-smoker_1339


title: Blood, Non-smoker_1334


title: Blood, Non-smoker_1337


title: Blood, Non-smoker_1333


title: Blood, Non-smoker_1330


title: Blood, Non-smoker_1331


title: Blood, Smoker_1328


title: Blood, Smoker_1332


title: Blood, Non-smoker_1326


title: Blood, Non-smoker_1329


title: Blood, Smoker_1323


title: Blood, Smoker_1325


title: Blood, Smoker_1320


title: Blood, Non-smoker_1321


title: Blood, Smoker_1322


title: Blood, Non-smoker_1318


title: Blood, Smoker_1319


title: Blood, Non-smoker_1344


title: Blood, Smoker_1315


title: Blood, Non-smoker_1316


title: Blood, Non-smoker_1317


title: Blood, Smoker_1314


title: Blood, Non-smoker_1313


title: Blood, Smoker_1335


title: Blood, Non-smoker_1336


title: Blood, Non-smoker_1312


title: Blood, Non-smoker_1309


title: Blood, Non-smoker_1308


title: Blood, Non-smoker_1307


title: Blood, Non-smoker_1306


title: Blood, Non-smoker_1305


title: Blood, Non-smoker_1311


title: Blood, Non-smoker_1302


title: Blood, Non-smoker_1324


title: Blood, Non-smoker_1304


title: Blood, Smoker_1300


title: Blood, Smoker_1301


title: Blood, Smoker_1299


title: Blood, Non-smoker_1303


title: Blood, Non-smoker_1297


title: Blood, Non-smoker_1296


title: Blood, Smoker_1298


title: Blood, Smoker_1294


title: Blood, Smoker_1293


title: Blood, Smoker_1295


title: Blood, Non-smoker_1292


title: Blood, Smoker_1291


title: Blood, Smoker_1289


title: Blood, Non-smoker_1310


title: Blood, Non-smoker_1288


title: Blood, Non-smoker_1287


title: Blood, Non-smoker_1286


title: Blood, Smoker_1283


title: Blood, Non-smoker_1282


title: Blood, Non-smoker_1285


title: Blood, Non-smoker_1281


title: Blood, Non-smoker_1284


title: Blood, Non-smoker_1278


title: Blood, Non-smoker_1277


title: Blood, Smoker_1279


title: Blood, Non-smoker_1275


title: Blood, Non-smoker_1276


title: Blood, Non-smoker_1272


title: Blood, Non-smoker_1273


title: Blood, Non-smoker_1271


title: Blood, Non-smoker_1270


title: Blood, Non-smoker_1269


title: Blood, Smoker_1267


title: Blood, Smoker_1290


title: Blood, Non-smoker_1266


title: Blood, Non-smoker_1265


title: Blood, Non-smoker_1264


title: Blood, Non-smoker_1263


title: Blood, Non-smoker_1262


title: Blood, Non-smoker_1261


title: Blood, Non-smoker_1260


title: Blood, Non-smoker_1259


title: Blood, Smoker_1258


title: Blood, Smoker_1280


title: Blood, Non-smoker_1256


title: Blood, Smoker_1274


title: Blood, Non-smoker_1253


title: Blood, Smoker_1252


title: Blood, Non-smoker_1255


title: Blood, Non-smoker_1250


title: Blood, Non-smoker_1249


title: Blood, Non-smoker_1254


title: Blood, Smoker_1248


title: Blood, Non-smoker_1247


title: Blood, Non-smoker_1246


title: Blood, Non-smoker_1268


title: Blood, Non-smoker_1244


title: Blood, Non-smoker_1245


title: Blood, Smoker_1243


title: Blood, Smoker_1242


title: Blood, Non-smoker_1241


title: Blood, Non-smoker_1238


title: Blood, Non-smoker_1240


title: Blood, Smoker_1237


title: Blood, Non-smoker_1235


title: Blood, Smoker_1239


title: Blood, Non-smoker_1236


title: Blood, Smoker_1233


title: Blood, Non-smoker_1257


title: Blood, Non-smoker_1231


title: Blood, Non-smoker_1230


title: Blood, Smoker_1251


title: Blood, Non-smoker_1229


title: Blood, Non-smoker_1222


title: Blood, Non-smoker_1225


title: Blood, Non-smoker_1227


title: Blood, Non-smoker_1226


title: Blood, Non-smoker_1221


title: Blood, Non-smoker_1223


title: Blood, Non-smoker_1220


title: Blood, Non-smoker_1224


title: Blood, Smoker_1219


title: Blood, Non-smoker_1217


title: Blood, Smoker_1212


title: Blood, Non-smoker_1215


title: Blood, Smoker_1213


title: Blood, Non-smoker_1232


title: Blood, Smoker_1234


title: Blood, Non-smoker_1214


title: Blood, Non-smoker_1211


title: Blood, Non-smoker_1204


title: Blood, Smoker_1216


title: Blood, Non-smoker_1210


title: Blood, Non-smoker_1205


title: Blood, Non-smoker_1206


title: Blood, Non-smoker_1203


title: Blood, Non-smoker_1228


title: Blood, Smoker_1202


title: Blood, Non-smoker_1201


title: Blood, Non-smoker_1199


title: Blood, Non-smoker_1200


title: Blood, Non-smoker_1198


title: Blood, Smoker_1193


title: Blood, Smoker_1327


title: Blood, Non-smoker_1195


title: Blood, Non-smoker_1218


title: Blood, Smoker_1207


title: Blood, Smoker_1208


title: Blood, Non-smoker_1209


title: Blood, Non-smoker_1191


title: Blood, Non-smoker_1190


title: Blood, Non-smoker_1189


title: Blood, Non-smoker_1187


title: Blood, Smoker_1188


title: Blood, Non-smoker_1186


title: Blood, Non-smoker_1182


title: Blood, Non-smoker_1185


title: Blood, Non-smoker_1196


title: Blood, Non-smoker_1179


title: Blood, Non-smoker_1197


title: Blood, Non-smoker_1181


title: Blood, Smoker_1194


title: Blood, Non-smoker_1180


title: Blood, Smoker_1173


title: Blood, Non-smoker_1177


title: Blood, Non-smoker_1192


title: Blood, Non-smoker_1175


title: Blood, Non-smoker_1174


title: Blood, Non-smoker_1178


title: Blood, Smoker_1176


title: Blood, Non-smoker_1172


title: Blood, Non-smoker_1171


title: Blood, Non-smoker_1170


title: Blood, Non-smoker_1169


title: Blood, Smoker_1168


title: Blood, Smoker_1166


title: Blood, Smoker_1167


title: Blood, Smoker_1184


title: Blood, Non-smoker_1183


title: Blood, Non-smoker_1164


title: Blood, Non-smoker_1163


title: Blood, Smoker_1162


title: Blood, Non-smoker_1161


title: Blood, Non-smoker_1160


title: Blood, Non-smoker_1159


title: Blood, Non-smoker_1158


title: Blood, Non-smoker_1155


title: Blood, Non-smoker_1156


title: Blood, Non-smoker_1154


title: Blood, Smoker_1153


title: Blood, Non-smoker_1152


title: Blood, Smoker_1157


title: Blood, Non-smoker_1150


title: Blood, Non-smoker_1149


title: Blood, Non-smoker_1148


title: Blood, Non-smoker_1147


title: Blood, Non-smoker_1151


title: Blood, Non-smoker_1144


title: Blood, Non-smoker_1146


title: Blood, Non-smoker_1145


title: Blood, Non-smoker_1143


title: Blood, Non-smoker_1141


title: Blood, Smoker_1139


title: Blood, Non-smoker_1138


title: Blood, Non-smoker_1142


title: Blood, Non-smoker_1140


title: Blood, Non-smoker_1165


title: Blood, Smoker_1137


title: Blood, Non-smoker_1136


title: Blood, Non-smoker_1135


title: Blood, Non-smoker_1134


title: Blood, Smoker_1131


title: Blood, Smoker_1132


title: Blood, Non-smoker_1130


title: Blood, Non-smoker_1133


title: Blood, Smoker_1126


title: Blood, Smoker_1125


title: Blood, Non-smoker_1123


title: Blood, Non-smoker_1122


title: Blood, Non-smoker_1127


title: Blood, Smoker_1121


title: Blood, Smoker_1124


title: Blood, Smoker_1128


title: Blood, Smoker_1120


title: Blood, Smoker_1116


title: Blood, Non-smoker_1117


title: Blood, Smoker_1118


title: Blood, Smoker_1115


title: Blood, Smoker_1113


title: Blood, Non-smoker_1111


title: Blood, Non-smoker_1110


title: Blood, Smoker_1108


title: Blood, Smoker_1107


title: Blood, Non-smoker_1105


title: Blood, Non-smoker_1109


title: Blood, Smoker_1129


title: Blood, Smoker_1106


title: Blood, Non-smoker_1104


title: Blood, Smoker_1103


title: Blood, Smoker_1102


title: Blood, Non-smoker_1101


title: Blood, Smoker_1119


title: Blood, Smoker_1100


title: Blood, Non-smoker_1112


title: Blood, Non-smoker_1114


title: Blood, Non-smoker_1097


title: Blood, Non-smoker_1096


title: Blood, Smoker_1098


title: Blood, Smoker_1095


title: Blood, Smoker_1093


title: Blood, Smoker_1094


title: Blood, Non-smoker_1091


title: Blood, Smoker_1092


title: Blood, Non-smoker_1089


title: Blood, Non-smoker_1090


title: Blood, Non-smoker_1088


title: Blood, Smoker_1085


title: Blood, Smoker_1086


title: Blood, Smoker_1087


title: Blood, Smoker_1082


title: Blood, Non-smoker_1081


title: Blood, Smoker_1083


title: Blood, Non-smoker_1079


title: Blood, Smoker_1080


title: Blood, Smoker_1077


title: Blood, Smoker_1078


title: Blood, Smoker_1084


title: Blood, Non-smoker_1073


title: Blood, Non-smoker_1072


title: Blood, Smoker_1074


title: Blood, Non-smoker_1071


title: Blood, Non-smoker_1076


title: Blood, Non-smoker_1075


title: Blood, Smoker_1070


title: Blood, Smoker_1099


title: Blood, Smoker_1067


title: Blood, Non-smoker_1068


title: Blood, Non-smoker_1066


title: Blood, Non-smoker_1069


title: Blood, Non-smoker_1065


title: Blood, Non-smoker_1063


title: Blood, Smoker_1064


title: Blood, Smoker_1062


title: Blood, Smoker_1060


title: Blood, Non-smoker_1059


title: Blood, Non-smoker_1061


title: Blood, Smoker_1057


title: Blood, Non-smoker_1058


title: Blood, Non-smoker_1056


title: Blood, Smoker_1052


title: Blood, Smoker_1055


title: Blood, Smoker_1053


title: Blood, Smoker_1050


title: Blood, Smoker_1043


title: Blood, Smoker_1045


title: Blood, Smoker_1046


title: Blood, Smoker_1044


title: Blood, Non-smoker_1042


title: Blood, Smoker_1049


title: Blood, Smoker_1047


title: Blood, Smoker_1051


title: Blood, Non-smoker_1041


title: Blood, Non-smoker_1039


title: Blood, Non-smoker_1040


title: Blood, Non-smoker_1036


title: Blood, Smoker_1037


title: Blood, Non-smoker_1033


title: Blood, Smoker_1032


title: Blood, Non-smoker_1038


title: Blood, Smoker_1035


title: Blood, Smoker_1031


title: Blood, Non-smoker_1029


title: Blood, Non-smoker_1028


title: Blood, Smoker_1048


title: Blood, Smoker_1030


title: Blood, Non-smoker_1026


title: Blood, Non-smoker_1025


title: Blood, Smoker_1024


title: Blood, Smoker_1054


title: Blood, Smoker_1023


title: Blood, Non-smoker_1021


title: Blood, Non-smoker_1027


title: Blood, Non-smoker_1014


title: Blood, Non-smoker_1020


title: Blood, Smoker_1017


title: Blood, Smoker_1015


title: Blood, Smoker_1019


title: Blood, Smoker_1018


title: Blood, Smoker_1034


title: Blood, Smoker_1016


title: Blood, Smoker_1013


title: Blood, Smoker_1010


title: Blood, Non-smoker_1012


title: Blood, Non-smoker_1009


title: Blood, Smoker_1011


title: Blood, Non-smoker_1008


title: Blood, Non-smoker_1006


title: Blood, Smoker_1007


title: Blood, Smoker_1002


title: Blood, Smoker_1005


title: Blood, Non-smoker_1004


title: Blood, Smoker_1003


title: Blood, Non-smoker_1001


title: Blood, Smoker_1022


title: Blood, Non-smoker_998


title: Blood, Non-smoker_994


title: Blood, Non-smoker_997


title: Blood, Smoker_992


title: Blood, Non-smoker_989


title: Blood, Smoker_995


title: Blood, Smoker_987


title: Blood, Non-smoker_996


title: Blood, Smoker_993


title: Blood, Smoker_985


title: Blood, Non-smoker_986


title: Blood, Non-smoker_990


title: Blood, Smoker_984


title: Blood, Non-smoker_982


title: Blood, Non-smoker_983


title: Blood, Non-smoker_981


title: Blood, Smoker_980


title: Blood, Smoker_979


title: Blood, Smoker_978


title: Blood, Smoker_977


title: Blood, Smoker_976


title: Blood, Smoker_1000


title: Blood, Non-smoker_975


title: Blood, Smoker_999


title: Blood, Smoker_973


title: Blood, Non-smoker_974


title: Blood, Smoker_988


title: Blood, Smoker_971


title: Blood, Smoker_970


title: Blood, Non-smoker_972


title: Blood, Smoker_991


title: Blood, Non-smoker_968


title: Blood, Smoker_963


title: Blood, Non-smoker_965


title: Blood, Smoker_962


title: Blood, Smoker_964


title: Blood, Non-smoker_966


title: Blood, Non-smoker_967


title: Blood, Smoker_961


title: Blood, Smoker_960


title: Blood, Smoker_958


title: Blood, Smoker_957


title: Blood, Smoker_955


title: Blood, Smoker_956


title: Blood, Smoker_959


title: Blood, Smoker_953


title: Blood, Smoker_954


title: Blood, Non-smoker_949


title: Blood, Non-smoker_950


title: Blood, Non-smoker_951


title: Blood, Non-smoker_948


title: Blood, Non-smoker_947


title: Blood, Smoker_943


title: Blood, Smoker_944


title: Blood, Smoker_969


title: Blood, Non-smoker_945


title: Blood, Smoker_942


title: Blood, Smoker_940


title: Blood, Non-smoker_941


title: Blood, Non-smoker_939


title: Blood, Smoker_938


title: Blood, Smoker_937


title: Blood, Smoker_935


title: Blood, Smoker_933


title: Blood, Smoker_934


title: Blood, Smoker_936


title: Blood, Smoker_932


title: Blood, Smoker_931


title: Blood, Smoker_930


title: Blood, Smoker_952


title: Blood, Non-smoker_927


title: Blood, Non-smoker_926


title: Blood, Smoker_929


title: Blood, Smoker_925


title: Blood, Non-smoker_946


title: Blood, Non-smoker_923


title: Blood, Non-smoker_921


title: Blood, Non-smoker_922


title: Blood, Smoker_916


title: Blood, Smoker_919


title: Blood, Non-smoker_918


title: Blood, Smoker_917


title: Blood, Smoker_915


title: Blood, Non-smoker_912


title: Blood, Smoker_914


title: Blood, Smoker_913


title: Blood, Smoker_910


title: Blood, Non-smoker_911


title: Blood, Smoker_909


title: Blood, Smoker_908


title: Blood, Non-smoker_907


title: Blood, Smoker_904


title: Blood, Non-smoker_928


title: Blood, Non-smoker_905


title: Blood, Smoker_906


title: Blood, Non-smoker_902


title: Blood, Smoker_901


title: Blood, Non-smoker_924


title: Blood, Smoker_897


title: Blood, Smoker_900


title: Blood, Smoker_903


title: Blood, Smoker_920


title: Blood, Smoker_894


title: Blood, Non-smoker_896


title: Blood, Non-smoker_898


title: Blood, Non-smoker_890


title: Blood, Non-smoker_891


title: Blood, Smoker_895


title: Blood, Non-smoker_892


title: Blood, Non-smoker_886


title: Blood, Smoker_887


title: Blood, Non-smoker_884


title: Blood, Smoker_883


title: Blood, Non-smoker_885


title: Blood, Smoker_882


title: Blood, Non-smoker_879


title: Blood, Smoker_899


title: Blood, Non-smoker_878


title: Blood, Non-smoker_875


title: Blood, Smoker_873


title: Blood, Non-smoker_874


title: Blood, Smoker_876


title: Blood, Smoker_893


title: Blood, Non-smoker_870


title: Blood, Non-smoker_869


title: Blood, Non-smoker_867


title: Blood, Non-smoker_889


title: Blood, Smoker_888


title: Blood, Non-smoker_865


title: Blood, Smoker_863


title: Blood, Smoker_864


title: Blood, Non-smoker_862


title: Blood, Smoker_861


title: Blood, Smoker_857


title: Blood, Smoker_880


title: Blood, Smoker_860


title: Blood, Smoker_877


title: Blood, Smoker_881


title: Blood, Non-smoker_859


title: Blood, Smoker_854


title: Blood, Non-smoker_856


title: Blood, Non-smoker_851


title: Blood, Smoker_853


title: Blood, Smoker_872


title: Blood, Non-smoker_871


title: Blood, Non-smoker_868


title: Blood, Non-smoker_852


title: Blood, Smoker_850


title: Blood, Non-smoker_849


title: Blood, Smoker_866


title: Blood, Smoker_847


title: Blood, Non-smoker_848


title: Blood, Smoker_845


title: Blood, Smoker_844


title: Blood, Smoker_843


title: Blood, Smoker_846


title: Blood, Smoker_840


title: Blood, Non-smoker_839


title: Blood, Smoker_841


title: Blood, Smoker_842


title: Blood, Non-smoker_858


title: Blood, Smoker_855


title: Blood, Non-smoker_838


title: Blood, Non-smoker_836


title: Blood, Non-smoker_832


title: Blood, Smoker_835


title: Blood, Smoker_833


title: Blood, Smoker_834


title: Blood, Non-smoker_837


title: Blood, Smoker_831


title: Blood, Non-smoker_826


title: Blood, Non-smoker_827


title: Blood, Smoker_829


title: Blood, Smoker_822


title: Blood, Non-smoker_823


title: Blood, Non-smoker_824


title: Blood, Smoker_819


title: Blood, Non-smoker_825


title: Blood, Non-smoker_820


title: Blood, Smoker_814


title: Blood, Non-smoker_828


title: Blood, Non-smoker_818


title: Blood, Non-smoker_816


title: Blood, Smoker_817


title: Blood, Non-smoker_815


title: Blood, Smoker_811


title: Blood, Non-smoker_812


title: Blood, Smoker_813


title: Blood, Smoker_821


title: Blood, Non-smoker_810


title: Blood, Non-smoker_830


title: Blood, Non-smoker_809


title: Blood, Non-smoker_807


title: Blood, Smoker_804


title: Blood, Smoker_803


title: Blood, Smoker_806


title: Blood, Smoker_805


title: Blood, Smoker_802


title: Blood, Smoker_799


title: Blood, Smoker_801


title: Blood, Non-smoker_800


title: Blood, Non-smoker_798


title: Blood, Smoker_794


title: Blood, Non-smoker_796


title: Blood, Non-smoker_793


title: Blood, Smoker_791


title: Blood, Smoker_790


title: Blood, Non-smoker_789


title: Blood, Non-smoker_792


title: Blood, Smoker_788


title: Blood, Smoker_786


title: Blood, Smoker_787


title: Blood, Smoker_784


title: Blood, Smoker_782


title: Blood, Smoker_785


title: Blood, Smoker_783


title: Blood, Non-smoker_808


title: Blood, Smoker_780


title: Blood, Non-smoker_779


title: Blood, Smoker_778


title: Blood, Smoker_776


title: Blood, Non-smoker_781


title: Blood, Smoker_775


title: Blood, Smoker_777


title: Blood, Smoker_774


title: Blood, Non-smoker_797


title: Blood, Non-smoker_772


title: Blood, Non-smoker_795


title: Blood, Smoker_769


title: Blood, Smoker_773


title: Blood, Non-smoker_770


title: Blood, Smoker_768


title: Blood, Smoker_766


title: Blood, Non-smoker_767


title: Blood, Smoker_765


title: Blood, Non-smoker_764


title: Blood, Non-smoker_762


title: Blood, Smoker_759


title: Blood, Smoker_758


title: Blood, Smoker_760


title: Blood, Non-smoker_761


title: Blood, Smoker_757


title: Blood, Smoker_763


title: Blood, Smoker_756


title: Blood, Non-smoker_771


title: Blood, Smoker_755


title: Blood, Non-smoker_754


title: Blood, Non-smoker_753


title: Blood, Smoker_752


title: Blood, Smoker_751


title: Blood, Smoker_749


title: Blood, Smoker_750


title: Blood, Smoker_748


title: Blood, Non-smoker_746


title: Blood, Smoker_747


title: Blood, Smoker_744


title: Blood, Non-smoker_743


title: Blood, Non-smoker_742


title: Blood, Non-smoker_745


title: Blood, Non-smoker_740


title: Blood, Non-smoker_741


title: Blood, Non-smoker_738


title: Blood, Non-smoker_739


title: Blood, Smoker_737


title: Blood, Smoker_736


title: Blood, Non-smoker_735


title: Blood, Non-smoker_731


title: Blood, Non-smoker_733


title: Blood, Smoker_732


title: Blood, Non-smoker_734


title: Blood, Smoker_727


title: Blood, Non-smoker_728


title: Blood, Smoker_729


title: Blood, Smoker_730


title: Blood, Non-smoker_726


title: Blood, Smoker_724


title: Blood, Smoker_719


title: Blood, Non-smoker_720


title: Blood, Non-smoker_721


title: Blood, Smoker_725


title: Blood, Smoker_722


title: Blood, Smoker_723


title: Blood, Non-smoker_716


title: Blood, Non-smoker_715


title: Blood, Non-smoker_711


title: Blood, Non-smoker_713


title: Blood, Non-smoker_709


title: Blood, Smoker_712


title: Blood, Smoker_714


title: Blood, Non-smoker_710


title: Blood, Non-smoker_708


title: Blood, Smoker_707


title: Blood, Smoker_706


title: Blood, Non-smoker_705


title: Blood, Smoker_704


title: Blood, Non-smoker_703


title: Blood, Smoker_702


title: Blood, Non-smoker_699


title: Blood, Non-smoker_698


title: Blood, Smoker_696


title: Blood, Non-smoker_697


title: Blood, Smoker_718


title: Blood, Smoker_695


title: Blood, Smoker_693


title: Blood, Non-smoker_717


title: Blood, Non-smoker_694


title: Blood, Smoker_691


title: Blood, Smoker_692


title: Blood, Non-smoker_690


title: Blood, Smoker_689


title: Blood, Non-smoker_687


title: Blood, Smoker_688


title: Blood, Non-smoker_686


title: Blood, Smoker_682


title: Blood, Non-smoker_685


title: Blood, Smoker_683


title: Blood, Non-smoker_680


title: Blood, Non-smoker_684


title: Blood, Smoker_681


title: Blood, Non-smoker_701


title: Blood, Non-smoker_679


title: Blood, Non-smoker_700


title: Blood, Smoker_676


title: Blood, Smoker_677


title: Blood, Smoker_674


title: Blood, Smoker_672


title: Blood, Non-smoker_673


title: a33f_after

type: SRA

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Rd.

department: Tongji Hospital

institute: Tongji University

library_source: transcriptomic

data_processing:
Cutadapt1.6 were used to remove adapter and primer sequences. Reads shor than 50 were removed.
Unmapped reads were mapped again with bowtie2 (v2.10) in local mode. Alignment results were merged by the SAMtools.
Normalized FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) of genes in the RefGene annotation (2015 Feb) were estimated by Cuffquant (Cufflinks v2.21) with [-b, -u] options followed by Cuffnormal (Cufflinks v2.21).
Genome_build: hg19
Supplementary_files_format_and_content: A Tab-separated values file including gene FPKMs of each sample.

molecule: total RNA

source_name: human PBMC_a33f

extract_protocol:
PBMCs were isolated and total RNA was extracted by TRIzol. Total RNA was checked for a RIN number to inspect RNA integrity by the Spectrophotometer NanoDrop ND-1000 and an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Ion Total RNA-Seq protocols.

tag: disease state

value: PD

tag: exercise

value: Tai chi

tag: time

value: after

tag: cell type

value: PBMC


title: a29f_after

source_name: human PBMC_a29f


title: a5f_after

source_name: human PBMC_a5f

value: MET


title: Blood, Non-smoker_671


title: a37f_after

source_name: human PBMC_a37f


title: a38f_after

source_name: human PBMC_a38f


title: Blood, Smoker_669


title: Blood, Smoker_670


title: a27f_after

source_name: human PBMC_a27f


title: a21f_after

source_name: human PBMC_a21f


title: a14f_after

source_name: human PBMC_a14f


title: Blood, Smoker_668


title: a3f_after

source_name: human PBMC_a3f


title: Blood, Non-smoker_667


title: Blood, Non-smoker_678


title: Blood, Smoker_665


title: Blood, Smoker_666


title: a22f_after

source_name: human PBMC_a22f


title: Blood, Smoker_663


title: a28f_after

source_name: human PBMC_a28f


title: Blood, Smoker_675


title: a4f_after

source_name: human PBMC_a4f


title: a8f_after

source_name: human PBMC_a8f


title: Blood, Non-smoker_662


title: a2f_after

source_name: human PBMC_a2f


title: a6f_after

source_name: human PBMC_a6f


title: Blood, Non-smoker_661


title: Blood, Non-smoker_660


title: a35f_after

source_name: human PBMC_a35f


title: Blood, Non-smoker_659

source_name: Blood


title: Blood, Smoker_658


title: a19f_after

source_name: human PBMC_a19f


title: a7f_after

source_name: human PBMC_a7f


title: a9f_after

source_name: human PBMC_a9f


title: a23f_after

source_name: human PBMC_a23f


title: a30f_after

source_name: human PBMC_a30f


title: a22_before

source_name: human PBMC_a22

value: before


title: Blood, Smoker_664


title: Blood, Smoker_654


title: Blood, Non-smoker_655


title: Blood, Non-smoker_657


title: a3_before

source_name: human PBMC_a3


title: Blood, Smoker_653


title: a14_before

source_name: human PBMC_a14


title: a29_before

source_name: human PBMC_a29


title: Blood, Non-smoker_652


title: Blood, Smoker_651


title: Blood, Non-smoker_649


title: Blood, Non-smoker_650


title: a35_before

source_name: human PBMC_a35


title: Blood, Non-smoker_648


title: a23_before

source_name: human PBMC_a23


title: a5_before

source_name: human PBMC_a5


title: Blood, Smoker_647


title: Blood, Non-smoker_646


title: a27_before

source_name: human PBMC_a27


title: a2_before

source_name: human PBMC_a2


title: Blood, Non-smoker_645


title: Blood, Non-smoker_656


title: Blood, Smoker_644


title: a7_before

source_name: human PBMC_a7


title: Blood, Smoker_643


title: a37_before

source_name: human PBMC_a37


title: a4_before

source_name: human PBMC_a4


title: Blood, Smoker_642

source_name: Blood


title: Blood, Smoker_641


title: Blood, Smoker_640


title: a30_before

source_name: human PBMC_a30


title: a33_before

source_name: human PBMC_a33


title: a6_before

source_name: human PBMC_a6


title: Blood, Non-smoker_639


title: Blood, Non-smoker_637


title: a8_before

source_name: human PBMC_a8


title: a38_before

source_name: human PBMC_a38


title: Blood, Non-smoker_638


title: a28_before

source_name: human PBMC_a28


title: Blood, Smoker_634


title: Blood, Non-smoker_632


title: Blood, Smoker_636


title: Blood, Non-smoker_631


title: Blood, Smoker_635


title: a9_before

source_name: human PBMC_a9


title: Blood, Smoker_630


title: T10

city: Minneapolis

first: emilyn

middle: U

last: alejandro

state: MN

department: Integrative Biology and Physiology

country: USA

institute: University of Minnesota

description:
T10
RNA-seq Run 1

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Bowtie2 (2.2.4.0)
Cuffdiff 2.2.1 was used to quantify the expression level of each known gene in units of FPKM (fragment mapped per kilobase of exons per million mapped reads)
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: mm10
Supplementary_files_format_and_content: raw read count and fpkm

organism: Mus musculus

source_name: KO

growth_protocol: Islets were isolated from freshly-harvested mouse pancreas using collagenase digestion and  hand-picked clean before culturing overnight in RPMI media (5 mM glucose, 10% FBS, penicillin-streptomycin) at 37°C, 5% CO2.

extract_protocol:
RNA was extracted using the RNAeasy Plus Micro Kit from Qiagen, including the Dnase treatment step
Clontech Smarter Stranded Total RNA. Pico Input Mammalian. Standard Scale in #38

treatment_protocol: Islet pellets were washed once in PBS then flash-frozen in RNAlater for storage before RNA isolation

value: Pancreatic Islets

tag: genotype

value: Rip-cre; Ogt f/f

tag: run pool

value: 1st Run

tag: Sex


title: 2040

description:
2040
RNA-seq Run 3

source_name: WT

value: Ogt f/f

value: 2nd Run


title: 2046

description:
2046
RNA-seq Run 3


title: 203941

description:
203941
RNA-seq Run 3


title: 2042

description:
2042
RNA-seq Run 3


title: Blood, Smoker_629

value: African-American


title: 1200

description:
1200
RNA-seq Run 1

value: Ogt f/+


title: Blood, Smoker_628

value: Smoker


title: 1123

description:
1123
RNA-seq Run 1


title: a21_before

source_name: human PBMC_a21


title: Blood, Smoker_626

value: Blood


title: Blood, Non-smoker_627

value: Male

value: Non-smoker


title: 1119

description:
1119
RNA-seq Run 1

value: Female


title: 1112

description:
1112
RNA-seq Run 1


title: Blood, Non-smoker_623


title: Blood, Smoker_625


title: a19_before

source_name: human PBMC_a19

value: PD


title: dKAT3_30d_snRNAseq_1

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

description:
processed data file:
dKAT3_30d_snRNAseq_matrix.tar
Paired-end
snRNAseq dKAT3_30days
Sample 19
single nucleus RNA

data_processing:
All sequenced datasets adapters were trimmed using cutadapt v1.18 (Martin, 2011) and aligned to mm10.
Only reads with mapq > 30 and mapping to nuclear chromosomes were used for the posterior analysis.
Data were processed with R custom scripts, Samtools (v1.9) (Li et al., 2009), bedtools v2.26.0 (Quinlan and Hall, 2010) and DeepTools v3.1.0 (Ramirez et al., 2016).
RNA-seq data: Reads were aligned with HISAT2 v2.1.0 (Kim et al., 2015).
ATAC-seq data: Reads were aligned with bowtie2 v2.2.6 (Langmead and Salzberg, 2012). Duplicated reads were removed with Picardtools and only paired reads were used for the posterior analysis.
ChIP-seq data: Reads were aligned with bowtie2 v2.2.6 (Langmead and Salzberg, 2012).
For ATAC and ChIP-seq peaks were called using MACS2 (Zhang et al., 2008) and peak replication was addressed with IDR (ENCODE consortium)
snRNAseq data analysis was performed using Cell Ranger v2.2.0 pipeline (10x Genomics), R package Seurat v2.3.4 and custom scripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files from whole genome alignments were normalized to 10 RPMs (read per million sequenced reads).
Supplementary_files_format_and_content: snRNAseq sequences were processed using Cell Ranger v2.2.0 pipeline (10x Genomics). Processed snRNAseq data consist of filtered feature-barcode matrix. This matrix contains only detected nuclear barcodes. Each matrix is stored in the Market Exchange Format (MEX) for sparse matrices. It also contains TSV files with feature (genes) and barcode sequences corresponding to row and column indices respectively. Features correspond to row indices. For each feature, its feature ID (Ensembl ID) and name (gene symbol) are stored in the first and second column of the file, respectively. Barcode sequences correspond to column indices. Each barcode sequence includes a suffix with a dash separator followed by a number. Additional information can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

source_name: Hippocampal tissue

growth_protocol: Mice were maintained and bred under standard conditions, consistent with Spanish and European regulations and approved by the Institutional Animal Care and Use Committee.

extract_protocol:
Hippocampi were micro-dissected after cervical dislocation, washed in ice-cold PBS and pooled together, when fixation was needed 1% FA was used. Nuclei were isolated using our improved FANS protocol for SUN1-GFP+ cells. Extensive description of protocols indicated in Supplemental Experimental Procedures.
For snRNAseq, the isolation of single nuclei was carried out at 4ºC. The two hippocampi of each mouse were dissected in cold PBS and transferred to a dounce homogeneizer containing 1 mL of ice cold MACS buffer (0.5% BSA, 2 mM EDTA, PBS 1x) and were homogenized 15-12 times with the pestle. The cell suspension was transferred to a 2 mL tube and centrifuge 15 min at 500g and 4ºC. Cell pellets were resuspended in 2 mL of lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0,1% IGEPAL) and kept 5 min on ice. Samples were then spun down at 500g for 30 min in a pre-chilled centrifuge. The nuclei pellet was resuspended in PBS 1x 1% BSA and sorted on a BD FACS Aria III. 15,000 nuclei per sample were loaded into the single cell A Chip and then generation of barcode-containing partitions were carried out with the Chromium Controller (10X Genomics).
snRNAseq libraries were prepared according to manufacturer instructions using Chromium Controller. Chromium Single Cell 3’ Library & Gel Bead Kit v2 and Chromium Single Cell A Chip Kit (10x Genomics)
snRNAseq library construction protocol: Chromium Single Cell 3’ Library & Gel Bead Kit v2 was employed for post-GEM-RT cleanup, cDNA amplification and the generation of barcoded (ChromiumTM i7 Multiplex Kit) libraries. Libraries were sequenced to an average depth of 290-310 Million reads per sample on an Illumina HiSeq2500 sequencer according to manufacturer instructions. Quality control of sequenced reads was performed using FastQC (Babraham Institute). Sequenced samples were processed using the Cell Ranger v2.2.0 pipeline (10x Genomics) and aligned to the CRGm38 (mm10) mouse reference genome customized to count reads in introns (pre-mRNA) (gene annotation version 94). We retrieved between 1.791 (control), 1.133 (dKAT3-ifKO 2w), and 1.465 (dKAT3-ifKO 1m) high quality nuclei per sample. Mean reads per nuclei were 172.879 (control), 271.535 (dKAT3-ifKO 2w), and 197.840 (dKAT3-ifKO 1m).
snRNAseq barcodes correspond to nucleotides 59-74 of read 1 (R1 files)

treatment_protocol: Mice received intragastric administration of tamoxifen when they were ~2 month-old, and we wait 3-4 weeks before experimentation.  For snRNAseq, nuclei were isolated 2 weeks or 5 weeks upon tamoxifen administration.

tag: replicate

value: Adult induced cbp p300 mutant

tag: strain

tag: fans antibody

tag: chip antibody

value: Adult Forebrain (hippocampus)

value: 4 month

value: male


title: Blood, Non-smoker_622

tag: ethnicity

tag: age


title: dKAT3_15d_snRNAseq_1

description:
processed data file:
dKAT3_15d_snRNAseq_matrix.tar
Paired-end
snRNAseq dKAT3 15days
Sample 18
single nucleus RNA

value: 14 weeks

tag: gender


title: wt_snRNAseq_1

description:
processed data file:
wt_snRNAseq_matrix.tar
Paired-end
snRNAseq control
Sample 17
single nucleus RNA

value: control (floxed)

value: 3 month


title: Blood, Smoker_633

tag: cpd

tag: hsi


title: Blood, Non-smoker_621

tag: ftnd

tag: tissue


title: wt_ChIP_INPUT

description:
processed data file:
none
Single-end
none (input)
input sample

library_source: genomic

extract_protocol:
Hippocampi were micro-dissected after cervical dislocation, washed in ice-cold PBS and pooled together, when fixation was needed 1% FA was used. Nuclei were isolated using our improved FANS protocol for SUN1-GFP+ cells. Extensive description of protocols indicated in Supplemental Experimental Procedures.
ChIP-seq was conducted as previously described (Lopez-Atalaya et al., 2013) using the anti-H3K27AC (AB4729 Abcam), anti-H3K9,14 (Home made), anti-CBP (sc-583) and anti-p300 (sc-585).
Libraries were prepared with TruSeq.

value: none (input)

value: 3-4 month


title: dKAT3-ifKO_ChIP-aH3K9,14ac_2

description:
processed data file:
dKAT3_ChIP-aH3K9,14ac.bw
Single-end
ChIP dKAT3 aH3K9,14ac
Sample 16

value: Anti-H3K9,14ac (Home made)


title: dKAT3-ifKO_ChIP-aH3K9,14ac_1


title: Blood, Non-smoker_619

value: African-American


title: Blood, Smoker_618

value: Smoker


title: wt_ChIP-aH3K9,14ac_2

description:
processed data file:
wt_ChIP-aH3K9,14ac.bw
Single-end
ChIP control aH3K9,14ac
Sample 15


title: Blood, Smoker_617

value: Blood


title: dKAT3-ifKO_ChIP-aH3K27Ac_2

description:
processed data file:
dKAT3-ifKO_ChIP_aH3K27Ac.bw
Single-end
ChIP dKAT3 aH3K27ac
Sample 14

value: anti-H3K27AC (AB4729 Abcam)


title: Blood, Smoker_615

value: Male


title: wt_ChIP-aH3K9,14ac_1


title: Blood, Smoker_614

value: Female


title: Blood, Smoker_624


title: wt_ChIP-aH3K27ac_1

description:
processed data file:
wt_ChIP_aH3K27Ac.bw
Single-end
ChIP control aH3K27ac
Sample 13


title: dKAT3-ifKO_ChIP-aP300_2

description:
processed data file:
dKAT3_aP300.bw
Single-end
ChIP dKAT3 aP300
Sample 12

value: anti-p300 (Santa Cruz sc-585)


title: Blood, Non-smoker_612

value: Non-smoker


title: Blood, Non-smoker_610


title: Blood, Non-smoker_608


title: dKAT3-ifKO_ChIP-aP300_1

value: Adult induced cbp p300 mutant

value: Adult Forebrain (hippocampus)


title: cbp-ifKO_ChIP-aP300_2

description:
processed data file:
cbp_aP300.bw
Single-end
ChIP cbp aP300
Sample 10

value: Adult induced cbp mutant

value: male


title: cbp-ifKO_ChIP-aP300_1


title: Blood, Smoker_620


title: cbp-ifKO_ChIP-aCBP_2

description:
processed data file:
cbp_aCBP.bw
Single-end
ChIP cbp aCBP
Sample 9

value: anti-CBP (Santa Cruz sc-583)


title: Blood, Smoker_616


title: dKAT3-ifKO_ChIP-aH3K27Ac_1


title: Blood, Smoker_605


title: cbp-ifKO_ChIP-aCBP_1


title: p300-ifKO_ChIP-aP300_2

description:
processed data file:
p300_aP300.bw
Single-end
ChIP p300 aP300
Sample 8

value: Adult induced p300 mutant


title: Blood, Smoker_604


title: Blood, Non-smoker_606


title: p300-ifKO_ChIP-aP300_1


title: wt_ChIP-aH3K27ac_2

value: control (floxed)


title: Blood, Non-smoker_603


title: Blood, Smoker_602


title: Blood, Non-smoker_613


title: Blood, Non-smoker_611


title: Blood, Smoker_601


title: dKAT3-ifKO_ChIP-aCBP_2

description:
processed data file:
dKAT3_aCBP.bw
Single-end
ChIP dKAT3 aCBP
Sample 11

value: 3-4 month


title: wt_ChIP-aP300_3

description:
processed data file:
wt_ChIP_aP300.bw
Single-end
ChIP control aP300
Sample 6


title: p300-ifKO_ChIP-aCBP_1

description:
processed data file:
p300_aCBP.bw
Single-end
ChIP p300 aCBP
Sample 7


title: Blood, Smoker_609


title: dKAT3-ifKO_ChIP-aCBP_1


title: Blood, Smoker_598


title: Blood, Smoker_599


title: Blood, Smoker_600


title: wt_ChIP-aP300_1


title: Blood, Smoker_607


title: Blood, Smoker_597


title: wt_ChIP-aCBP_2

description:
processed data file:
wt_ChIP_aCBP.bw
Single-end
ChIP control aCBP
Sample 5


title: Blood, Non-smoker_595


title: wt_ChIP-aCBP_1


title: ATAC_dKAT3-ifKO_2

description:
processed data file:
ATAC_dKAT3-ifKO.bw
Paired-end
ATAC dKAT3
Sample 4

source_name: Hippocampal excitatory neurons

extract_protocol:
Hippocampi were micro-dissected after cervical dislocation, washed in ice-cold PBS and pooled together, when fixation was needed 1% FA was used. Nuclei were isolated using our improved FANS protocol for SUN1-GFP+ cells. Extensive description of protocols indicated in Supplemental Experimental Procedures.
ATAC-seq experiments were conducted as the original protocol (Buenrostro et al., 2013), using anti-NeuN (Millipore MAB377) to select mature neurons.
Libraries were prepared with TruSeq.

value: anti-NeuN (Millipore MAB377)


title: Blood, Smoker_593

value: African-American


title: Blood, Smoker_594

value: Smoker


title: ATAC_dKAT3-ifKO_1


title: p300-ifKO_ChIP-aCBP_2


title: ATAC_wt_1

description:
processed data file:
ATAC_wt.bw
Paired-end
ATAC control
Sample 3


title: ATAC_wt_2


title: Blood, Smoker_591

value: Blood


title: Blood, Smoker_592


title: Blood, Smoker_590


title: Blood, Non-smoker_589


title: RNAseq_dKAT3-ifKO_3

description:
processed data file:
RNAseq_dKAT3-ifKO.bw
Single-end
RNAseq dKAT3
Sample 2

extract_protocol:
Hippocampi were micro-dissected after cervical dislocation, washed in ice-cold PBS and pooled together, when fixation was needed 1% FA was used. Nuclei were isolated using our improved FANS protocol for SUN1-GFP+ cells. Extensive description of protocols indicated in Supplemental Experimental Procedures.
Extraction of RNA was performed using TRI-reagent (MERCK) as previously described (Scandaglia et al., 2017).
Libraries were prepared with TruSeq.


title: RNAseq_dKAT3-ifKO_2


title: RNAseq_dKAT3-ifKO_1


title: wt_ChIP-aP300_2


title: Blood, Non-smoker_588


title: Blood, Smoker_587


title: Blood, Non-smoker_586


title: RNAseq_wt_1

description:
processed data file:
RNAseq_wt.bw
Single-end
RNAseq control
Sample 1


title: Blood, Non-smoker_585


title: RNAseq_wt_2


title: Blood, Smoker_584


title: NN190_LCA

city: Rochester

first: Vyacheslav

last: Korshunov

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15
Genome Alignment - STAR_2.5.2b, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.5.0p3, featurecounts, -s 2 -t exon -g gene_name
Genome_build: GRCm38 + gencode M12
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

source_name: Ligated left carotid artery

extract_protocol:
Tissue homogenization by Next Advance Bullet Blender with zirconium oxide beads and Trizol. Total RNA isolation using Trizol and Qiagen RNeasy Micro kit.
Illumina TruSeq Stranded mRNA

treatment_protocol: To compare protective effects of Sacubitril/valsartan (Sac/val; 60 mg/kg/day) and Valsartan (Val; 27 mg/kg/day) to the Vehicle (Veh; 2 mL/kg/day), we induced vascular remodeling in these mice by carotid ligation, and treated 129X1/SvJ (129X1) or C57BL/6J (B6) mice with two protocols: 1) a prophylactic regimen began 2 days before ligation (“-P”); 2) a therapeutic regimen started 7 days after ligation (“-T”). Mice were randomly divided into twelve experimental groups: 1) B6, Veh-P, n=3; 2) 129X1, Veh-P, n=3; 3) B6, Val-P, n=3; 4) 129X1, Val-P, n=3; 5) B6, Sac/val-P, n=3; 6) 129X1, Sac/val-P, n=3; 7) B6, Veh-T, n=3; 8) 129X1, Veh-T, n=3; 9) B6, Val-T, n=3; 10) 129X1, Val-T, n=3; 11) B6, Sac/val-T, n=3; 12) 129X1, Sac/val-T, n=3. Fresh carotid arteries were collected 14 days after the carotid ligation.

value: Carotid artery

tag: treatment regimen

value: Therapeutic, 7 days

tag: treatment

value: Sacubitril/valsartan, 60 mg/kg/day


title: Blood, Smoker_583

value: Male


title: NN159_LCA


title: Blood, Smoker_581


title: NN186_LCA

value: Valsartan, 27 mg/kg/day


title: Blood, Smoker_582


title: NN192_LCA

value: Vehicle, 2 mL/kg/day


title: NN130_LCA


title: Blood, Smoker_580

value: Female


title: NN131_LCA


title: Blood, Smoker_579


title: Blood, Smoker_578


title: Blood, Smoker_577


title: NN185_LCA


title: Blood, Smoker_575


title: NN154_LCA


title: NN176_LCA


title: NN191_LCA


title: NN142_LCA


title: Blood, Smoker_574


title: RNAseq_wt_3

value: Adult Forebrain (hippocampus)


title: NN111_LCA


title: Blood, Non-smoker_572

value: Non-smoker


title: NN174_LCA


title: Blood, Smoker_573


title: NN140_LCA


title: wt_ChIP-aCBP_3

value: anti-CBP (Santa Cruz sc-583)

value: male


title: Blood, Smoker_571


title: NN110_LCA


title: Blood, Smoker_596


title: NN172_LCA


title: Blood, Smoker_568


title: NN171_LCA


title: Blood, Smoker_569


title: Blood, Smoker_567


title: Blood, Smoker_570


title: Blood, Smoker_565


title: NN151_LCA

value: Prophylactic, 16 days


title: Blood, Smoker_576


title: Blood, Smoker_566


title: NN120_LCA


title: Blood, Smoker_564


title: NN116_LCA


title: NN117_LCA


title: NN182_LCA


title: NN146_LCA


title: Blood, Smoker_562


title: Blood, Smoker_561


title: Blood, Smoker_563


title: Blood, Smoker_560


title: Blood, Smoker_558


title: Blood, Smoker_559


title: Blood, Smoker_557


title: NN113_LCA


title: NN169_LCA


title: NN145_LCA


title: NN107_LCA


title: NN137_LCA


title: Blood, Smoker_556


title: Blood, Smoker_554


title: Blood, Smoker_555


title: Blood, Smoker_553


title: NN168_LCA


title: Blood, Smoker_551


title: NN164_LCA


title: Blood, Non-smoker_550


title: NN178_LCA


title: NN106_LCA


title: NN167_LCA


title: Blood, Smoker_548


title: Blood, Smoker_552


title: Blood, Non-smoker_547


title: NN104_LCA


title: M2_0hr 2

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

description: Stable mesenchymal Clone 2

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to MM10 version of mouse genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout")
Counts are obtained using qcount in qusaR and CPM (counts per million) was computed for each sample
Genome_build: mm10
Supplementary_files_format_and_content: txt file and contains counts as CPM values for each sample

source_name: Breast cancer cells

growth_protocol: Py2T cells and M clone cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with glutamine, penicillin, streptomycin and 10% FBS (Sigma-Aldrich). Py2T cells were treated with 2ng/ml TGFb1 and the medium was replenished every 3 days. All cells were cultured at 37°C with 5% CO2 in a humid incubator.

extract_protocol:
Total RNA was isolated from cells of 2 independent experiments using the miRNeasy mini kit (217004, Qiagen) according to the manufacturer’s instruction.
200ng of RNA was utilized for library preparation with the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina).

treatment_protocol: Cells were treated with 2µM CI994 for 72 hours.

tag: cell type

value: Breast cancer

value: MMTV-PyMT


title: M3_0hr 1

description: Stable mesenchymal Clone 3


title: M3_0hr 2

description: Stable mesenchymal Clone 3


title: Blood, Smoker_546

value: African-American


title: NN163_LCA


title: Blood, Non-smoker_545


title: Blood, Smoker_549

value: Smoker


title: M1_0hr 2

description: Stable mesenchymal Clone 1


title: Blood, Non-smoker_544

value: Blood


title: Py2T LT_0hr 2

description: Py2T cells + TGFβ >10 days

value: Py2T LT


title: M2_0hr 1

description: Stable mesenchymal Clone 2


title: Py2T LT_0hr 1

description: Py2T cells + TGFβ >10 days


title: Blood, Non-smoker_543


title: Blood, Non-smoker_542


title: Blood, Non-smoker_539


title: Blood, Non-smoker_540


title: Blood, Non-smoker_538


title: Blood, Smoker_535


title: Blood, Non-smoker_537


title: NN109_LCA

value: Carotid artery

value: Therapeutic, 7 days


title: Blood, Smoker_536


title: Blood, Non-smoker_534


title: Blood, Non-smoker_533


title: Blood, Smoker_532


title: Blood, Non-smoker_530


title: M1_0hr 1

description: Stable mesenchymal Clone 1


title: Series15_COVID19Lung_1

city: New York

first: Daniel

last: Blanco Melo

state: NY

address: One Gustave L. Levy Place, Box 1124

department: Microbiology

institute: Icahn School of Medicine at Mount Sina

description:
COVID-1-Cornell-indexC10
processed data file: RawReadCounts_Human.tsv

data_processing:
cDNA libraries were sequenced using an Illumina NextSeq 500 platform
Raw sequencing reads were aligned to the human genome (hg19) or Ferret genome (MusPutFur1.0) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA)
Differential gene expression analysis was performed using DESeq2 (implemented in the RNA Express App (v1.1.0) on Basespace (Illumina, CA)) comparing Infected samples to their correspondent mock treated sample, for each virus/cell type.
Genome_build: human (hg19), Ferret (MusPutFur1.0)
Supplementary_files_format_and_content: Tab separated value (tsv) matrix of raw read counts per gene for each sample.

molecule: polyA RNA

source_name: Lung sample from postmortem COVID-19 patient

extract_protocol:
TruSeq RNA Library Prep Kit v2
Total RNA was extracted using RNeasy Mini Kit (Qiagen)

tag: subject status

value: No treatment; >60 years old male COVID-19 deceased patient

tag: tissue/cell type

value: Lung Biopsy


title: Series15_COVID19Lung_2

description:
COVID-2-Cornell-indexC11
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_529

source_name: Blood


title: Blood, Non-smoker_528

value: Male


title: Blood, Non-smoker_541

value: Female


title: Series9_NHBE_IFNB_6h_2

description:
IFN_6_2
processed data file: RawReadCounts_Human.tsv

source_name: human IFNB treated NHBE cells

value: primary human bronchial epithelial cells

value: human IFNB treatment (100U/ml)

tag: time after treatment

value: 6 hours


title: Series9_NHBE_IAVdNS1_4

description:
dNS1-LD-4
processed data file: RawReadCounts_Human.tsv

source_name: IAVdNS1 infected NHBE cells

value: IAVdNS1 infected (MOI 3)

value: A/Puerto Rico/8/1934 (H1N1) (dNS1)

value: 12 hours


title: Series9_NHBE_IFNB_4h_2

description:
IFN_4_2
processed data file: RawReadCounts_Human.tsv

value: 4 hours


title: Series9_NHBE_IFNB_12h_1

description:
IFN_12_1
processed data file: RawReadCounts_Human.tsv


title: Series9_NHBE_IFNB_4h_1

description:
IFN_4_1
processed data file: RawReadCounts_Human.tsv


title: Series9_NHBE_IFNB_6h_1

description:
IFN_6_1
processed data file: RawReadCounts_Human.tsv


title: Series9_NHBE_IFNB_12h_2

description:
IFN_12_2
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_526

value: African-American

value: Non-smoker


title: Series9_NHBE_IAVdNS1_3

description:
dNS1-LD-3
processed data file: RawReadCounts_Human.tsv


title: Series9_NHBE_IAVdNS1_1

description:
dNS1-LD-1
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_525

value: Blood


title: Series9_NHBE_IAV_3

description:
IAV-LD-3
processed data file: RawReadCounts_Human.tsv

source_name: IAV infected NHBE cells

value: IAV infected (MOI 3)

value: A/Puerto Rico/8/1934 (H1N1)


title: Series9_NHBE_IAVdNS1_2

description:
dNS1-LD-2
processed data file: RawReadCounts_Human.tsv


title: Series9_NHBE_IAV_4

description:
IAV-LD-4
processed data file: RawReadCounts_Human.tsv


title: Blood, Smoker_523

value: Smoker


title: Blood, Non-smoker_524


title: Blood, Non-smoker_522


title: Blood, Non-smoker_521


title: Blood, Non-smoker_531


title: Series9_NHBE_IAV_2

description:
IAV-LD-2
processed data file: RawReadCounts_Human.tsv


title: Series9_NHBE_IAV_1

description:
IAV-LD-1
processed data file: RawReadCounts_Human.tsv


title: Series9_NHBE_Mock_2

description:
NHBE-Mock-2
processed data file: RawReadCounts_Human.tsv

source_name: Mock treated NHBE cells

value: Mock treatment


title: Blood, Non-smoker_519


title: Series9_NHBE_Mock_3

description:
NHBE-Mock-3
processed data file: RawReadCounts_Human.tsv


title: Series9_NHBE_Mock_4

description:
NHBE-Mock-4
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_518


title: Blood, Non-smoker_520


title: Blood, Non-smoker_515


title: Blood, Non-smoker_517


title: Series8_A549_HPIV3_2

description:
A549-HPIV3-MOI2-2-indexD2
processed data file: RawReadCounts_Human.tsv

source_name: HPIV3 infected A549 cells

extract_protocol:
TruSeq Stranded mRNA LP
Total RNA was extracted using RNeasy Mini Kit (Qiagen)

tag: cell line

value: Lung adenocarcinoma

value: HPIV3 infected (MOI 3)

value: JS

value: 24 hours


title: Series8_A549_HPIV3_1

description:
A549-HPIV3-MOI2-1-indexD1
processed data file: RawReadCounts_Human.tsv

tag: strain


title: Blood, Smoker_516

value: Male


title: Series9_NHBE_Mock_1

description:
NHBE-Mock-1
processed data file: RawReadCounts_Human.tsv

value: primary human bronchial epithelial cells


title: Series8_A549_RSV_3

description:
RSV_A549-RSV-MOI2-1
processed data file: RawReadCounts_Human.tsv

source_name: RSV infected A549 cells

value: RSV infected (MOI 2)


title: Series8_A549_HPIV3_3

description:
A549-HPIV3-MOI2-3-indexD3
processed data file: RawReadCounts_Human.tsv


title: Series8_A549_RSV_1

description:
RSV_A549-RSV-MOI2-3
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_511


title: Series8_A549_Mock_3

description:
RSV_A549-mock1
processed data file: RawReadCounts_Human.tsv

source_name: Mock treated A549 cells


title: Blood, Non-smoker_510

value: Female


title: Series8_A549_RSV_2

description:
RSV_A549-RSV-MOI2-2
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_513


title: Blood, Non-smoker_508


title: Blood, Non-smoker_509


title: Blood, Non-smoker_507


title: Series8_A549_Mock_1

description:
RSV_A549-mock3
processed data file: RawReadCounts_Human.tsv


title: Series7_Calu3_SARS-CoV-2_3

description:
Calu3-SARSCoV2-1
processed data file: RawReadCounts_Human.tsv

source_name: SARS-CoV-2 infected Calu-3 cells

value: SARS-CoV-2 infected (MOI 2)


title: Series7_Calu3_SARS-CoV-2_2

description:
Calu3-SARSCoV2-2
processed data file: RawReadCounts_Human.tsv


title: Blood, Smoker_506


title: Series7_Calu3_SARS-CoV-2_1

description:
Calu3-SARSCoV2-3
processed data file: RawReadCounts_Human.tsv


title: Series7_Calu3_Mock_3

description:
Calu3-mock1
processed data file: RawReadCounts_Human.tsv

source_name: Mock treated Calu-3 cells


title: Blood, Non-smoker_505


title: Blood, Non-smoker_514


title: Series7_Calu3_Mock_2

description:
Calu3-mock2
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_503


title: Blood, Non-smoker_502


title: Blood, Smoker_504


title: Series7_Calu3_Mock_1

description:
Calu3-mock3
processed data file: RawReadCounts_Human.tsv


title: Blood, Smoker_501


title: Blood, Non-smoker_512


title: Series6_A549-ACE2_SARS-CoV-2_2

description:
A549-Adeno-GFP-ACE2-SARS-CoV2-2
processed data file: RawReadCounts_Human.tsv

source_name: SARS-CoV-2 infected A549 cells trasnduced with a vector expressing human ACE2

value: SARS-CoV-2 infected (MOI 0.2)


title: Series6_A549-ACE2_SARS-CoV-2_1

description:
A549-Adeno-GFP-ACE2-SARS-CoV2-3
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_500

value: African-American


title: Blood, Non-smoker_499

value: Non-smoker


title: Series8_A549_Mock_2

description:
RSV_A549-mock2
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_497

value: Blood


title: Blood, Non-smoker_496


title: Series6_A549-ACE2_Mock_2

description:
A549-Adeno-GFP-ACE2-mock2
processed data file: RawReadCounts_Human.tsv

source_name: Mock treated A549 cells trasnduced with a vector expressing human ACE2


title: Blood, Smoker_495


title: Series5_A549_SARS-CoV-2_3

description:
CoV_A549-SARSCoV2-1
processed data file: RawReadCounts_Human.tsv

source_name: SARS-CoV-2 infected A549 cells


title: Blood, Non-smoker_494


title: Series5_A549_SARS-CoV-2_2

description:
CoV_A549-SARSCoV2-2
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_493


title: Blood, Non-smoker_492


title: Series5_A549_Mock_3

description:
CoV_A549-mock1
processed data file: RawReadCounts_Human.tsv


title: Series5_A549_Mock_2

description:
CoV_A549-mock2
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_490


title: Blood, Non-smoker_491


title: Blood, Non-smoker_488


title: Series5_A549_Mock_1

description:
CoV_A549-mock3
processed data file: RawReadCounts_Human.tsv


title: Series6_A549-ACE2_Mock_3

description:
A549-Adeno-GFP-ACE2-mock1
processed data file: RawReadCounts_Human.tsv


title: Series6_A549-ACE2_Mock_1

description:
A549-Adeno-GFP-ACE2-mock3
processed data file: RawReadCounts_Human.tsv


title: Blood, Non-smoker_486


title: Drops_DMSO

city: Lausane

first: Nathalie

last: Brandenberg

state: VD

address: AI 1116 (Bâtiment AI) Station 15

department: SV IBI-SV

institute: Ecole Polytechnique Federale de Lausane

data_processing:
RNA-seq reads were aligned to the hg38 Human reference genome (GRCh38.p10) with STAR (version 2.5).
Abundance measurements for genes in the gencode primary assembly (v17) was done from uniquely mapped reads, using HTSeq-count (version 0.9).
Lowly expressed genes (<50 reads in all 4 samples ) were excluded and the log2 normalised CPM values of the remaining 13’668 genes were calculated using the R package edgeR (version 3.14)
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: file combined_htseqcounts_ENSG_withGeneInfos_norm.csv contains results for all samples, and reports the normalised expressions, the log2 Fold Changes and the mean normalised expressions of gene cross samples.

source_name: Primary colorectal cancer cells

growth_protocol: Human colorectal tissues were obtained from the Centre Hospitalier Universitaire Vaudois (CHUV) with informed consent. The study was approved by the local regulatory body, CER-VD, under the ID: 2017-00359. The primary tumor resections were processed as described previously, and the organoids were expanded and maintained in Advanced DMEM/F12 containing Glutamax, HEPES, penicillin/streptomycin, B27 (Life technologies), 1mM N-acetylcysteine (Sigma) supplemented with growth factors; EGF (50 ng/ml; R&D), Noggin (100 ng/ml; produced in-house). The organoids were maintained and expanded as follows: the full medium was changed every three days, and the cells were passaged every 6-8 days.

extract_protocol:
CRC organoids grown in Organoid arrays or Matrigel® drops exposed to 1μM afuresertib or vehicle were lyzed and the mRNA was extracted using the RNeasy mini kit according to the supplier’s information. The different samples were quality controlled using a TapeStation 4200 (Agilent) and sequenced using an Illumina NextSeq500. An average of 41Mio reads per sample was uniquely aligned to the hg38 Human reference genome (GRCh38) with STAR (version 2.5) and about 90% of those were confidently assigned to genes (gencode primary assembly v27) using HTSeq-count (version 0.9). Genes with less than 50 reads in all 4 samples were excluded and the log2 normalised CPM values of the remaining 13’668 genes were calculated using the R package edgeR (version 3.14).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Organoids were generated as described above. Once the microtissues grown into the different conditions, i.e. three days of expansion for CRC organoids, respectively, they were exposed to 1μΜ Afuresertib or DMSO 1:100 for three additional days.

value: Primary colorectal cancer derived organoids

tag: tumor type

value: Primary colorectal tumor resection

value: DMSO

tag: substrate

value: Matrigel drops


title: Arrays_DMSO

description: combined_htseqcounts_ENSG_withGeneInfos_norm.csv

value: Organoid arrays


title: Arrays_1uM

value: 1uM Afuresertib


title: Blood, Non-smoker_498

tag: ethnicity


title: Blood, Smoker_485

tag: age

value: Smoker


title: Drops_1uM


title: 10631602_S10

city: Marseille

first: Paul

last: Pascale

address: 27 Bd Jean Moulin

department: Faculté de Pharmacie

country: France

data_processing:
The reads generated were single-end and of 76-nt length. FastQC (version 0.11.5) was used to examine the read quality.
Trimming of reads was performed using Trimmomatic (version 0.33) on the base of an average phred quality of 20.
Then the raw single-ends reads were mapped against the human genome (GRCh38.90) from Ensembl database using STAR (version 2.5.3a) sequence mapper. The resulting BAM files were examined by Qualimap (version 2.2). The duplicates reads were removed using the function MarkDuplicates of picard tools (version 2.9.0).
Unduplicated reads were used to count reads per gene with FeatureCounts (version 1.5.2)
Genome_build: GRCh38.90
Supplementary_files_format_and_content: tab-delimited txt files including raw count values

source_name: Stromal vascular fraction

growth_protocol: Perirenal adipose tissue (at least 30g) was collected under aseptic conditions during the multi-organ retrieval for cadaveric donors or during laparoscopic nephrectomy for living donor renal transplantation. Excised fat was manually sliced with scissors into units of approximately 3mm x 3mm x 3mm. Enzymatic digestion was performed using 0.25UI/mL collagenase NB4 (Serva, Heidelberg, Germany) for one hour at 37°C under constant agitation. Three cycles of wash/centrifugation were performed to eliminate adipose and red blood cells.

extract_protocol:
Total RNA was isolated from PRAT-SVF using RNeasy mini kits (QIAGEN Inc., Valencia, CA, USA) including a DNase I digestion step removing genomic DNA.
Generation of libraries was performed using PerklinElmer technologies with the NEXTflex qRNA-Seq kit v2 after total RNA enrichment by NEXTflex Poly(A) beads following manufacturer's recommendations (PerkinElmer).  RNA-seq library were sequenced on Illumina Nextseq sequencer.

value: Perirenal adipose tissue

tag: statuts

value: nonECD


title: 10631483_S9


title: 10631482_S8


title: Blood, Non-smoker_483

tag: gender

tag: cpd


title: 10631481_S7


title: 10631480_S6


title: 10631479_S5

value: ECD


title: Blood, Non-smoker_480

tag: hsi

tag: ftnd


title: Blood, Smoker_487

tag: tissue


title: 10631478_S4


title: Blood, Non-smoker_479


title: 10631477_S3


title: Blood, Smoker_478


title: 10631475_S2


title: Blood, Smoker_477


title: Blood, Non-smoker_489


title: 10631474_S1


title: Blood, Non-smoker_476


title: Blood, Non-smoker_484


title: Blood, Non-smoker_475


title: Blood, Non-smoker_473


title: My-La_RNA

city: Manchester

last: Martin

state: Greater Manchester

address: Oxford Road

department: Centre for Genetics and Genomics Versus Arthritis

country: United Kingdom

institute: Univeristy of Manchester

description:
This Sample represents 1 replicate
RNA-seq, My-La CD8+ T lymphocyte cells, replicate 1

data_processing:
CHi-C: Fastq files were filtered and mapped to the hg19 genome by the Hi-C User Pipeline (HiCUP) v0.5.8. The filtered files for two biological replicates were simultaneously run through the Capture Hi-C Analysis of Genomic Organisation (CHiCAGO) v1.1.8, with a score threshold of 5. Interactions were limited to same-chromosome (cis) and to psoriasis-specific loci.
Hi-C: Fastq files were filtered and adapters removed using fastp v0.19.4. Reads were mapped to the GRCh38 genome with Hi-C Pro v2.11.0 using default settings. Hi-C interaction matrices were normalised within Hi-C Pro using iterative correction and eigenvector decomposition (ICE). Topologically associating domains (TADs) were then called in TADtool software using insulation score with the normalised Hi-C contact matrices, binned with 40 kb resolution. For comparison, TADs were lifted over to the hg19 genome using UCSC LiftOver.
Hi-ChIP: Fastq files were filtered and the adapters were removed using fastp v0.19.4. The reads were then mapped to the GRCh38 genome with Hi-C Pro v2.11.0, using default settings. Genome-wide anchors for H3K27ac were called in hichipper v0.7.3 using the self-circle and dangling end reads for the first replicate, extended for 147 bp. For interactions, two replicates were merged and loops were identified using FitHiChIP using the following settings: Coverage normalisation, stringent background with merging enabled, peaks generated from HiChIP data using the included tool and 5kb bin size.
RNA-seq: Reads were quality trimmed using Trimmomatic v0.38 using a sliding window of 5 with a mean minimum quality of 20. Adapters and poly A/poly G tails were removed using Cutadapt v1.18 and then UMIs were extracted from the 5’ of the reads using UMI-tools v0.5.5. Reads were then mapped using STAR v2.5.3a on the GRCh38 genome with GENCODE annotation v29. Reads were de-duplicated using UMIs with UMI-tools and then counted using HTSeq v0.11.2. Count matrixes were analysed in R 3.5.1 and normalisation and differential expression analysis was conducted using DESeq2 v1.22.2.
Genome_build: hg19
Supplementary_files_format_and_content: TADs.bed.gz: TAD coordinates (chromosome, start, end)
Supplementary_files_format_and_content: Ps_bait_fragments.bed.gz: HindIII fragments tagged by psoriasis-associated GWAS SNPs (chromsosome, start, end, SNP)
Supplementary_files_format_and_content: CHi-C_interactions.txt.gz: Significant CHi-C interacting HindIII fragments involving psoriasis loci (bait chromosome, bait start, bait end, other-end chromosome, other-end start, other-end end, CHiCAGO score, SNP)
Supplementary_files_format_and_content: HiChIP_9q31_interactions.txt.gz: Significant HiChIP interactions originating from the H3K27ac peak at KLF4 in 9q31 (peak chromosome, peak start, peak end, other-end chromosome, other-end start, other-end end, Hichipper score)
Supplementary_files_format_and_content: combined_RNA-seq_counts.csv: Raw RNA-seq counts for all experimental samples
Supplementary_files_format_and_content: 27ac.anchors.bed.gz: Standard bed files
Supplementary_files_format_and_content: HiChIP_interactions.txt.gz: FitHiChIP interaction files (with header)

source_name: My-La CD8+ T lymphocyte cells

growth_protocol: My-La cells were cultured in RPMI 1640 medium supplemented with 10% AB human serum, 100 U/mL recombinant human IL-2 and 1% penicillin-streptomycin in 25cm2 vented culture flasks at 37C/5% CO2

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen) and RNA integrity was assessed using the Bioanalyzer Agilent RNA 6000 Nano Kit (Agilent Technologies).
Sequencing library was generated using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

value: My-La CD8+ T lymphocyte cell line

tag: stimulation

tag: biomaterial provider

tag: restriction enzyme


title: Blood, Smoker_474

value: Male


title: Blood, Non-smoker_527

value: Female


title: Blood, Non-smoker_471


title: HaCaT_stimulated_RNA

description:
This Sample represents 3 replicates
RNA-seq, HaCaT Keratinocyte cells, stimulated, replicates 1-3

source_name: HaCaT Keratinocyte cells

growth_protocol: HaCaT cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in 75cm2 vented culture flasks at 37C/5% CO2. Cells were stimulated with 100 ng/mL recombinant human IFN-γ (285-IF-100; R&D Systems) for 8 hours.

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen) and RNA integrity was assessed using the Bioanalyzer Agilent RNA 6000 Nano Kit (Agilent Technologies).
Sequencing libraries were generated using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

value: HaCaT Keratinocyte cell line

value: 100 ng/mL recombinant human IFN-γ for 8 hours


title: HaCaT_unstimulated_RNA

description:
This Sample represents 4 replicates
RNA-seq, HaCaT Keratinocyte cells, unstimulated, replicates 1-4

growth_protocol: HaCaT cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in 75cm2 vented culture flasks at 37C/5% CO2


title: Blood, Non-smoker_470

source_name: Blood

value: African-American

value: Non-smoker


title: HaCaT_p300_ctrl_RNA

description:
This Sample represents 3 replicates
RNA-seq, HaCaT Keratinocyte cells, p300 + ctrl gRNA, replicates 1-3

growth_protocol: HaCaT cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in 75cm2 vented culture flasks at 37C/5% CO2. Cells were transduced with dCas9 P300 plasmid (Addgene 83889) and selected using with 1 µg/mL puromycin for 7 days, and afterwards maintained with 0.5 µg/mL puromycin. Cells underwent a second transduction with pLKO5.sgRNA.EFS.GFP empty plasmid (Addgene 57822) and selected by flow cytometry for GFP.


title: My-La_CHiC

description:
This Sample represents 2 replicates
Capture Hi-C, My-La CD8+ T lymphocyte cells, replicate 1 & 2

data_processing:
Library strategy: Capture Hi-C
CHi-C: Fastq files were filtered and mapped to the hg19 genome by the Hi-C User Pipeline (HiCUP) v0.5.8. The filtered files for two biological replicates were simultaneously run through the Capture Hi-C Analysis of Genomic Organisation (CHiCAGO) v1.1.8, with a score threshold of 5. Interactions were limited to same-chromosome (cis) and to psoriasis-specific loci.
Hi-C: Fastq files were filtered and adapters removed using fastp v0.19.4. Reads were mapped to the GRCh38 genome with Hi-C Pro v2.11.0 using default settings. Hi-C interaction matrices were normalised within Hi-C Pro using iterative correction and eigenvector decomposition (ICE). Topologically associating domains (TADs) were then called in TADtool software using insulation score with the normalised Hi-C contact matrices, binned with 40 kb resolution. For comparison, TADs were lifted over to the hg19 genome using UCSC LiftOver.
Hi-ChIP: Fastq files were filtered and the adapters were removed using fastp v0.19.4. The reads were then mapped to the GRCh38 genome with Hi-C Pro v2.11.0, using default settings. Genome-wide anchors for H3K27ac were called in hichipper v0.7.3 using the self-circle and dangling end reads for the first replicate, extended for 147 bp. For interactions, two replicates were merged and loops were identified using FitHiChIP using the following settings: Coverage normalisation, stringent background with merging enabled, peaks generated from HiChIP data using the included tool and 5kb bin size.
RNA-seq: Reads were quality trimmed using Trimmomatic v0.38 using a sliding window of 5 with a mean minimum quality of 20. Adapters and poly A/poly G tails were removed using Cutadapt v1.18 and then UMIs were extracted from the 5’ of the reads using UMI-tools v0.5.5. Reads were then mapped using STAR v2.5.3a on the GRCh38 genome with GENCODE annotation v29. Reads were de-duplicated using UMIs with UMI-tools and then counted using HTSeq v0.11.2. Count matrixes were analysed in R 3.5.1 and normalisation and differential expression analysis was conducted using DESeq2 v1.22.2.
Genome_build: hg19
Supplementary_files_format_and_content: TADs.bed.gz: TAD coordinates (chromosome, start, end)
Supplementary_files_format_and_content: Ps_bait_fragments.bed.gz: HindIII fragments tagged by psoriasis-associated GWAS SNPs (chromsosome, start, end, SNP)
Supplementary_files_format_and_content: CHi-C_interactions.txt.gz: Significant CHi-C interacting HindIII fragments involving psoriasis loci (bait chromosome, bait start, bait end, other-end chromosome, other-end start, other-end end, CHiCAGO score, SNP)
Supplementary_files_format_and_content: HiChIP_9q31_interactions.txt.gz: Significant HiChIP interactions originating from the H3K27ac peak at KLF4 in 9q31 (peak chromosome, peak start, peak end, other-end chromosome, other-end start, other-end end, Hichipper score)
Supplementary_files_format_and_content: combined_RNA-seq_counts.csv: Raw RNA-seq counts for all experimental samples
Supplementary_files_format_and_content: 27ac.anchors.bed.gz: Standard bed files
Supplementary_files_format_and_content: HiChIP_interactions.txt.gz: FitHiChIP interaction files (with header)

extract_protocol:
Cells were thawed on ice and re-suspended in 50ml ice-cold lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal CA-630, one protease inhibitor cocktail tablet). Cells were lysed on ice for a total of 30 min, with 2x10 strokes of a dounce homogeniser with a 5 minute break between douncing. The nuclei were pelleted and permeabilised and the chromatin was digested with HindIII. Ends were marked with biotin followed by in-nucleus ligation, decrosslinking and biotin pulldown according to the previously established Hi-C protocol (Dryden et al., 2014; P. Martin et al., 2015). Genomic regions of interest were captured using biotinylated RNA baits (Agilent Technologies).
Sequencing libraries were generated with 6-8 cycles of PCR using Truseq single indexes (Illumina) and Phusion polymerase (NEB)

treatment_protocol: Cells were fixed in 2% formaldehyde for 10 minutes at room temperature, Fixation was quenched by the addition of cold 1M glycine to a final concentration of 0.125M. Pelleted cells were frozen on dry ice and stored at -80C.

value: HindIII


title: HaCaT_p300_P3_RNA

description:
This Sample represents 3 replicates
RNA-seq, HaCaT Keratinocyte cells, p300 + P3 gRNA, replicates 1-3

growth_protocol: HaCaT cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in 75cm2 vented culture flasks at 37C/5% CO2. Cells were transduced with dCas9 P300 plasmid (Addgene 83889) and selected using with 1 µg/mL puromycin for 7 days, and afterwards maintained with 0.5 µg/mL puromycin. Cells underwent a second transduction with pLKO5.sgRNA.EFS.GFP plasmid (Addgene 57822) containing a sgRNA for the 9q31 locus and selected by flow cytometry for GFP.


title: Blood, Non-smoker_469

value: Blood


title: Blood, Non-smoker_481


title: Blood, Non-smoker_467


title: Blood, Non-smoker_466


title: Blood, Non-smoker_468


title: PRDX1_input_2-mRNA

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of PRDX1 on genome using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

source_name: HeLa cell

growth_protocol: HeLa cells were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from Prdx1-RNA complexes and another for the western blotting assay for Prdx1 immunoprecipitation.The Prdx1-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

tag: cell type

value: HeLa cell


title: Blood, Non-smoker_464

extract_protocol: Genomic DNA was extracted from EDTA-treated peripheral venous blood of each subject using the Qiagen DNA purification kit. All DNA samples were treated with RNase A to remove potential contaminating RNA, and DNA quality and the concentration of each sample was determined by the A260/A280 absorbance ratio.


title: PRDX1_input_1-mRNA


title: Blood, Non-smoker_472


title: Blood, Non-smoker_465


title: M3 shTet2.CI994 1

description: Stable mesenchymal Clone 3

source_name: Breast cancer cells

value: Breast cancer

value: MMTV-PyMT


title: PRDX1_IP_1-mRNA


title: M3 shMbd3.CI994 2

description: Stable mesenchymal Clone 3


title: Blood, Non-smoker_462


title: Blood, Non-smoker_463


title: PRDX1_IP_2-mRNA


title: M3 shMbd3.CI994 1

description: Stable mesenchymal Clone 3


title: M3 shTet2.CI994 2

description: Stable mesenchymal Clone 3


title: Blood, Non-smoker_461


title: M3 shControl.CI994 2

description: Stable mesenchymal Clone 3


title: M3 shControl.CI994 1

description: Stable mesenchymal Clone 3


title: M3 shMbd3 2

description: Stable mesenchymal Clone 3


title: Blood, Smoker_3398


title: Blood, Smoker_3399


title: Blood, Smoker_3396


title: M3 shTet2 1

description: Stable mesenchymal Clone 3


title: Blood, Smoker_3395


title: Blood, Smoker_3391


title: Series6_A549-ACE2_SARS-CoV-2_3

description:
A549-Adeno-GFP-ACE2-SARS-CoV2-1
processed data file: RawReadCounts_Human.tsv

tag: tissue/cell type

value: Lung adenocarcinoma

tag: treatment

value: SARS-CoV-2 infected (MOI 0.2)

tag: time after treatment

value: 24 hours


title: Blood, Smoker_3390

value: Smoker


title: HepG2 Nucleosome

city: Perth

first: Zhaoyu

last: Li

state: Western Australia

address: QE II, M block, 225C

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

data_processing:
Low quality bases in the short reads were dynamically trimmed from both 5' and 3' end, and the trimmed bases number were also recorded.
The trimmed reads were mapped to version hg19 of human genome sequences with BWA.0.7.12. Uniquely mapped reads were extracted, and the mapped location were restored according to previous trimming record. Then pair-end reads were converted to DNA fragment by combining the 5’ end location of the paired reads.
Nucleosome peaks were called by DANPOS 2.1.4 with default parameters.
Genome_build: hg19

extract_protocol:
For nucleosome mapping data, native chromatin was isolated from freshly cultured cells and digested with micrococcal nuclease or nuclease S7 (MNase, Roche).
Nucleosomal DNA was isolated and used for the library preparation with the TureSeq DNA PCR-free Library Prep kit (Illumina) and sequenced using the HiSeq 2000 (Illumina).

tag: cell line


title: Blood, Smoker_3389


title: Blood, Smoker_3392


title: HepG2 H3K9me3

data_processing:
Low quality bases in the short reads were dynamically trimmed from both 5' and 3' end, and the trimmed bases number were also recorded.
The trimmed reads were mapped to version hg19 of human genome sequences with BWA.0.7.12. Uniquely mapped reads were extracted, and the mapped location were restored according to previous trimming record. Then pair-end reads were converted to DNA fragment by combining the 5’ end location of the paired reads.
Duplicated DNA fragments were removed, and single nucleosome resolution histone modification peaks were called by NUCLIZE 1.0 with default parameters.
Genome_build: hg19

extract_protocol:
For ChIP-Seq data of histone markers, crosslinked chromatin was isolated from freshly cultured cells and sonicated into small fragments for immunoprecipitation with antibodies against each histone modification marker, including anti-H3K4me3 (Abcam, ab8580; Active Motif, 39915), anti-H3K9ac (Abcam, ab4441; Active Motif, 39917), anti-H3K9me3 (Abcam, ab8898; Active Motif, 39161), anti-H3K27ac (Abcam, ab4729; Active Motif, 39133), and anti-H3K27me3 (Cell Signaling, C36B11; Active Motif, 39155) antibodies.
ChIP DNA was used for the library preparation using the NEBNext ChIP-Seq Library Prep kit (NEB) following manufacturer's protocol and sequenced using the HiSeq 2000 (Illumina).

tag: chip antibody


title: Blood, Smoker_3393

tag: ethnicity


title: Blood, Smoker_3394

tag: age


title: Blood, Smoker_3388


title: Blood, Smoker_3397


title: HepG2 H3K27me3


title: HepG2 H3K4me3


title: Blood, Smoker_3387


title: M3 shMbd3 1

description: Stable mesenchymal Clone 3

tag: strain


title: Blood, Smoker_3386

tag: gender


title: HepG2 H3K27ac


title: Blood, Smoker_3385

tag: cpd


title: M3 shTet2 2

description: Stable mesenchymal Clone 3


title: M3 shControl 2

description: Stable mesenchymal Clone 3


title: Blood, Smoker_3384

tag: hsi


title: M3 shControl 1

description: Stable mesenchymal Clone 3


title: HepG2 mRNA

data_processing:
Low quality bases in the short reads were dynamically trimmed from both 5' and 3' end, and the trimmed bases number were also recorded.
The trimmed reads were mapped to version hg19 of human genome sequences with Tophat 2.1.0(with bowtie1). Uniquely mapped reads were extracted, and the mapped location were restored according to previous trimming record.
HOMER 4.7 was used to calculated the RPKM for each transcript, and EdgeR was employed to calculate differentially expressed genes.
Genome_build: hg19

extract_protocol:
For RNA-Seq, RNA was extracted from freshly cultured cells with Trizol reagents (Invitrogen). Total RNA was used for the mRNA-Seq library preparation using the NEBNext mRNA-Seq Library Prep kit (NEB) after removing ribosomal RNA using the Ribo-Zero kit (Epicenter). mRNA-Seq libraries were sequenced using the HiSeq 2000 (illumina).
For RNA-Seq, RNA was extracted from freshly cultured cells with Trizol reagents (Invitrogen). Total RNA was used for the mRNA-Seq library preparation using the NEBNext mRNA-Seq Library Prep kit (NEB) after removing ribosomal RNA using the Ribo-Zero kit (Epicenter). mRNA-Seq libraries were sequenced using the HiSeq 2000 (illumina).


title: NonTargetControl_48h

city: Stanford

first: James

middle: D.

last: Brooks

state: CA

address: 300 Pasteur Drive

department: Department of Urology

institute: Stanford University

data_processing:
mapping by Tophat v2.0.0 using default parameters
quantilifcation by Cufflinks v2.0.2 using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: Kidney

growth_protocol: RLC 8° cells were seeded in 12-well plate at a density of 20,0000 cells/well in 1 ml DMEM/F12 + GlutaMAX-I™ supplemented with 10% fetal bovine serum, human transferrin (5 µg/ml) without antibiotics.

extract_protocol:
Total RNA was extracted by Qiagen RNAeasy Mini
Barcoded cDNA libraries were then prepared from total RNA using the Illumina TruSeq RNAseq kit
single-end 101-bp reads sequencing  on an Illumina HiSeq 2000 instrument (Stanford Center for Genomics and Personalized Medicine)

treatment_protocol: miR22 mimic and negative control were introduced to the cell lines RLC. After 24 and 48 hours total RNA were extracted. Barcoded cDNA libraries were then prepared from total RNA using the Illumina TruSeq RNAseq kit, and sequenced (single-end 101-bp reads) on an Illumina HiSeq instrument.

tag: tumor type

value: ccRCC

value: Kidney

tag: protocol

value: NonTargetControl

tag: time point


title: miR22_Mimic_48h

tag: tissue

value: miR22 mimic


title: Blood, Smoker_3383

value: Female

tag: ftnd


title: HepG2 H3K9ac


title: NonTargetControl_24h


title: Blood, Smoker_3382

value: Male


title: miR22_Mimic_24h


title: LTS-IR03_298bp: MAm

city: Taipei

first: John

last: WANG

address: Academia Rd sec 2

department: Biodiversity Research Center

country: Taiwan

institute: Academia Sinica

data_processing:
Genome-based pipeline: We mapped reads onto gnH and went through Tuxedo pipeline to generate a common assembled gene set (3ampClontech_pool) and tested DEGs with Cuffdiff
Transcriptome-based pipeline: We mapped reads onto the OGS-plus genes using Bowtie2
We estimated gene expression using RSEM
We tested differentially expressed gene using EBSeq
Genome_build: Si_gnH (NCBI access number AEAQ00000000)
Supplementary_files_format_and_content: gtf file contains gene loci
Supplementary_files_format_and_content: Tab-delimited files contain expression level and DEG test
Supplementary_files_format_and_content: Tab-delimited files with 4Nugenpool prefix were generated by the Tuxedo pipeline
Supplementary_files_format_and_content: Tab-delimited files with Nugen-IR prefix were generated by RSEM
Supplementary_files_format_and_content: Spreadsheet file summary DEG test results by EBSeq

organism: Solenopsis invicta

extract_protocol:
We used a droplet of honey to attract workers in the forage area and collected workers of ca. 1.5 cm in length. Workers were decapitated one-by-one on a pre-chilled -20oC metal block sitting on ice. Worker heads were placed individually in 5 ul cold RNAlater ICE (AM7023, ThermoFisher) in a numbered 0.2 ml PCR-tube and temporarily stored in liquid nitrogen. Worker bodies were put in 2 ml tubes containing 50 ul QuickExtract solution (QE09050, Epicenter) and processed for Gp-9 genotyping. The processing of each individual, from sampling to head storage in liquid nitrogen was less than a minute. We sampled 96 individuals/polygyne and 50 individuals/monogyne colony each time. The head samples were stored in a -80oC freezer for subsequent antennae dissection. We sampled polygyne workers until we obtained at least 45 individuals of each genotype. We dissected the antennae of workers of the same genotype on a metal block sitting on ice, under a dissecting microscope (Leica, 20X magnification). We used a clean sheet of Kimwipe tissue to blot away any remaining RNAlater ICE on the samples before placing them into 200 ul cold TRIzol (15596018, Invitrogen). To minimize RNA degradation, we processed at most five heads at once. To minimize cross-sample contamination, we cleaned the metal block and forceps with RNase-Zap after each dissection. Antennae were stored in a -80oC freezer until RNA extraction.
We extracted RNA using the Direct-zol RNA MiniPrep kit (R2050, ZymoResearch) following a modification of the manufacturer's instructions (Zhang et al. 2013). Frozen antennae in 200 ul Trizol were homogenized using a FastPrep-24 bead homogenizer (MP Biomedicals). Tissue destruction was checked under a microscope. If extra homogenization was required, we re-froze the sample in liquid nitrogen and repeated the homogenization (three times was the maximum needed). After the tissue was completely homogenized, we added an additional 400 ul Trizol into each sample, followed by vortexing for 10 secs and incubation at room temperature for 15 minutes. Samples were then phase separated with 120 ul chloroform. The aqueous phase was kept for RNA purification using the Direct-zol column with on-column DNase I treatment. RNA was eluted once in 25 ul RNase-free water.
cDNA was amplified from each RNA samples using the Nugen Ovation V.2 kit (M01206, NuGEN Technologies), following the manufacturer’s instructions.
To prepare sequencing samples, we mixed four bioreplicates of amplified cDNA of the same genotype. Samples of the same bioreplicate contributed same amount of cDNA.
follow the manufacturer's instructions of Illumina

value: Antennae

tag: caste

value: worker

tag: colony organization type

value: monogyne

tag: colony name

value: Rui7, Zhuang3,Tan1, Rui1

tag: genotype

value: SB/SB


title: Blood, Smoker_3380

data_processing:
After genotyping, we performed the following quality control analyses on all genotyped SNPs. First, among 242 901 genotyped variants, we excluded all insertions and deletions to ensure that all base pair positions were unique and referred to the same variant. Second, any SNP with a call rate of <95% was excluded. Third, we removed those SNPs that were not in Hardy–Weinberg equilibrium at a p value of < 1.0 × 10−6. Finally, we used a 5% minor allele frequency (MAF) as a threshold to define rare and common variants, and any SNP with an MAF of <0.05 was excluded from the analysis.
[value definition]  Genotype: AA,AB,BB,or NC (no call)

value: African-American

value: Blood