title: colon_1088_LibRep_A_SeqRep_B


title: colon_1375_LibRep_A_SeqRep_B

status: Public on Mar 05 2018

type: SRA

city: Huntsville

first: Brian

middle: Scott

last: Roberts

state: AL

address: 601 Genome Way

country: USA

institute: HudsonAlpha Institute for Biotechnology

library_source: transcriptomic

data_processing:
Fastqs from multiple lanes of the same flowcell were merged with zcat.
Reads were adaptor trimmed for both 5' adaptors (4 separate) and 3' adaptors.  See script "adaptor_trim_example.sh" for help (raw files provided are not trimmed, in accordance with GEO guidelines).
Trimmed reads were aligned to hg19 reference using bowtie2-2.1.0 keeping only perfect alignments.  Reads aligning to mutliple locii were assigned to each locii proportionally to the total number of reads.  Reads were filtered to keep only features with counts in at least 10 samples, and with a count average of at least 1.
Reads as processed above were read into R and sequencing replicates and library replicates were summed.  Reads were normalized and regression analysis were performed with the R package DESeq2.
Classifiers were constructed from normalized reads via LASSO regression using the R package glmnet.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text and Excel files

molecule: total RNA

organism: Homo sapiens

source_name: blood plasma

extract_protocol:
RNA was isolated from 1 mL of plasma using the Plasma/Serum Circulating and Exosomal RNA Purification Kit (Slurry Format) from Norgen Biotek using manufacturer's protocols.
Libraries were constructed exactly as detailed in "Blocking of targeted microRNAs from next-generation sequencing libraries", Roberts et al, PMID:26209131

treatment_protocol: Blood was drawn from patients prior to undergoing colonoscopy. Plasma was isolated within 30 min using standard centrifugation protocol.

tag: Sex

value: F

tag: self-identified ancestry

value: AA

tag: age

tag: finding

tag: patient id

tag: library id

tag: library replicate

value: A

tag: sequencing replicate

value: B

tag: library bath id


title: colon_1279_LibRep_B_SeqRep_B

value: C

value: adenoma


title: colon_1286_LibRep_B_SeqRep_B

value: M


title: colon_1291_LibRep_A_SeqRep_B


title: colon_1247_LibRep_B_SeqRep_B


title: colon_1290_LibRep_B_SeqRep_B


title: colon_1219_LibRep_A_SeqRep_B


title: colon_1283_LibRep_A_SeqRep_B


title: colon_1218_LibRep_A_SeqRep_B


title: colon_1214_LibRep_A_SeqRep_B


title: colon_1212_LibRep_A_SeqRep_B

value: ASIAN


title: colon_1198_LibRep_A_SeqRep_B


title: colon_1197_LibRep_A_SeqRep_B


title: colon_1289_LibRep_B_SeqRep_B


title: colon_1191_LibRep_A_SeqRep_B


title: colon_1207_LibRep_A_SeqRep_B


title: colon_1370_LibRep_A_SeqRep_B


title: colon_1184_LibRep_A_SeqRep_B


title: colon_1167_LibRep_B_SeqRep_B


title: colon_1168_LibRep_A_SeqRep_B


title: colon_1165_LibRep_A_SeqRep_B


title: colon_1389_LibRep_A_SeqRep_B


title: colon_1182_LibRep_A_SeqRep_B


title: colon_1159_LibRep_A_SeqRep_B


title: colon_1154_LibRep_A_SeqRep_B


title: colon_1390_LibRep_A_SeqRep_B


title: colon_1153_LibRep_B_SeqRep_B


title: colon_1151_LibRep_B_SeqRep_B


title: colon_1158_LibRep_B_SeqRep_B


title: colon_1234_LibRep_A_SeqRep_B


title: colon_1149_LibRep_B_SeqRep_B


title: colon_1156_LibRep_A_SeqRep_B


title: colon_1144_LibRep_B_SeqRep_B


title: colon_1113_LibRep_B_SeqRep_B


title: colon_1091_LibRep_B_SeqRep_B


title: colon_1080_LibRep_A_SeqRep_B


title: colon_1044_LibRep_A_SeqRep_B


title: colon_1122_LibRep_B_SeqRep_B


title: colon_1196_LibRep_B_SeqRep_B


title: colon_1186_LibRep_A_SeqRep_B


title: colon_1506_LibRep_A_SeqRep_A


title: colon_1530_LibRep_B_SeqRep_A


title: colon_1257_LibRep_A_SeqRep_A


title: colon_1491_LibRep_A_SeqRep_A


title: colon_1433_LibRep_A_SeqRep_A


title: colon_1498_LibRep_A_SeqRep_A


title: colon_1432_LibRep_A_SeqRep_A


title: colon_1405_LibRep_A_SeqRep_A


title: colon_1401_LibRep_A_SeqRep_A


title: colon_1500_LibRep_A_SeqRep_A


title: colon_1398_LibRep_A_SeqRep_A


title: colon_1400_LibRep_A_SeqRep_A


title: colon_1397_LibRep_A_SeqRep_A


title: colon_1383_LibRep_A_SeqRep_A


title: colon_1391_LibRep_A_SeqRep_A


title: colon_1385_LibRep_A_SeqRep_A


title: colon_1095_LibRep_A_SeqRep_A


title: colon_1382_LibRep_A_SeqRep_A


title: colon_1381_LibRep_A_SeqRep_A


title: colon_1523_LibRep_B_SeqRep_A


title: colon_1375_LibRep_A_SeqRep_A


title: colon_1370_LibRep_A_SeqRep_A


title: colon_1088_LibRep_A_SeqRep_A


title: colon_1354_LibRep_B_SeqRep_A


title: colon_1374_LibRep_A_SeqRep_A


title: colon_1390_LibRep_A_SeqRep_A


title: colon_1290_LibRep_B_SeqRep_A


title: colon_1408_LibRep_A_SeqRep_A


title: colon_1289_LibRep_B_SeqRep_A


title: colon_1283_LibRep_A_SeqRep_A


title: colon_1279_LibRep_B_SeqRep_A


title: colon_1247_LibRep_B_SeqRep_A


title: colon_1389_LibRep_A_SeqRep_A


title: colon_1286_LibRep_B_SeqRep_A


title: colon_1234_LibRep_A_SeqRep_A


title: colon_1212_LibRep_A_SeqRep_A


title: colon_1198_LibRep_A_SeqRep_A


title: colon_1214_LibRep_A_SeqRep_A


title: colon_1218_LibRep_A_SeqRep_A


title: colon_1207_LibRep_A_SeqRep_A


title: colon_1197_LibRep_A_SeqRep_A


title: colon_1184_LibRep_A_SeqRep_A


title: colon_1186_LibRep_A_SeqRep_A


title: colon_1196_LibRep_B_SeqRep_A


title: colon_1291_LibRep_A_SeqRep_A


title: colon_1167_LibRep_B_SeqRep_A


title: colon_1219_LibRep_A_SeqRep_A


title: colon_1159_LibRep_A_SeqRep_A


title: colon_1158_LibRep_B_SeqRep_A


title: colon_1165_LibRep_A_SeqRep_A


title: colon_1168_LibRep_A_SeqRep_A


title: colon_1191_LibRep_A_SeqRep_A


title: colon_1154_LibRep_A_SeqRep_A


title: colon_1182_LibRep_A_SeqRep_A


title: colon_1156_LibRep_A_SeqRep_A


title: colon_1153_LibRep_B_SeqRep_A


title: colon_1151_LibRep_B_SeqRep_A


title: colon_1149_LibRep_B_SeqRep_A


title: colon_1144_LibRep_B_SeqRep_A


title: colon_1044_LibRep_A_SeqRep_A


title: colon_1113_LibRep_B_SeqRep_A


title: colon_1403_LibRep_B_SeqRep_C


title: colon_1080_LibRep_A_SeqRep_A


title: colon_1467_LibRep_A_SeqRep_C


title: colon_1259_LibRep_B_SeqRep_C


title: colon_1332_LibRep_B_SeqRep_E

value: E


title: colon_1018_LibRep_B_SeqRep_C


title: colon_1004_LibRep_B_SeqRep_C


title: colon_1296_LibRep_C_SeqRep_C


title: colon_1304_LibRep_B_SeqRep_C


title: colon_1402_LibRep_B_SeqRep_C


title: colon_1418_LibRep_A_SeqRep_C


title: colon_1195_LibRep_C_SeqRep_C


title: colon_1303_LibRep_A_SeqRep_C


title: colon_1333_LibRep_B_SeqRep_C


title: colon_1342_LibRep_B_SeqRep_C


title: colon_1018_LibRep_A_SeqRep_C


title: colon_1189_LibRep_B_SeqRep_C


title: colon_1394_LibRep_A_SeqRep_C


title: colon_1093_LibRep_B_SeqRep_C


title: colon_1155_LibRep_A_SeqRep_E


title: colon_1418_LibRep_B_SeqRep_C


title: colon_1122_LibRep_B_SeqRep_A


title: colon_1059_LibRep_B_SeqRep_C


title: colon_1081_LibRep_B_SeqRep_C


title: colon_1331_LibRep_C_SeqRep_C


title: colon_1091_LibRep_B_SeqRep_A


title: colon_1324_LibRep_B_SeqRep_E


title: colon_1099_LibRep_C_SeqRep_C


title: colon_1251_LibRep_B_SeqRep_C


title: colon_1109_LibRep_B_SeqRep_E


title: colon_1256_LibRep_B_SeqRep_C


title: colon_1439_LibRep_A_SeqRep_C


title: colon_1087_LibRep_A_SeqRep_C


title: colon_1124_LibRep_C_SeqRep_C


title: colon_1105_LibRep_B_SeqRep_E


title: colon_1439_LibRep_B_SeqRep_C


title: colon_1331_LibRep_B_SeqRep_D

value: D


title: colon_1320_LibRep_B_SeqRep_C


title: colon_1365_LibRep_A_SeqRep_B


title: colon_1353_LibRep_B_SeqRep_C


title: colon_1303_LibRep_A_SeqRep_B


title: colon_1004_LibRep_B_SeqRep_B


title: colon_1332_LibRep_B_SeqRep_D


title: colon_1403_LibRep_B_SeqRep_B


title: colon_1418_LibRep_B_SeqRep_B


title: colon_1338_LibRep_B_SeqRep_C


title: colon_1018_LibRep_B_SeqRep_B


title: colon_1059_LibRep_B_SeqRep_B


title: colon_1269_LibRep_A_SeqRep_C


title: colon_1081_LibRep_B_SeqRep_B


title: colon_1342_LibRep_B_SeqRep_B


title: colon_1296_LibRep_C_SeqRep_B


title: colon_1338_LibRep_B_SeqRep_B


title: colon_1418_LibRep_A_SeqRep_B


title: colon_1124_LibRep_C_SeqRep_B


title: colon_1467_LibRep_A_SeqRep_B


title: colon_1259_LibRep_B_SeqRep_B


title: colon_1195_LibRep_C_SeqRep_B


title: colon_1304_LibRep_B_SeqRep_B


title: colon_1439_LibRep_A_SeqRep_B


title: colon_1199_LibRep_B_SeqRep_E


title: colon_1394_LibRep_A_SeqRep_B


title: colon_1018_LibRep_A_SeqRep_B


title: colon_1189_LibRep_B_SeqRep_B


title: colon_1195_LibRep_A_SeqRep_B


title: colon_1296_LibRep_B_SeqRep_B


title: colon_1087_LibRep_A_SeqRep_B


title: colon_1136_LibRep_A_SeqRep_B


title: colon_1081_LibRep_A_SeqRep_B


title: colon_1103_LibRep_A_SeqRep_B


title: colon_1124_LibRep_A_SeqRep_B


title: colon_1282_LibRep_B_SeqRep_B

value: HISPANIC


title: colon_1402_LibRep_B_SeqRep_B


title: colon_1333_LibRep_B_SeqRep_B


title: colon_1353_LibRep_A_SeqRep_B


title: colon_1269_LibRep_A_SeqRep_B


title: colon_1258_LibRep_A_SeqRep_B


title: colon_1324_LibRep_B_SeqRep_D


title: colon_1304_LibRep_A_SeqRep_B


title: colon_1099_LibRep_C_SeqRep_B


title: colon_1270_LibRep_B_SeqRep_B


title: colon_1261_LibRep_A_SeqRep_B


title: colon_1233_LibRep_B_SeqRep_B


title: colon_1251_LibRep_B_SeqRep_B


title: colon_1303_LibRep_B_SeqRep_B


title: colon_1448_LibRep_B_SeqRep_B


title: colon_1256_LibRep_A_SeqRep_B


title: colon_1355_LibRep_B_SeqRep_B


title: colon_1105_LibRep_B_SeqRep_D


title: colon_1331_LibRep_B_SeqRep_C


title: colon_1331_LibRep_C_SeqRep_B


title: colon_1059_LibRep_A_SeqRep_B


title: colon_1353_LibRep_B_SeqRep_B


title: colon_1532_LibRep_B_SeqRep_B


title: colon_1467_LibRep_B_SeqRep_B


title: colon_1532_LibRep_A_SeqRep_B


title: colon_1439_LibRep_B_SeqRep_B


title: colon_1065_LibRep_B_SeqRep_B


title: colon_1269_LibRep_B_SeqRep_B


title: colon_1394_LibRep_B_SeqRep_B


title: colon_1256_LibRep_B_SeqRep_B


title: colon_1343_LibRep_A_SeqRep_B


title: colon_1330_LibRep_B_SeqRep_C


title: colon_1093_LibRep_B_SeqRep_B


title: colon_1237_LibRep_B_SeqRep_B


title: colon_1147_LibRep_A_SeqRep_B


title: colon_1109_LibRep_B_SeqRep_D


title: colon_1087_LibRep_B_SeqRep_B


title: colon_1155_LibRep_A_SeqRep_D


title: colon_1086_LibRep_B_SeqRep_D


title: colon_1350_LibRep_B_SeqRep_B


title: colon_1320_LibRep_B_SeqRep_B


title: colon_1403_LibRep_C_SeqRep_B


title: colon_1199_LibRep_B_SeqRep_D


title: colon_1016_LibRep_C_SeqRep_B


title: colon_1322_LibRep_B_SeqRep_B


title: colon_1151_LibRep_A_SeqRep_A


title: colon_1153_LibRep_A_SeqRep_A


title: colon_1356_LibRep_A_SeqRep_A


title: colon_1189_LibRep_A_SeqRep_B


title: colon_1352_LibRep_A_SeqRep_A


title: colon_1357_LibRep_A_SeqRep_A


title: colon_1335_LibRep_A_SeqRep_A


title: colon_1149_LibRep_A_SeqRep_A


title: colon_1348_LibRep_A_SeqRep_A


title: colon_1346_LibRep_A_SeqRep_A


title: colon_1530_LibRep_A_SeqRep_A


title: colon_1313_LibRep_A_SeqRep_A


title: colon_1523_LibRep_A_SeqRep_A


title: colon_1289_LibRep_A_SeqRep_A


title: colon_1247_LibRep_A_SeqRep_A


title: colon_1286_LibRep_A_SeqRep_A


title: colon_1093_LibRep_A_SeqRep_B


title: colon_1251_LibRep_A_SeqRep_B


title: colon_1290_LibRep_A_SeqRep_A


title: colon_1215_LibRep_A_SeqRep_A


title: colon_1210_LibRep_A_SeqRep_A


title: colon_1196_LibRep_A_SeqRep_A


title: colon_1167_LibRep_A_SeqRep_A


title: colon_1158_LibRep_A_SeqRep_A


title: colon_1354_LibRep_A_SeqRep_A


title: colon_1494_LibRep_B_SeqRep_A


title: colon_1474_LibRep_B_SeqRep_A


title: colon_1122_LibRep_A_SeqRep_A


title: colon_1457_LibRep_B_SeqRep_A


title: colon_1394_LibRep_B_SeqRep_A


title: colon_1345_LibRep_A_SeqRep_A


title: colon_1113_LibRep_A_SeqRep_A


title: colon_1284_LibRep_B_SeqRep_A


title: colon_1269_LibRep_B_SeqRep_A


title: colon_1259_LibRep_B_SeqRep_A


title: colon_1233_LibRep_B_SeqRep_A


title: colon_1237_LibRep_B_SeqRep_A


title: colon_1489_LibRep_B_SeqRep_A


title: colon_1395_LibRep_B_SeqRep_A


title: colon_1448_LibRep_B_SeqRep_A


title: colon_1256_LibRep_B_SeqRep_A


title: colon_1359_LibRep_B_SeqRep_A


title: colon_1362_LibRep_B_SeqRep_A


title: colon_1303_LibRep_B_SeqRep_A


title: colon_1004_LibRep_B_SeqRep_A


title: colon_1251_LibRep_B_SeqRep_A


title: colon_1018_LibRep_B_SeqRep_A


title: colon_1144_LibRep_A_SeqRep_A


title: colon_1091_LibRep_A_SeqRep_A


title: colon_1439_LibRep_B_SeqRep_A


title: colon_1418_LibRep_B_SeqRep_A


title: colon_1404_LibRep_B_SeqRep_A


title: colon_1507_LibRep_B_SeqRep_A


title: colon_1366_LibRep_B_SeqRep_A


title: colon_1402_LibRep_B_SeqRep_A


title: colon_1355_LibRep_B_SeqRep_A


title: colon_1350_LibRep_B_SeqRep_A


title: colon_1365_LibRep_B_SeqRep_A


title: colon_1338_LibRep_B_SeqRep_A


title: colon_1337_LibRep_B_SeqRep_A


title: colon_1334_LibRep_B_SeqRep_A


title: colon_1342_LibRep_B_SeqRep_A


title: colon_1333_LibRep_B_SeqRep_A


title: colon_1282_LibRep_B_SeqRep_A


title: colon_1119_LibRep_B_SeqRep_A


title: colon_1266_LibRep_A_SeqRep_A


title: colon_1018_LibRep_A_SeqRep_A


title: colon_1404_LibRep_A_SeqRep_A


title: colon_1418_LibRep_A_SeqRep_A


title: colon_1366_LibRep_A_SeqRep_A


title: colon_1322_LibRep_B_SeqRep_A


title: colon_1350_LibRep_A_SeqRep_A


title: colon_1004_LibRep_A_SeqRep_A


title: colon_1355_LibRep_A_SeqRep_A


title: colon_1333_LibRep_A_SeqRep_A


title: colon_1439_LibRep_A_SeqRep_A


title: colon_1532_LibRep_B_SeqRep_A


title: colon_1365_LibRep_A_SeqRep_A


title: colon_1279_LibRep_A_SeqRep_A


title: colon_1303_LibRep_A_SeqRep_A


title: colon_1338_LibRep_A_SeqRep_A


title: colon_1334_LibRep_A_SeqRep_A


title: colon_1321_LibRep_A_SeqRep_A


title: colon_1474_LibRep_A_SeqRep_A


title: colon_1337_LibRep_A_SeqRep_A


title: colon_1494_LibRep_A_SeqRep_A


title: colon_1342_LibRep_A_SeqRep_A


title: colon_1457_LibRep_A_SeqRep_A


title: colon_1393_LibRep_A_SeqRep_A


title: colon_1394_LibRep_A_SeqRep_A


title: colon_1266_LibRep_B_SeqRep_A


title: colon_1402_LibRep_A_SeqRep_A


title: colon_1379_LibRep_A_SeqRep_A


title: colon_1322_LibRep_A_SeqRep_A


title: colon_1233_LibRep_A_SeqRep_A


title: colon_1237_LibRep_A_SeqRep_A


title: colon_1362_LibRep_A_SeqRep_A


title: colon_1488_LibRep_B_SeqRep_A


title: colon_1284_LibRep_A_SeqRep_A


title: colon_1251_LibRep_A_SeqRep_A


title: colon_1395_LibRep_A_SeqRep_A


title: colon_1308_LibRep_A_SeqRep_A


title: colon_1256_LibRep_A_SeqRep_A


title: colon_1386_LibRep_A_SeqRep_A


title: colon_1359_LibRep_A_SeqRep_A


title: colon_1343_LibRep_B_SeqRep_A


title: colon_1259_LibRep_A_SeqRep_A


title: colon_1325_LibRep_B_SeqRep_A


title: colon_1339_LibRep_B_SeqRep_A


title: colon_1347_LibRep_B_SeqRep_A


title: colon_1304_LibRep_B_SeqRep_A


title: colon_1467_LibRep_B_SeqRep_A


title: colon_1269_LibRep_A_SeqRep_A


title: colon_1448_LibRep_A_SeqRep_A


title: colon_1065_LibRep_B_SeqRep_A


title: colon_1353_LibRep_B_SeqRep_A


title: colon_1318_LibRep_B_SeqRep_A


title: colon_1336_LibRep_B_SeqRep_A


title: colon_1270_LibRep_B_SeqRep_A


title: colon_1265_LibRep_B_SeqRep_A


title: colon_1489_LibRep_A_SeqRep_A


title: colon_1261_LibRep_B_SeqRep_A


title: colon_1258_LibRep_B_SeqRep_A


title: colon_1517_LibRep_B_SeqRep_A


title: colon_1097_LibRep_B_SeqRep_A


title: colon_1189_LibRep_B_SeqRep_A


title: colon_1087_LibRep_B_SeqRep_A


title: colon_1147_LibRep_B_SeqRep_A


title: colon_1136_LibRep_B_SeqRep_A


title: colon_1134_LibRep_B_SeqRep_A


title: colon_1200_LibRep_B_SeqRep_A


title: colon_1103_LibRep_B_SeqRep_A


title: colon_1059_LibRep_B_SeqRep_A


title: colon_1093_LibRep_B_SeqRep_A


title: colon_1143_LibRep_B_SeqRep_A


title: colon_1081_LibRep_B_SeqRep_A


title: colon_1057_LibRep_B_SeqRep_A


title: colon_1141_LibRep_B_SeqRep_A


title: colon_1331_LibRep_C_SeqRep_A


title: colon_1320_LibRep_C_SeqRep_A


title: colon_1403_LibRep_C_SeqRep_A


title: colon_1003_LibRep_B_SeqRep_A


title: colon_1296_LibRep_C_SeqRep_A


title: colon_1195_LibRep_C_SeqRep_A


title: colon_1099_LibRep_C_SeqRep_A


title: colon_1124_LibRep_C_SeqRep_A


title: colon_1016_LibRep_C_SeqRep_A


title: colon_1328_LibRep_B_SeqRep_C


title: colon_1332_LibRep_B_SeqRep_C


title: colon_1082_LibRep_B_SeqRep_A


title: colon_1271_LibRep_B_SeqRep_C


title: colon_1176_LibRep_B_SeqRep_A


title: colon_1330_LibRep_C_SeqRep_A


title: colon_1105_LibRep_B_SeqRep_C


title: colon_1155_LibRep_B_SeqRep_C


title: colon_1173_LibRep_B_SeqRep_C


title: colon_1101_LibRep_B_SeqRep_C


title: colon_1199_LibRep_B_SeqRep_C


title: colon_1086_LibRep_B_SeqRep_C


title: colon_1043_LibRep_B_SeqRep_C


title: colon_1228_LibRep_B_SeqRep_B


title: colon_1006_LibRep_B_SeqRep_C


title: colon_1072_LibRep_A_SeqRep_C


title: colon_1109_LibRep_B_SeqRep_C


title: colon_1332_LibRep_B_SeqRep_B


title: colon_1199_LibRep_A_SeqRep_B


title: colon_1271_LibRep_A_SeqRep_B


title: colon_1324_LibRep_B_SeqRep_C


title: colon_1213_LibRep_A_SeqRep_B


title: colon_1330_LibRep_B_SeqRep_B


title: colon_1106_LibRep_B_SeqRep_B


title: colon_1105_LibRep_B_SeqRep_B


title: colon_1101_LibRep_B_SeqRep_B


title: colon_1173_LibRep_B_SeqRep_B


title: colon_1072_LibRep_A_SeqRep_B


title: colon_1213_LibRep_B_SeqRep_B


title: colon_1072_LibRep_B_SeqRep_B


title: colon_1331_LibRep_B_SeqRep_B


title: colon_1155_LibRep_A_SeqRep_C


title: colon_1226_LibRep_B_SeqRep_C


title: colon_1232_LibRep_B_SeqRep_B


title: colon_1062_LibRep_B_SeqRep_B


title: colon_1323_LibRep_B_SeqRep_B


title: colon_1043_LibRep_B_SeqRep_B


title: colon_1155_LibRep_B_SeqRep_B


title: colon_1226_LibRep_B_SeqRep_B


title: colon_1006_LibRep_B_SeqRep_B


title: colon_1324_LibRep_B_SeqRep_B


title: colon_1271_LibRep_B_SeqRep_B


title: colon_1331_LibRep_A_SeqRep_B


title: colon_1173_LibRep_A_SeqRep_B


title: colon_1135_LibRep_A_SeqRep_B


title: colon_1155_LibRep_A_SeqRep_B


title: colon_1328_LibRep_B_SeqRep_B


title: colon_1109_LibRep_B_SeqRep_B


title: colon_1048_LibRep_A_SeqRep_B


title: colon_1086_LibRep_B_SeqRep_B


title: colon_1043_LibRep_A_SeqRep_B


title: colon_1240_LibRep_B_SeqRep_B


title: colon_1248_LibRep_B_SeqRep_B


title: colon_1199_LibRep_B_SeqRep_B


title: colon_1332_LibRep_A_SeqRep_B


title: colon_1063_LibRep_B_SeqRep_B


title: colon_1045_LibRep_B_SeqRep_B


title: colon_1353_LibRep_A_SeqRep_A


title: colon_1012_LibRep_B_SeqRep_B


title: colon_1351_LibRep_A_SeqRep_A


title: colon_1339_LibRep_A_SeqRep_A


title: colon_1304_LibRep_A_SeqRep_A


title: colon_1325_LibRep_A_SeqRep_A


title: colon_1282_LibRep_A_SeqRep_A


title: colon_1200_LibRep_A_SeqRep_A


title: colon_1136_LibRep_A_SeqRep_A


title: colon_1119_LibRep_A_SeqRep_A


title: colon_1265_LibRep_A_SeqRep_A


title: colon_1065_LibRep_A_SeqRep_A


title: colon_1270_LibRep_A_SeqRep_A


title: colon_1097_LibRep_A_SeqRep_A


title: colon_1038_LibRep_A_SeqRep_A


title: colon_1003_LibRep_A_SeqRep_A


title: colon_1336_LibRep_A_SeqRep_A


title: colon_1332_LibRep_B_SeqRep_A


title: colon_1517_LibRep_A_SeqRep_A


title: colon_1271_LibRep_B_SeqRep_A


title: colon_1296_LibRep_B_SeqRep_A


title: colon_1293_LibRep_B_SeqRep_A


title: colon_1258_LibRep_A_SeqRep_A


title: colon_1261_LibRep_A_SeqRep_A


title: colon_1189_LibRep_A_SeqRep_A


title: colon_1467_LibRep_A_SeqRep_A


title: colon_1176_LibRep_A_SeqRep_A


title: colon_1141_LibRep_A_SeqRep_A


title: colon_1143_LibRep_A_SeqRep_A


title: colon_1135_LibRep_B_SeqRep_A


title: colon_1134_LibRep_A_SeqRep_A


title: colon_1103_LibRep_A_SeqRep_A


title: colon_1082_LibRep_A_SeqRep_A


title: colon_1081_LibRep_A_SeqRep_A


title: colon_1059_LibRep_A_SeqRep_A


title: colon_1072_LibRep_B_SeqRep_A


title: colon_1403_LibRep_B_SeqRep_A


title: colon_1062_LibRep_B_SeqRep_A


title: colon_1043_LibRep_B_SeqRep_A


title: colon_1403_LibRep_A_SeqRep_A


title: colon_1048_LibRep_B_SeqRep_A


title: colon_1146_LibRep_A_SeqRep_A


title: colon_1271_LibRep_A_SeqRep_A


title: colon_1135_LibRep_A_SeqRep_A


title: colon_1343_LibRep_A_SeqRep_A


title: colon_1296_LibRep_A_SeqRep_A


title: colon_1048_LibRep_A_SeqRep_A


title: colon_1147_LibRep_A_SeqRep_A


title: colon_1213_LibRep_B_SeqRep_A


title: colon_1293_LibRep_A_SeqRep_A


title: colon_1078_LibRep_A_SeqRep_A


title: colon_1318_LibRep_A_SeqRep_A


title: colon_1093_LibRep_A_SeqRep_A


title: colon_1199_LibRep_B_SeqRep_A


title: colon_1072_LibRep_A_SeqRep_A


title: colon_1240_LibRep_B_SeqRep_A


title: colon_1332_LibRep_A_SeqRep_A


title: colon_1232_LibRep_B_SeqRep_A


title: colon_1063_LibRep_B_SeqRep_A


title: colon_1057_LibRep_A_SeqRep_A


title: colon_1226_LibRep_B_SeqRep_A


title: colon_1330_LibRep_B_SeqRep_A


title: colon_1328_LibRep_B_SeqRep_A


title: colon_1181_LibRep_B_SeqRep_A


title: colon_1324_LibRep_B_SeqRep_A


title: colon_1173_LibRep_B_SeqRep_A


title: colon_1155_LibRep_B_SeqRep_A


title: colon_1109_LibRep_B_SeqRep_A


title: colon_1101_LibRep_B_SeqRep_A


title: colon_1105_LibRep_B_SeqRep_A


title: colon_1086_LibRep_B_SeqRep_A


title: colon_1106_LibRep_B_SeqRep_A


title: colon_1062_LibRep_A_SeqRep_A


title: colon_1323_LibRep_B_SeqRep_A


title: colon_1016_LibRep_B_SeqRep_A


title: colon_1331_LibRep_B_SeqRep_A


title: colon_1248_LibRep_B_SeqRep_A


title: colon_1320_LibRep_B_SeqRep_A


title: colon_1006_LibRep_B_SeqRep_A


title: colon_1045_LibRep_B_SeqRep_A


title: colon_1228_LibRep_B_SeqRep_A


title: colon_1013_LibRep_B_SeqRep_A


title: colon_1012_LibRep_B_SeqRep_A


title: colon_1330_LibRep_A_SeqRep_A


title: colon_1331_LibRep_A_SeqRep_A


title: colon_1049_LibRep_B_SeqRep_A


title: colon_1323_LibRep_A_SeqRep_A


title: colon_1324_LibRep_A_SeqRep_A


title: colon_1328_LibRep_A_SeqRep_A


title: colon_1320_LibRep_A_SeqRep_A


title: colon_1312_LibRep_A_SeqRep_A


title: colon_1248_LibRep_A_SeqRep_A


title: colon_1245_LibRep_A_SeqRep_A


title: colon_1240_LibRep_A_SeqRep_A


title: colon_1232_LibRep_A_SeqRep_A


title: colon_1228_LibRep_A_SeqRep_A


title: Nt-Mock-rep1

type: RNA

city: Valencia

first: Héctor

last: Cervera Benet

state: Valencia

address: Ingeniero Fausto Elio s/n

department: IBMCP

country: Spain

institute: CSIC-UPV

description:
Experimental block 1
Negative_1_4

hyb_protocol: Hybridization and slide washing were performed with the Gene Expression Hybridization Kit (Agilent 5188-5242) and Gene Expression Wash Buffers (Agilent 5188-5326) as detailed in G4140-90040 GeneExpression one Color v6.6 procedure. An Agilent One color Spike-In Kit (Agilent 5188-5282) was used to assess the labeling and hybridization efficiencies.

scan_protocol: Slides were scanned in GenePix 4000B (Axon) microarray scanner, at 5 µm resolution. Image files were extracted with the Feature Extraction software 9.5.1.

data_processing: Interarray analyses were performed with the Babelomics 5 software.

organism: Nicotiana tabacum

source_name: N. tabacum non-infected mock-inoculated replicate1

label_protocol: Sample RNA (200 ng) was amplified and labeled with the Agilent Low Input Quick Amp Labeling Kit (Agilent 5190-2306).

growth_protocol: All plants were at similar growth stages and were maintained in a Biosafety Level-2 greenhouse at 25ºC under a 16-h light and 8-h dark photoperiod.

extract_protocol: RNA extraction from 100 mg of fresh tissue per plant was performed using Agilent Plant RNA Isolation Mini Kit (Agilent Technologies) following the manufacturer’s instructions. The integrity of the RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent) before and after hybridization.

treatment_protocol: Batches of 8-week-old N. tabacum plants were inoculated with ≈5 µg of RNA of each viral genotype by abrasion of the third true leaf. Inoculations were done in two experimental blocks, first one including HC-Pro:AS13, HC-Pro:CLA2, HC-Pro:CLA11, NIb:PC95 and their controls, and second one including CI:PC48, CI:PC55 and their controls. All infected tobacco plants showed symptoms 5–8 dpi (not HC-Pro:AS13 infected plants). At 8 dpi virus-infected leafs and apexes for each plant were collected individually (HC-Pro:AS13 infected plants that were collected at 15 dpi). Plant tissue was frozen, homogenized, aliquoted and stored at -80ºC.

tag: cultivar

value: Xanthi NN

tag: tissue

value: Leaves and apex

tag: dpi


title: Nt-Mock-rep2

description:
Experimental block 1
Negative_1_6

source_name: N. tabacum non-infected mock-inoculated replicate2


title: Nt-Mock-rep3

description:
Experimental block 2
Negative_2_1

source_name: N. tabacum non-infected mock-inoculated replicate3


title: Nt-WT-rep3

description:
Experimental block 2
WT_2_1

source_name: N. tabacum infected with WT replicate3


title: Nt-WT-rep1

description:
Experimental block 1
WT_1_1

source_name: N. tabacum infected with WT replicate1


title: Nt-WT-rep2

description:
Experimental block 1
WT_1_4

source_name: N. tabacum infected with WT replicate2


title: Nt-Mock-rep4

description:
Experimental block 2
Negative_2_3

source_name: N. tabacum non-infected mock-inoculated replicate4


title: Nt-PC48-rep2

description:
Experimental block 2
CIPC48_18

source_name: N. tabacum infected with CIPC48 replicate2


title: colon_1226_LibRep_A_SeqRep_A


title: colon_1086_LibRep_A_SeqRep_A


title: colon_1049_LibRep_A_SeqRep_A


title: Nt-PC48-rep3

description:
Experimental block 2
CIPC48_24

source_name: N. tabacum infected with CIPC48 replicate3


title: colon_1045_LibRep_A_SeqRep_A


title: Nt-WT-rep4

description:
Experimental block 2
WT_2_2

source_name: N. tabacum infected with WT replicate4


title: Nt-PC55-rep1

description:
Experimental block 2
CIPC55_24

source_name: N. tabacum infected with CIPC55 replicate1


title: Nt-PC55-rep2

description:
Experimental block 2
CIPC55_26

source_name: N. tabacum infected with CIPC55 replicate2


title: Nt-PC55-rep3

description:
Experimental block 2
CIPC55_36

source_name: N. tabacum infected with CIPC55 replicate3


title: Nt-PC95-rep1

description:
Experimental block 1
NIbPC95_7

source_name: N. tabacum infected with NIbPC95 replicate1


title: Nt-PC95-rep2

description:
Experimental block 1
NIbPC95_8

source_name: N. tabacum infected with NIbPC95 replicate2


title: Nt-PC48-rep1

description:
Experimental block 2
CIPC48_7

source_name: N. tabacum infected with CIPC48 replicate1


title: Nt-CLA2-rep3

description:
Experimental block 1
HC-ProCLA2_10

source_name: N. tabacum infected with HC-ProCLA2 replicate3


title: colon_1030_LibRep_A_SeqRep_A

source_name: blood plasma


title: colon_1053_LibRep_A_SeqRep_A


title: Nt-PC95-rep3

description:
Experimental block 1
NIbPC95_11

source_name: N. tabacum infected with NIbPC95 replicate3


title: colon_1013_LibRep_A_SeqRep_A


title: Nt-CLA2-rep2

description:
Experimental block 1
HC-ProCLA2_7

source_name: N. tabacum infected with HC-ProCLA2 replicate2


title: Nt-CLA11-rep2

description:
Experimental block 1
HC-ProCLA11_5

source_name: N. tabacum infected with HC-ProCLA11 replicate2


title: Nt-CLA2-rep1

description:
Experimental block 1
HC-ProCLA2_1

source_name: N. tabacum infected with HC-ProCLA2 replicate1


title: colon_1012_LibRep_A_SeqRep_A


title: colon_1007_LibRep_A_SeqRep_A


title: colon_1213_LibRep_A_SeqRep_A


title: Nt-AS13-rep3

description:
Experimental block 1
HC-ProAS13_29

source_name: N. tabacum infected with HC-ProAS13 replicate3


title: colon_1199_LibRep_A_SeqRep_A


title: colon_1181_LibRep_A_SeqRep_A


title: Nt-AS13-rep1

description:
Experimental block 1
HC-ProAS13_12

source_name: N. tabacum infected with HC-ProAS13 replicate1


title: DNase-seq Late Th2 Bcl 11b KO-1

city: Bethesda

first: Andrew

middle: J

last: Oler

state: MD

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

description:
GB4919
Cell culture
DNase-Seq

library_source: genomic

data_processing:
Basecalls performed using CASAVA 2.18.
Sequence reads were mapped to mouse genome (mm9) by using bowtie 2 with default settings (PMID: 22388286 ). Reads mapped to multiple positions (MAPQ < 10) were discarded. Only one read for genomic site with multiple alignment hits were retained.
SICER v1.1 was used to call peaks (window size is 200bp, gap size is 400bp, bp-shift is 75, E-value = 1 and others by defaults) (PMID: 19505939).
Genome_build: mm9
Supplementary_files_format_and_content: *.scoreisland.txt.gz: gzipped peak file recoding peak call from SICER. Columns from left to right denote: chrom, start, end, score.

molecule: genomic DNA

organism: Mus musculus

source_name: Late Th2

extract_protocol:
ChIP-Seq experiments were performed following iDeal ChIP-seq Kit for Histones (C01010051, Diagenode) using anti-H3K27ac (C15410196, Diagenode). DNase-Seq followed the protocols described previously in (PMID: 26605532).
Library constructions ChIP-Seq and DNase-Seq follow the protocols described previously in (PMID: 19528076) and (PMID: 26605532).

tag: strain/background

value: Bcl11b[fl/fl]-CreERT2 mice on C57BL/6 background

tag: isolated cell type

value: Naive CD4 T cells

tag: sorting condition

tag: culture condition

value: Late Th2

tag: genotype/variation

value: Bcl11b KO


title: colon_1010_LibRep_A_SeqRep_A

tag: Sex

value: F


title: DNase-seq Late Th2 WT-1

description:
GB4917
Cell culture
DNase-Seq

value: Bcl11b WT


title: DNase-seq Early Th2 Bcl 11b KO-2

description:
GB4916
Cell culture
DNase-Seq

source_name: Early Th2

value: Early Th2


title: DNase-seq Late Th2 Bcl 11b KO-2

description:
GB4920
Cell culture
DNase-Seq


title: DNase-seq Late Th2 WT-2

description:
GB4918
Cell culture
DNase-Seq


title: colon_1195_LibRep_A_SeqRep_A

tag: self-identified ancestry

value: A


title: Late Th2 Bcl11bKO2 H3K27ac

description:
GA9780
Cell culture

tag: chip antibody


title: DNase-seq Early Th2 WT-1

description:
GB4913
Cell culture
DNase-Seq


title: colon_1235_LibRep_A_SeqRep_A

value: C

tag: age

tag: finding


title: colon_1155_LibRep_A_SeqRep_A

value: adenoma

tag: patient id

tag: library id


title: colon_1138_LibRep_A_SeqRep_A

value: AA

tag: library replicate

tag: sequencing replicate


title: Late Th2 Bcl11bWT1 H3K27ac

description:
GA9777
Cell culture


title: Early Th2 Bcl11bWT2 H3K27ac

description:
GA9775
Cell culture


title: colon_1109_LibRep_A_SeqRep_A

value: M

tag: library bath id


title: colon_1116_LibRep_A_SeqRep_A


title: Late Th2 Bcl11bKO1 H3K27ac

description:
GA9778
Cell culture


title: DNase-seq Early Th2 WT-2

description:
GB4914
Cell culture
DNase-Seq


title: Early Th2 Bcl11bKO2 H3K27ac

description:
GA9776
Cell culture


title: Early Th2 Bcl11bKO1 H3K27ac

description:
GA9774
Cell culture


title: Nt-AS13-rep2

description:
Experimental block 1
HC-ProAS13_28

source_name: N. tabacum infected with HC-ProAS13 replicate2

tag: cultivar

tag: tissue


title: colon_1106_LibRep_A_SeqRep_A


title: colon_1173_LibRep_A_SeqRep_A


title: Early Th2 Bcl11bWT1 H3K27ac

description:
GA9773
Cell culture

tag: strain/background


title: Nt-CLA11-rep3

description:
Experimental block 1
HC-ProCLA11_7

source_name: N. tabacum infected with HC-ProCLA11 replicate3

tag: dpi


title: Nt-CLA11-rep1

description:
Experimental block 1
HC-ProCLA11_2

source_name: N. tabacum infected with HC-ProCLA11 replicate1


title: colon_1105_LibRep_A_SeqRep_A


title: DNase-seq Early Th2 Bcl 11b KO-1

description:
GB4915
Cell culture
DNase-Seq

tag: isolated cell type

tag: sorting condition


title: colon_1099_LibRep_A_SeqRep_A


title: colon_1063_LibRep_A_SeqRep_A


title: colon_1032_LibRep_A_SeqRep_A


title: colon_1124_LibRep_A_SeqRep_A


title: colon_1033_LibRep_A_SeqRep_A


title: colon_1023_LibRep_A_SeqRep_A


title: colon_1016_LibRep_A_SeqRep_A


title: colon_1532_LibRep_A_SeqRep_A


title: colon_1488_LibRep_A_SeqRep_A


title: colon_1347_LibRep_A_SeqRep_A


title: colon_1140_LibRep_A_SeqRep_A

value: OTHER


title: colon_1087_LibRep_A_SeqRep_A


title: colon_1043_LibRep_A_SeqRep_A


title: colon_1101_LibRep_A_SeqRep_A


title: Late Th2 Bcl11bWT2 H3K27ac

description:
GA9779
Cell culture

tag: culture condition

tag: genotype/variation


title: colon_1006_LibRep_A_SeqRep_A

tag: Sex

tag: self-identified ancestry


title: LCCTam-no4HT, biological rep3

city: Washington

first: Rebecca

middle: B.

last: Riggins

state: DC

address: E412 Research Building, 3970 Reservoir Rd. NW

department: Oncology, and Lombardi Comprehensive Cancer Center

institute: Georgetown University

description: cell line original publication: PMID 8425198

hyb_protocol: standard Affymetrix protocol

scan_protocol: Standard Protocol for Affymetrix GeneChip Scanner 3000

data_processing: RMA

label: biotin

source_name: LCCTam cell line

label_protocol: standard one-cycle Affymetrix protocol

growth_protocol: cultured in SFIH (Ham's F12) to 70% confluency

extract_protocol: Trizol (Invitrogen; Carlsbad, CA), 2 ml per T-25 cm^2 flask, followed by Qiagen RNeasy cleanup protocol

treatment_protocol: For SUM44+500nM 4HT, cells were cultured in the presence of 4HT for 24 hours. For LCCTam-no4HT, cells were cultured in the absence of 4HT for 14 days

tag: breast tumor type

value: ER+/PR+ invasive lobular breast carcinoma cell line

tag: tamoxifen phenotype

value: resistant

tag: treatment

value: cultured in the absence of 500 nM 4HT for 14d


title: LCCTam-no4HT, biological rep1


title: LCCTam-no4HT, biological rep2


title: SUM44+500nM4HT, biological rep3

source_name: SUM44 cell line

value: sensitive

value: 500 nM 4-hydroxytamoxifen (4HT) for 24h


title: SUM44+500nM4HT, biological rep2


title: DKO DT40 B cells rep2

city: Turku

first: Paulina

last: Budzynska

address: Kiinamyllynkatu 13

country: Finland

institute: University of Turku

description: replicate 2

hyb_protocol: 1.65 ug of Cy-3 labeled sample was hybridized onto Agilent’s 4x44K Chicken V2 array (Design ID 026441) at 65 °C overnight using Agilent’s GE Hybridization Kit (Product number 5188-5242) following manufacturer's instructions.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2565CA. Scan Profile: AgilentHD_GX_1Color

data_processing: gProcessedSignal column in the Agilent raw data files was used as the input for the analysis. The data were normalised using quantile normalisation with limma package in R/Bioconductor tool (Bioconductor version 2.7, R version 2.12.0)

organism: Gallus gallus

source_name: IRF4KOBCL6KO DT40 B cell line

label_protocol: Cy3-labeled with Agilent’s one-color Low Input Quick Amp Labeling kit, one-color according to manufacturer's instructions.

extract_protocol: Total RNA was prepared from 5x10^6 cells of three independent cultures of WT and IRF4KO cells with RNeasy Mini Kit (Qiagen) with RNase- Free DNase treatment according to manufacturer’s instructions.

tag: tag

value: cell line:DT40


title: WT_DT40 B cells rep2

description: replicate 2

source_name: WT DT40 B cell

value: Genotype/variation:wild type


title: SUM44+500nM4HT, biological rep1


title: DKO DT40 B cells rep1

description: replicate 1


title: WT_DT40 B cells rep1

description: replicate 1


title: DKO DT40 B cells rep3

description: replicate 3


title: WT_DT40 B cells rep3

description: replicate 3


title: IWP2G9

city: Dallas

first: Lawrence

last: Lum

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

scan_protocol: Standard

data_processing: Quantile normalization

source_name: LSC

label_protocol: Biotin

growth_protocol: Cells isolated from mice and used for the assay

extract_protocol: Standard

treatment_protocol: Oral gavage

tag: background strain

tag: cell type

value: leukemic stem cells


title: BCL6KO DT40 B cells rep2

description: replicate 2

source_name: BCL6KO DT40 B cell


title: Wls_KO

treatment_protocol: Wls Genetic knockout

value: leukemic stem cells (LSC)

tag: wls genotype

value: Wntless (Wls) KO


title: BCL6KO DT40 B cells rep1

description: replicate 1


title: IWR107


title: Vehicle


title: hPSCs hMSGN1-Venus -positive at day4-5, Chir/Ldn (CL medium) differentiation, biological rep2

city: Boston

first: Jerome

last: Chal

state: MA

address: 77 ave Louis Pasteur

institute: Brigham and Women's Hospital

description: Gene expression data from differentiated hPSC in Chir  and Ldn medium for 4-5 days and sorted for hMSGN1+

hyb_protocol: Following fragmentation, cRNAs were hybridized for 16 hours at 45oC on GeneChip® Human Genome arrays. Each microarray was then washed and stained on a GeneChip® fluidics station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G. Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.1.

data_processing: The data were analyzed with GC-RMA

source_name: hPSC hMSGN1Venus+, CL, day4-5

label_protocol: Biotinylated cRNA targets were prepared from total RNA using a double amplification protocol according to the GeneChip® Expression Analysis Technical Manual: Two-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

growth_protocol: Undifferentiated hPSCs were cultured on a Matrigel (Corning)/mTESR1 system (StemCell Technologies)

extract_protocol: Total RNA was extracted from PSC populations using Trizol (Invitrogen) or with the RNAeasy plus mini-kit (Qiagen).

treatment_protocol: hPS were plated at approximatively at 30,000 cells/cm2 in mTeSR, and after recovery medium  was changed to a DMEM-based medium supplemented with insulin-transferrin- selenium (ITS, Gibco), 3 μMCHIRON99021 (Axon MedChem,  Tocris) (C medium) and  additionally 0.5 μM LDN-193189 (Axon MedChem, Stemgent) (CL  medium). On day 3, 20 ng/ml FGF2 (R&D Systems) was added .

tag: Stage

value: day 4-5

tag: strain

value: hPSC hiPSC11a

tag: marker

value: Serum-free- CHIRON99021, LDN193191


title: hPSCs undifferentiated at day0, biological rep3

description: Gene expression data from undifferentiated hPSC

source_name: hPSC, non treated, day0

value: day 0

value: Serum-free- mTeSR


title: hPSCs undifferentiated at day0, biological rep2


title: hPSCs hMSGN1-Venus -positive at day4-5, Chir/Ldn (CL medium) differentiation, biological rep1


title: hPSCs hMSGN1-Venus -positive at day4-5, Chir/Ldn (CL medium) differentiation, biological rep3


title: Mutant

city: 上海

first: tang

middle: gui

last: rong

address: fenglin road 300

department: Shanghai Institutes for Biological Sciences

country: China

institute: University of Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Agrobacterium tumefaciens C58  whole genome using bowtie2(version: 2- 2.0.5)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using protocol from Mortazavi A et al., Nat Methods, 2008; Anders S et al, Bioinformatics, 2015; Robinson MD, Ge nome Biol, 2010.
Genome_build: Agrobacterium fabrum C58, ASM9202v1
Supplementary_files_format_and_content: EXCEL files include RPKM values for each Sample

organism: Agrobacterium fabrum str. C58

source_name: Mutant

growth_protocol: Subcultures were started by inoculation of 50 mL of fresh TY medium with 5% of overnight cultures and allowed to grow to log phase (OD600 = 0.5-0.6)

extract_protocol:
RNA was isolated using TRIZOL Reagent (Invitrogen, 15596026)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: lsrB mutant


title: hPSCs hMSGN1-Venus -positive at day4-5, Chir (C medium) differentiation, biological rep2

description: Gene expression data from differentiated hPSC in Chir only medium for 4-5 days and sorted for hMSGN1+

source_name: hPSC hMSGN1Venus+, C, day4-5

value: Serum-free- CHIRON99021


title: hPSCs hMSGN1-Venus -positive at day4-5, Chir (C medium) differentiation, biological rep3


title: AML LSC rep1

description: AML LSC rep1

data_processing:
Sequencing reads were aligned to mouse genome assembly (mm9) using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized by total read count for ATAC-seq data generated by NextSeq500.
Genome_build: mm9
Supplementary_files_format_and_content: wig file and peak bed file

source_name: leukemic stem cells

growth_protocol: Normal adult mice or adult mice of AML driven by oncofusion protein MLLAF9

extract_protocol:
For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference mouse genome (mm9) were retained for downstream data analysis.
Following protocols established by Buenrostro et al. (Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-9)

treatment_protocol: FACS sorting

tag: developmental stage

value: adult


title: AML LSC rep2

description: AML LSC rep2


title: WT LSK rep2

description: WT LSK rep2

source_name: hematopoietic stem/progenitor cells

value: hematopoietic stem/progenitor cells


title: Wls_WT

value: wildtype


title: WT LSK rep1

description: WT LSK rep1


title: hPSCs hMSGN1-Venus -positive at day4-5, Chir (C medium) differentiation, biological rep1


title: tumor MSCs_sipa1 KO_rep1

city: Kyoto

first: Yan

last: Xu

address: 53 Shogoin Kawahara-cho

country: Japan

institute: Kyoto University

description: Gene expression in  mesenchymal stroma cells  in sipa1 KO Bcr-abl+ tumor tissue

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mesenchymal stroma cells, sipa1 KO mice,  replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the TRIzol RNA Isolation Reagents (Invitrogen, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The Bcr-abl+ HPCs cells were injected subcutaneously into wild type B6 mice and sipa-1 konck out mice at 1.5×104 cells per mouse. For subcutaneous injection, the GFP+ HPCs were placed in Matrigel matrix (Corning, MA, USA) to prevent rapid cell diffusion. On day 12 after subcutaneous injection, the tumor tissue were collected form wide type mice and sipa-1 knock mice recipient respectively. Tumor tissues were cut into small pieces in 1 mg/mL Collagenases IV and Dnase I in 2% RPMI-1640 medium. After 60 min of incubation with gentle shaking at 37°C, the cells were strained through a 40-μm nylon mesh to produce a single cell suspension. To isolate mesenchymal stroma cells (MSCs), the cell suspensions were stained with anti-CD45-BV510 (30-F11; BD Bioscience), anti-TER119-BV510 (TER119; BD Bioscience), anti-CD31-APC (390; BioLegend). The GFP– CD45– Ter119– CD31– cell population was sorted with FACS Aria III (BD Bioscience, San Jose, CA, USA).To isolate CD8 T cells, the cell suspensions were stained with anti-CD8 (53-6.7; TONBO),  anti-TCRb-BV421 (H57-597; BioLegend). The GFP– TCRb+CD8+ cell population was sorted with FACS Aria III (BD Bioscience, San Jose, CA, USA).

tag: tissue

value: Bcr-abl+  tumor

value: sipa1 KO

tag: age


title: Wt

source_name: Wt

value: wild type


title: UC3D

type: genomic

city: Sendai

first: Yoichi

last: Kakuta

state: Miyagi

address: 1-1 Seiryo Aoba

institute: Tohoku University

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 13

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: The genotype calling was performed using Axiom Analysis suites with default parameters.

label: Biotin

source_name: T cell from LPMC

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: LPMCs in the diseased areas of the resected small or large intestines were isolated by the dithiothreitol (DTT)–ethylenediaminetetraacetic acid (EDTA)–collagenase sequences. D4+ T cells in the diseased areas of intestines were purified from LPMCs by negative selection using Easy Sep Magnet (STEMCELL Technology, Vancouver, Canada) with Easy Sep Human CD4+ T cell Enrichment (STEMCELL Technology). The isolated CD4+ T cells were purified using FACS aria II cell sorter (BD Biosciences, Franklin Lake, NJ). Cells were stained with anti-CD3-FITC, CD4-PE, CD45RO-APC, CD197 (CCR7)-BV421, and 7ADD-Cell Viability Solution (BD Biosciences), and Tem were purified. Genomic DNA  were purified from isolated Tem using the AllPrep DNA/RNA mini kit (QIAGEN, Hilden, Germany).

treatment_protocol: DNA was digested using a cocktail of three MSREs: HpaII (5′-CˆCGG-3′), HhaI (5′-GCGˆC-3′), and AciI (5′-CˆCGC-3′) (New England BioLabs, Ipswich, USA)

value: CD4+ T cells

tag: disease

value: Ulcerative Colitis

tag: percentage of normal paneth cells


title: IL36B_24_lineB_batch4

status: Public on Mar 04 2018

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description:
RNA extracted from monolayer KC cultures
Sample_469_14208

data_processing:
Illumina adaptor sequences were removed using CutAdapt (version 1.6).
Reads were trimmed to remove bases with low PHRED quality scores (CutAdapt and Fast-X toolkit)
Filtered reads were mapped to the UCSC GRCh37/hg19 genome using Tophat2 (version 2.0.12)
Overlap between mapped reads and known human genes was tabulated using the htseq-count function from the HTSeq python library (version 0.5.4p3)
Cufflinks (version 2.2.1) was used to calculate fragments per kilobase of exon per million fragments mapped (FPKM) for each gene feature.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Processed data includes raw read counts and FPKM values for all human genes (GRCh37/hg19) and each sample (.txt files).

growth_protocol: Normal human epidermal keratinocyte cultures were established from sun-protected skin of 3 unrelated donors (donors A, B and C). Cultures were maintained until 4 days post-confluence with serum-free medium (Medium 154, Invitrogen/Cascade Biologics, Portland, OR). Only 2nd or 3rd passage cells were used in experiments with a calcium concentration of 0.1 mM.

extract_protocol:
Total RNA was isolated using the RNeasy plus isolation kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.  An Agilent Bioanalzyer (Agilent Technologies, Santa Clara, CA) was used to assess RNA quality and quantity.
Polyadenylated RNA was purified and used to prepare complementary DNA libraries for high throughput sequencing using the Illumina mRNA-Seq kit according to the manufacturer’s protocol (Illumina, San Diego, CA). Sequencing of fragmented complementary cDNA was performed using the Illumina Genome Analyzer Iix

treatment_protocol: Cultures were starved of growth factors for a 24 hour period prior to cytokine treatment. Cultures were treated with truncated recombinant human IL-1B, IL-36A, IL-36B or IL-36G (10 ng/ml for IL-1B; 2000 ng/ml for IL-36 cytokines). Three cell lines were used (lines A, B and C) with samples processed in 4 batches. Samples within the same batch are comparable. Experiments were performed with 8 and 24 hours of cytokine treatment (n = 2-3 per time point).

tag: cell line

value: B

value: Monolayer keratinocytes

tag: time

value: 24 hours

tag: batch


title: IL36A_24_lineA_batch4

description:
RNA extracted from monolayer KC cultures
Sample_469_14223

value: A

tag: treatment


title: IL36G_24_lineC_batch4

description:
RNA extracted from monolayer KC cultures
Sample_469_14217

value: C


title: IL36B_24_lineA_batch4

description:
RNA extracted from monolayer KC cultures
Sample_469_14224


title: IL36B_24_lineC_batch4

description:
RNA extracted from monolayer KC cultures
Sample_469_14216


title: IL36G_24_lineA_batch4

description:
RNA extracted from monolayer KC cultures
Sample_469_14225


title: UC2D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 12


title: tumor CD8 T_sipa1 KO_rep1

description: Gene expression in CD8 T cells in sipa1 knock out mice Bcr-abl+ tumor tissue

source_name: tumor CD8 T, sipa1 KO mice,  replicate 1

tag: genotype/variation


title: UC4D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 14


title: tumor CD8 T_WT_rep1

description: Gene expression in CD8 T cells in wild type mice Bcr-abl+ tumor tissue

source_name: tumor CD8 T, wild type mice,  replicate 1


title: tumor MSCs_WT_rep1

description: Gene expression in  mesenchymal stroma cells  in wild type Bcr-abl+ tumor tissue

source_name: mesenchymal stroma cells, wild type mice,  replicate 1


title: IL36A_24_lineB_batch4

description:
RNA extracted from monolayer KC cultures
Sample_469_14207


title: CTL_24_lineA_batch4

description:
RNA extracted from monolayer KC cultures
Sample_469_14222

value: CTL


title: UC5D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 15


title: UC1D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 11


title: CD9D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 9

value: Crohn's disease


title: CD10D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 10


title: IL36A_24_lineC_batch4

description:
RNA extracted from monolayer KC cultures
Sample_469_14215


title: CTL_24_lineB_batch4

description:
RNA extracted from monolayer KC cultures
Sample_469_14206


title: IL36B_8_lineC_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14212

value: 8 hours


title: CTL_24_lineC_batch4

description:
RNA extracted from monolayer KC cultures
Sample_469_14214


title: IL36G_8_lineC_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14213


title: CTL_8_lineC_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14210


title: IL36B_8_lineA_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14220


title: IL36G_8_lineB_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14205


title: CD7D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 7


title: CD4D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 4


title: IL36G_8_lineA_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14221


title: CTL_8_lineA_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14218


title: CTL_8_lineB_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14202


title: CD5D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 5


title: IL36B_8_lineB_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14204


title: CD8D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 8


title: IL36A_8_lineB_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14203


title: IL36A_8_lineA_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14219


title: IL1B_24_lineC_batch2

description:
RNA extracted from monolayer KC cultures
Sample_463_14174


title: IL1B_24_lineA_batch2

description:
RNA extracted from monolayer KC cultures
Sample_463_14197


title: IL36A_8_lineC_batch3

description:
RNA extracted from monolayer KC cultures
Sample_469_14211


title: IL1B_24_lineB_batch2

description:
RNA extracted from monolayer KC cultures
Sample_463_14154


title: CD2D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 2


title: CTL_24_lineB_batch2

description:
RNA extracted from monolayer KC cultures
Sample_460_14141


title: CD3D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 3


title: CD1D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 1


title: IL1B_8_lineB_batch1

description:
RNA extracted from monolayer KC cultures
Sample_460_14137


title: 07g39940 over 2

status: Public on Mar 03 2018

city: Yongin-si

first: Moon

last: Sunok

state: Gyeonggi-do

address: 1732, Deogyeong-daero

department: genetic engineering

country: South Korea

institute: kyung hee university

description: Gene expression in root hairs

hyb_protocol: Finally labeled cRNA with cyanine-3-CTP was hybridized onto the Rice Gene Expression Microarray, 4x44K containing 43,803 probes (Agilent, G2519F-015241).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer, then dried immediately by brief centrifugation.

scan_protocol: After washing, the arrays were scanned using an Agilent Surescan microarray scanner (Agilent Technologies). Feature Extraction software (version 11.5.1.1; Agilent Technologies) was used to analyze the array images and obtain raw data. Technologies) was used to analyze the array images and obtain raw data.

organism: Oryza sativa

source_name: root hairs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low input quick amp labeling kit, one-color, (Agilent, 5190-2305) according to the manufacturer's instructions.

growth_protocol: After sterilizing, seeds of rice were placed on an MSO medium during 3 day.

extract_protocol: Total RNA was extracted with TRIzol and then purified using RNeasy plant mini Kit (Qiagen, 74903)

treatment_protocol: The seminal roots were detached and submerged in liquid nitrogen and then gently were rubbed to purify root hairs

value: Root hairs

tag: cultivar

value: Don-gin


title: CTL_8_lineA_batch1

description:
RNA extracted from monolayer KC cultures
Sample_463_14179

tag: cell type


title: IL36G_24_lineB_batch4

description:
RNA extracted from monolayer KC cultures
Sample_469_14209


title: 07g39940 over 1

description: Gene expression in root hairs


title: CTL_24_lineA_batch2

description:
RNA extracted from monolayer KC cultures
Sample_463_14184


title: IL1B_8_lineA_batch1

description:
RNA extracted from monolayer KC cultures
Sample_463_14180


title: hPSCs undifferentiated at day0, biological rep1

description: Gene expression data from undifferentiated hPSC

value: day 0

value: hPSC hiPSC11a

value: Serum-free- mTeSR


title: CD6D

description:
DNA was digested with a cocktail of methylation-sensitive restriction enzymes
Patient No 6


title: Hippocampus_Paroxetine_P75_rep5

city: Blacksburg

first: Matthew

last: Glover

state: VA

address: 1981 Kraft Drive, Integrated Life Science

department: Neuroscience

institute: Virginia Tech

hyb_protocol: Microarrays were hybridized at 42°C 16-20h with 4μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner. Slides were scanned at 5μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level files and Gene level files were generated after normalization.

data_processing: All gene level files were imported into Agilent GeneSpring GX software (version 12.6) for further analysis. Probes with a raw expression value less than 50 for any sample were excluded from the analysis. The samples were then filtered to exclude any probes designated “predicted mRNA model”, as determined by the most recent RefSeq database annotations. Following experimental grouping (i.e., perinatal SSRI- versus vehicle-exposed LR at a particular developmental time point and specific brain region), differentially expressed genes with statistical significance were identified through volcano plot filtering, using cutoffs of fold change >1.5, p-value <0.05 [Bonferroni family-wise error rate (FWER)].

organism: Rattus norvegicus

label_protocol: Total RNA from each sample was linearly amplified with Agilent's Low Input Quick Amp Kit (Agilent Technology). Double-stranded cDNA (ds-cDNA) was synthesized from the amplified cRNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One microgram of ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5M EDTA, and the labeled ds-cDNA was purified by isopropanol/ethanol precipitation.

growth_protocol: Standard rat housing conditions

extract_protocol: RNA was isolated and purified using the TRIzol method. Briefly, tissue was homogenized in TRIzol (Life Technologies) and incubated at room temperature to allow dissociation of nucleoproteins. Chloroform was then added to each homogenized sample and centrifuged at 12,000g for 15 min at 4°C. Next, RNA was precipitated with isopropyl alcohol and spun down at 12,000g for 10 min at 4°C. The pellet was washed in ethanol, allowed to air dry, and resuspended in 100µl DEPC-H2O. RNA quantity and quality were measured by NanoDrop ND-1000; RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Adult females received paroxetine (10mg/kg/day) through their drinking water (or normal drinking water in the case of controls) beginning one week prior to conception, throughout gestation, until the offspring were weaned on postnatal day (P)21.

tag: gender

value: Male

tag: brain region

value: Hippocampus

tag: treatment condition

value: Paroxetine


title: Hippocampus_Paroxetine_P14_rep3


title: Hippocampus_Paroxetine_P14_rep4


title: Hippocampus_Paroxetine_P75_rep1


title: Hippocampus_Paroxetine_P75_rep2


title: Hippocampus_Paroxetine_P21_rep3


title: Hippocampus_Paroxetine_P21_rep5


title: Hippocampus_Paroxetine_P75_rep3


title: Hippocampus_Paroxetine_P14_rep2


title: Hippocampus_Paroxetine_P21_rep2


title: Hippocampus_Paroxetine_P75_rep4


title: Hippocampus_Paroxetine_P14_rep5


title: Hippocampus_Paroxetine_P21_rep4


title: Hippocampus_Paroxetine_P21_rep1


title: CTL_8_lineB_batch1

description:
RNA extracted from monolayer KC cultures
Sample_460_14136


title: Hippocampus_Control_P75_rep3

value: Control


title: Hippocampus_Paroxetine_P14_rep1


title: Hippocampus_Paroxetine_P7_rep2


title: Hippocampus_Control_P75_rep5


title: Hippocampus_Paroxetine_P7_rep3


title: Hippocampus_Control_P75_rep4


title: Hippocampus_Paroxetine_P7_rep1


title: Hippocampus_Paroxetine_P7_rep4


title: Hippocampus_Control_P75_rep2


title: Hippocampus_Control_P21_rep5


title: Hippocampus_Control_P75_rep1


title: X06277_hESC_female_rep1

city: shanghai

first: cuiqing

last: zhong

address: yueyang road 320

institute: institute of biochemistry and cell biology

description: ESC from PB2 transfer

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to illumina Inginium Human MethylationEPIC Beadchip following standard Illumina protocol

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

data_processing: GenomeStudio and Minfi R pachage

source_name: Normal diploid ESCs from PB2 transfer reconstructed embryos

label_protocol: Standard Illumina Protocol

growth_protocol: human ESCs were cultured on feeder in human ES medium supplemented with 10μM Y-27635

extract_protocol: Total DNA was extracted using DNeasy Blood & Tissue Kit (50 QIAGEN Cat No. 69504)

treatment_protocol: When ESCs conlonies achieved its maximum size and 80% coverage, aspirate spent medium followed by washing with DPBS and digesting with Accutase for 5 mins. After digestion, the samples were centrifuged for 5min at 1000 rpm then quick-froze in liquid nitrogen and stored at -80℃.

value: female

value: ESCs


title: X07138_hESC_female_rep1

description: ESC from PB2 transfer


title: X061427_hESC_male_rep1

description: ESC from PB1 transfer

source_name: Normal diploid ESCs from PB1 transfer reconstructed embryos

value: male


title: X07133_hESC_female_rep1

description: ESC from PB2 transfer


title: Hippocampus_Control_P14_rep4


title: X061422_hESC_male_rep1

description: ESC from PB1 transfer


title: Hippocampus_Control_P21_rep2


title: X06144_hESC_female_rep1

description: ESC from PB1 transfer


title: Hippocampus_Control_P14_rep3


title: Hippocampus_Control_P7_rep5


title: Hippocampus_Control_P21_rep3


title: Hippocampus_Control_P7_rep4


title: Hippocampus_Control_P21_rep1


title: Hippocampus_Control_P14_rep1


title: Hippocampus_Control_P7_rep3


title: Hippocampus_Control_P14_rep5


title: Amygdala_Paroxetine_P75_rep5

value: Amygdala


title: Hippocampus_Control_P21_rep4


title: Amygdala_Paroxetine_P75_rep4


title: Hippocampus_Control_P7_rep1


title: Hippocampus_Control_P14_rep2


title: Amygdala_Paroxetine_P75_rep1


title: Amygdala_Paroxetine_P75_rep3


title: Hippocampus_Control_P7_rep2


title: Amygdala_Paroxetine_P75_rep2


title: Amygdala_Paroxetine_P21_rep5


title: Amygdala_Paroxetine_P21_rep4


title: CTL_24_lineC_batch2

description:
RNA extracted from monolayer KC cultures
Sample_463_14161

value: C

value: Monolayer keratinocytes

value: 24 hours


title: Amygdala_Paroxetine_P21_rep3


title: Amygdala_Paroxetine_P14_rep4


title: Amygdala_Paroxetine_P14_rep5


title: Amygdala_Paroxetine_P21_rep2


title: Amygdala_Paroxetine_P14_rep3


title: Amygdala_Paroxetine_P21_rep1


title: Amygdala_Paroxetine_P7_rep2


title: Amygdala_Paroxetine_P14_rep1


title: Amygdala_Paroxetine_P7_rep4


title: Amygdala_Paroxetine_P7_rep3


title: Amygdala_Control_P75_rep5


title: Amygdala_Control_P75_rep2


title: Amygdala_Control_P75_rep1


title: Amygdala_Control_P75_rep3


title: Amygdala_Control_P21_rep4


title: Amygdala_Control_P21_rep1


title: Amygdala_Control_P21_rep3


title: Amygdala_Control_P14_rep4


title: Amygdala_Control_P21_rep2


title: Amygdala_Control_P14_rep3


title: Amygdala_Control_P21_rep5


title: Amygdala_Control_P14_rep1


title: Amygdala_Control_P7_rep5


title: Amygdala_Control_P14_rep2


title: Amygdala_Control_P75_rep4


title: Amygdala_Paroxetine_P14_rep2


title: Amygdala_Control_P14_rep5


title: BIN_UQMoore_UTE_2060

city: Brisbane

first: Marina

last: Fortes

state: Queensland

address: SCMB, room 454 bld 76

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

data_processing:
Sequencing libraries made using Illumina TrueSeq stranded mRNA Sample Preparation kit
mRNA was purified and converted to double stranded cDNA with adapters and indexes added to each sample
HiSeq 2000 sequencer analyzer (Illumina San Diego, CA) was used on each sample
Sequenced reads were analyzed using CLCBio Genomic workbench software
Quality control was performed using NGS tool
Genome_build: UMD3.1.74
Supplementary_files_format_and_content: Reads were normalized and RPKM was calculated using CLCBio Genomics workbench software for counts data text files

organism: Bos indicus

source_name: Uterus, animal 2060

extract_protocol:
Trizol and Rneasy mini kit (QIAGEN)
TruSeq RNA sample preparation kit (illumina)
libraries were multiplex per lane and paried-end sequenced, with Illumina HiSeq 2000 analyzer

tag: breed

value: Brahman

tag: animal id

tag: puberty status

value: pre-puberty

value: Uterus


title: BIN_UQMoore_UTE_2059

source_name: Uterus, animal 2059

tag: tissue


title: BIN_UQMoore_UTE_2054

source_name: Uterus, animal 2054

value: post-puberty


title: BIN_UQMoore_OVA_R_2047

source_name: Ovarian tissues right, animal 2047

value: Ovarian tissues right


title: BIN_UQMoore_UTE_2056

source_name: Uterus, animal 2056


title: BIN_UQMoore_UTE_2057

source_name: Uterus, animal 2057


title: Amygdala_Paroxetine_P7_rep1

tag: age


title: BIN_UQMoore_UTE_2048

source_name: Uterus, animal 2048


title: BIN_UQMoore_UTE_2061

source_name: Uterus, animal 2061


title: BIN_UQMoore_UTE_2046

source_name: Uterus, animal 2046


title: BIN_UQMoore_UTE_2047

source_name: Uterus, animal 2047


title: BIN_UQMoore_UTE_2064

source_name: Uterus, animal 2064


title: BIN_UQMoore_UTE_2049

source_name: Uterus, animal 2049


title: BIN_UQMoore_OVA_R_2046

source_name: Ovarian tissues right, animal 2046


title: BIN_UQMoore_OVA_R_2064

source_name: Ovarian tissues right, animal 2064


title: BIN_UQMoore_OVA_R_2060

source_name: Ovarian tissues right, animal 2060


title: BIN_UQMoore_OVA_R_2061

source_name: Ovarian tissues right, animal 2061


title: Amygdala_Control_P7_rep2


title: BIN_UQMoore_OVA_R_2059

source_name: Ovarian tissues right, animal 2059


title: Amygdala_Control_P7_rep3


title: BIN_UQMoore_UTE_2055

source_name: Uterus, animal 2055


title: Amygdala_Control_P7_rep4


title: BIN_UQMoore_OVA_R_2054

source_name: Ovarian tissues right, animal 2054


title: Amygdala_Control_P7_rep1


title: BIN_UQMoore_OVA_R_2049

source_name: Ovarian tissues right, animal 2049


title: BIN_UQMoore_OVA_R_2055

source_name: Ovarian tissues right, animal 2055


title: BIN_UQMoore_OVA_R_2056

source_name: Ovarian tissues right, animal 2056


title: BIN_UQMoore_OVA_R_2048

source_name: Ovarian tissues right, animal 2048


title: BIN_UQMoore_OVA_L_2047

source_name: Ovarian tissues left, animal 2047

value: Ovarian tissues left


title: BIN_UQMoore_OVA_R_2057

source_name: Ovarian tissues right, animal 2057


title: BIN_UQMoore_OVA_L_2060

source_name: Ovarian tissues left, animal 2060


title: BIN_UQMoore_OVA_L_2061

source_name: Ovarian tissues left, animal 2061


title: BIN_UQMoore_LIV_2060

source_name: Liver, animal 2060

value: Liver


title: BIN_UQMoore_LIV_2061

source_name: Liver, animal 2061


title: BIN_UQMoore_LIV_2047

source_name: Liver, animal 2047


title: BIN_UQMoore_OVA_L_2046

source_name: Ovarian tissues left, animal 2046


title: BIN_UQMoore_OVA_L_2056

source_name: Ovarian tissues left, animal 2056


title: BIN_UQMoore_OVA_L_2059

source_name: Ovarian tissues left, animal 2059


title: BIN_UQMoore_OVA_L_2057

source_name: Ovarian tissues left, animal 2057


title: transgenic kidney

city: Storrs

first: Yueh-chiang

last: Han

state: CT

address: 92 N. Eagleville Rd., Unit 3125, TLS 415

department: Molecular and cell biology

institute: University of Connecticut

data_processing:
Non-transgenic samples were sequenced by Illumina HiSeqTM 2000
The reads of adaptor, reads of >5% unknown nucleotides and reads with low quality bases were removed to gain clean reads.
De novo assembly was done by Trinity software to construct the unigenes as reference database.
Transgenic samples were sequenced by Illumina HiSeqTM 2000, and clean reads were collected by the same procedure. Then, clean reads were mapped to reference database by SOAPaligner/SOAP2 software.
Reads per kilobase of transcript per million mapped reads (RPKM) was calculated by BGI in tissue specific manner. The ratio among transgenic and non-transgenic was then determined, and log2 ratio of RPKM was used to represent the differential expression level.
Genome_build: non-transgenic unigenes reference database
Supplementary_files_format_and_content: rpkm.xlsx containing RPKM values for each sample
Supplementary_files_format_and_content: annotated non-transgenic unigenes.xlsx: unigene list with FPKM & annotation

organism: Oncorhynchus mykiss

source_name: kidney

growth_protocol: OSU protocol # 4282

extract_protocol:
Tissues were collected and flash frozen in dry ice. Total RNA was extracted by TRIzol reagen (Invitrogen, Carlsbad, CA) with standard protocols from manufacturer. Genomic DNA was removed by treating samples with RNase free DNase-I (M610A, Promega, Madison, WI).
RNA library was prepared by Beijing Genomic Institute (BGI) using non-transgenic samples with standard Illumina protocols as a commercial service.

treatment_protocol: OSU protocol # 4282

tag: genotype

value: transgenic  bearing cecropin P1 transgene

value: 1 year

value: kidney


title: BIN_UQMoore_OVA_L_2055

source_name: Ovarian tissues left, animal 2055


title: transgenic liver

source_name: liver

value: liver


title: transgenic spleen

source_name: spleen

value: spleen


title: BIN_UQMoore_OVA_L_2054

source_name: Ovarian tissues left, animal 2054


title: non-transgenic kidney

value: wild type


title: BIN_UQMoore_LIV_2056

source_name: Liver, animal 2056


title: BIN_UQMoore_OVA_L_2064

source_name: Ovarian tissues left, animal 2064


title: BIN_UQMoore_OVA_L_2049

source_name: Ovarian tissues left, animal 2049


title: BIN_UQMoore_OVA_L_2048

source_name: Ovarian tissues left, animal 2048


title: BIN_UQMoore_LIV_2054

source_name: Liver, animal 2054


title: BIN_UQMoore_LIV_2064

source_name: Liver, animal 2064


title: BIN_UQMoore_LIV_2048

source_name: Liver, animal 2048


title: BIN_UQMoore_LIV_2049

source_name: Liver, animal 2049


title: non-transgenic liver


title: BIN_UQMoore_LIV_2057

source_name: Liver, animal 2057


title: BIN_UQMoore_LIV_2046

source_name: Liver, animal 2046


title: BIN_UQMoore_PIT_2047

source_name: Pituitary gland, animal 2047

value: Pituitary gland


title: BIN_UQMoore_LIV_2059

source_name: Liver, animal 2059


title: BIN_UQMoore_LIV_2055

source_name: Liver, animal 2055


title: non-trasngenic spleen


title: BIN_UQMoore_PIT_2060

source_name: Pituitary gland, animal 2060


title: BIN_UQMoore_PIT_2064

source_name: Pituitary gland, animal 2064


title: BIN_UQMoore_PIT_2059

source_name: Pituitary gland, animal 2059


title: BIN_UQMoore_PIT_2046

source_name: Pituitary gland, animal 2046


title: BIN_UQMoore_PIT_2049

source_name: Pituitary gland, animal 2049


title: BIN_UQMoore_PIT_2057

source_name: Pituitary gland, animal 2057


title: BIN_UQMoore_HYP_2046

source_name: Hypothalamus, animal 2046

value: Hypothalamus


title: BIN_UQMoore_HYP_2047

source_name: Hypothalamus, animal 2047


title: BIN_UQMoore_HYP_2057

source_name: Hypothalamus, animal 2057


title: BIN_UQMoore_HYP_2054

source_name: Hypothalamus, animal 2054


title: BIN_UQMoore_HYP_2048

source_name: Hypothalamus, animal 2048


title: BIN_UQMoore_HYP_2056

source_name: Hypothalamus, animal 2056


title: BIN_UQMoore_PIT_2055

source_name: Pituitary gland, animal 2055


title: BIN_UQMoore_HYP_2060

source_name: Hypothalamus, animal 2060


title: BIN_UQMoore_HYP_2061

source_name: Hypothalamus, animal 2061


title: BIN_UQMoore_HYP_2064

source_name: Hypothalamus, animal 2064


title: BIN_UQMoore_PIT_2061

source_name: Pituitary gland, animal 2061


title: BIN_UQMoore_HYP_2049

source_name: Hypothalamus, animal 2049


title: BIN_UQMoore_PIT_2056

source_name: Pituitary gland, animal 2056


title: BIN_UQMoore_PIT_2054

source_name: Pituitary gland, animal 2054


title: BIN_UQMoore_PIT_2048

source_name: Pituitary gland, animal 2048


title: ID-014: HFH (High F-hemoglobin)

city: Augusta

first: Biaoru

last: Li

state: GA

department: Pediatrics

institute: MCG

description:
harvest protocol: Peripheral blood
HFH replicate 5 of 6

hyb_protocol: The Hy3-labeled RNA samples were mixed with reference Hy5-labeled RNA (from company for purpose of density normalization) and co-hybridized to miRCURY LNA Arrays version Dx10 and version 11 (Exiqon), which contain Tm-normalized capture probes that target miRNAs from human, mouse, and rat, as registered in miRBase version 19.0 at the Sanger Institute

scan_protocol: Scanned on an Agilent G2565AA scanner. After washing and drying, the microarray slides were scanned in a G2565BA Microarray Scanner System (Agilent, Santa Clara, CA). The resulting images were quantified with Imagene software version 8.0 (BioDiscovery, El Segundo, CA).

data_processing: the data were normalized using quantile normalization with R environment analysis

label_protocol: In the current study, we applied the two-channel labeling, 1 µg of total RNA from each sample was labeled using the miRCURY™ LNA 25 µM Cy3-label and reference RNA from Exiqon labeled by Cy5

extract_protocol: RNA was extracted with Trizol reagent, followed by quality check using the BioRad Experion system

value: child

value: CD71 red blood cells

tag: disease state

value: Sickle Cell disease

tag: disease type

value: High F-hemoglobin

source_name: Total RNA from Exiqon universal reference RNA

tag: source

value: Universal RNA

value: Normal tissue


title: BIN_UQMoore_HYP_2059

source_name: Hypothalamus, animal 2059

value: Brahman

value: post-puberty


title: BIN_UQMoore_HYP_2055

source_name: Hypothalamus, animal 2055

value: pre-puberty


title: ID-016: HFH (High F-hemoglobin)

description:
harvest protocol: Peripheral blood
HFH replicate 6 of 6


title: ID-008A: HFH (High F-hemoglobin)

description:
harvest protocol: Peripheral blood
HFH replicate 4 of 6

value: adult


title: ID-015: HFH (High F-hemoglobin)

description:
harvest protocol: Peripheral blood
HFH replicate 3 of 6


title: GC-2 B1

city: ChongqingPR China

first: Li

last: Yin

address: 69 Hongguang Road Huaxi Street, Banan District

department: College of Pharmacy and Biological Engineering

institute: Chongqing University of Technology

description: DNA methylation proﬁling in GC-2 cells following 2×10-5M diethylstilbestrol exposure

hyb_protocol: Affymetrix Chromatin Immunoprecipitation Assay Protocol

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: Affymetrix GCOS processed image files to generate CEL files. The Affymetrix CEL files were analyzed  by  R package Starr to obtain enrichment peaks() and annotated the result with Ensembl(mm10).

source_name: mouse spermatocyte-derived GC-2 cell line

growth_protocol: GC-2 cells were cultured in high-glucose DMEM containing 10% fetal bovine serum at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol: Sonicate sample to lyse cells and shear DNA to 100-1000 bp fragments.

treatment_protocol: GC-2 cells were exposed to 8×10-5M bisphenol A for 72h

tag: cell line

value: 8×10-5M bisphenol A exposure for 72h


title: control 6

city: Wuhan

first: M.

last: Peng

address: Wujiadun 156

department: Oncology Center

institute: Wuhan Union Hospital

description: control group

hyb_protocol: The pre-hybridization of HOA v6.1 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on HOA v6.1 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| â‰¥ 1 and P < 0.05).

source_name: NCI-H446 treat with 17ul DMSO

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: Cells were subcultured into culture flasks. When reached 80% area of the flasks, they were used for treatment.

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: Three control group were treated with DMSO 15ul, while the drug group with a kind of chemotherapy drug of the same concertration.(Because the article has not been published, so I can not provide the name of it.)

tag: treatment

value: 15 ul DMSO


title: drug 1

description: sample

source_name: NCI-H446 treat with chemotheraputic drug

value: chemotheraputic drug


title: control 5

description: control group

source_name: NCI-H446 treat with 16ul DMSO


title: drug 4

description: sample

source_name: NCI-H448 treat with chemotheraputic drug


title: control 2

description: control group

source_name: NCI-H446 treat with 15ul DMSO


title: drug 3

description: sample

source_name: NCI-H447 treat with chemotheraputic drug


title: ID-001: HFH (High F-hemoglobin)

description:
harvest protocol: Peripheral blood
HFH replicate 1 of 6


title: 8_235_489-14-dpi-SIV_61ECU_81

city: Ames

first: Laura

last: Miller

state: Iowa

address: 1920 Dayton Ave

department: Virus and Prion Research Unit

institute: USDA-ARS-National Animal Disease Center

data_processing:
Illumina fastq files for the infected and control libraries were processed by a custom perl script that created the three column Filtered Tag Count File consisting of: the first 20 bases of the tag sequence, raw tag count, and the normalized tag count in units of Tag Per Million (TPM). A tpm (transcripts per million) value for a specified transcriptional unit (TU) was calculated by counting appearance of DEGTP tags for a given TU, divided by the total number of TU counts obtained from a particular tissue and normalized per million.
Take 16bp tag blast against Pig EST DB
Download hit table and extract GI# and genbank ID
Convert the Genbank IDs to gene names
Reads calculated using Featurecounts version 1.4.6.p5
Differential gene expression calculated using DeSeq2 version 2.11.39
Genome_build: S.scrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files with tag counts

organism: Sus scrofa domesticus

source_name: Tracheobronchial lymph node, IAV-S 8_235_489-14-dpi-SIV_61ECU_81

growth_protocol: 80  conventionally raised 4-5 week old pigs, free of clinical disease, were purchased from a Porcine Circovirus 2-, Swine Influenza Virus-, Porcine Respiratory and Reproductive Virus -, and PRV-negative herd. Pigs were equally allotted to two equal treatment groups and each group was housed in an isolation room for about one week prior to the beginning of the experiment

extract_protocol:
One gram of TBLN from each pig was collected immediately upon necropsy, minced and stored in RNAlater at -80°C until homogenized for extraction of total RNA with MagMAX™-96 for Microarrays Total RNA Isolation Kit (Applied Biosystems, Carlsbad, CA) using the manufacturer's protocol. The integrity of the RNA was confirmed using a 2100 Bioanalyzer and RNA 6000 Nano-chip (Agilent, Santa Clara, CA). The samples used had an average RIN value of 7.8 and 28S:18S rRNA ratio of 1.9.
Tag library preparation was performed at Iowa State University DNA facility using a DGETP DpnII Sample Prep kit and protocol (Illumina, Hayward, CA). In brief, total RNA aliquots (1 mg) were diluted in 50 mL of nuclease-free H2O and heated at 65°C for 5 min to disrupt secondary structure prior to incubation with magnetic oligo-dT beads to capture the poly-adenlyated RNA fraction. First and second-strand cDNA was synthesized and bead-bound cDNA was subsequently digested with DpnII to retain a cDNA fragment from the most 3‘ GATC to the poly(A)-tail. Unbound cDNA fragments were washed away prior to ligation with GEX DpnII adapter to the 5’ end of the bead-bound digested cDNA fragments. This adapter contains a restriction site for MmeI which cuts 17 bp downstream from the DpnII site. After subsequent digestion with MmeI, 21 bp tags starting with the DpnII recognition sequence were recovered from the beads and dephosphorylated prior to phenol/chloroform extraction. Then, a second adapter (GEX adapter 2) was ligated onto the 3’ end of the cDNA tag at the MmeI cleavage site. The adapter-ligated cDNA tags were enriched by a 15 cycle PCR amplification using Phusion polymerase (Finnzymes) and primers complementary to the adapter sequences. The resulting fragments were purified by excision from a 6% polyacrylamide TBE gel. The DNA was eluted from the gel debris with 1× NEBuffer 2 by gentle rotation for 2 h at room temperature. Gel debris were removed using Spin-X Cellulose Acetate Filter (2 ml, 0.45 µm) and the DNA was precipitated by adding 10 µl of 3 M sodium acetate (pH 5.2) and 325 µl of ethanol (–20°C), followed by centrifugation at 14,000 r.p.m. for 20 min. After washing the pellet with 70% ethanol, the DNA was resuspended in 10 µl of 10 mM Tris–HCl, pH8.5 and quantified with a Nanodrop 1000 spectrophotometer. Sequencing using Solexa/Illumina Whole Genome SequencerCluster generation was performed according to the manufacturer's instructions.

treatment_protocol: On 0 dpi pigs received an intranasal challenge with 2 ml of either sham or virus  382 inoculum. Challenge viruses were PRRSV SDSU73, PCV-2 Group 2 European-like, and  383 IAV-S H1N1 OH07, used previously in our laboratory and given at a similar dose [63-  384 65]. Sham inoculum was prepared from the 3 cell cultures (MARC-145, PK-15, and  385 MDCK cells) used to propagate the viruses. Five pigs from each group were euthanized  386 and necropsied on 1, 3, 6, and 14 dpi

value: Cross-bred

tag: inoculation

value: IAV-S H1N1 OH07


title: 8_207_489-6-dpi-PRRSV_611LY_89

source_name: Tracheobronchial lymph node, PRRSV 8_207_489-6-dpi-PRRSV_611LY_89

value: PRRSV SDSU73


title: ID-008: LFH (low F-hemoglobin)

description:
harvest protocol: Peripheral blood
LFH replicate 5 of 6

value: low F-hemoglobin


title: ID-011: LFH (low F-hemoglobin)

description:
harvest protocol: Peripheral blood
LFH replicate 6 of 6

value: child


title: 13C bicarbonate

city: Livermore

first: Xavier

last: Mayali

state: CA

address: 7000 East Ave

department: Chemical Science

institute: Lawrence Livermore National Laboratory

description: isotope (bicarbonate)

hyb_protocol: 1 microgram RNA was hybridized with Nimblegen Hybridization buffer at 42 degrees Celsius for 18 hours, and washed with Nimblegen Wash buffers I, II, and III

scan_protocol: samples 1-3 were scanned with a Genepix 4000B at PMT = 800, other samples scanned with a NanoSIMS 50 according to protocol from Mayali et al. (2012) ISME J 6:1210-1221.

data_processing: Raw ion counts can be found on  12C 14N and 13C 14N columns of .txt files. Isotope ratios extracted using software package LIMAGE (L. Nittle, Carnegie Institute, Washington DC)

label: 13C bicarbonate

organism: Bacteria

source_name: stable isotope incubations of Pacifica pier surface water

label_protocol: samples 1-3 were labeled with Alexafluor 532 with the Ulysis labeling kit from Life Technologies

growth_protocol: seawater samples incubated in 1 Liter bottles at 16 degrees Celsius for 12 hours

extract_protocol: RNA was extracted using the Qiagen Rneasy kit

treatment_protocol: samples included various additions of isotope labeled substrates as indicated in the sample descriptions above

tag: sample collection

value: surface marine microbes <1 micron


title: 13C lactose

description: isotope (lactose)

label: 13C lactose


title: 13C maltose

description: isotope (maltose)

label: 13C maltose


title: ID-009: LFH (low F-hemoglobin)

description:
harvest protocol: Peripheral blood
LFH replicate 4 of 6

tag: cell type

value: CD71 red blood cells

value: Sickle Cell disease


title: ID-012A: LFH (low F-hemoglobin)

description:
harvest protocol: Peripheral blood
LFH replicate 2 of 6

value: Universal RNA


title: ID-011A: LFH (low F-hemoglobin)

description:
harvest protocol: Peripheral blood
LFH replicate 3 of 6

value: Normal tissue


title: 8_205_489-1-dpi-PRRSV_42RYV_69

source_name: Tracheobronchial lymph node, PRRSV 8_205_489-1-dpi-PRRSV_42RYV_69


title: ID-004: LFH (low F-hemoglobin)

description:
harvest protocol: Peripheral blood
LFH replicate 1 of 6


title: 8_202_489-3-dpi-PCV2_42RYU_55

source_name: Tracheobronchial lymph node,PCV2 8_202_489-3-dpi-PCV2_42RYU_55

value: PCV-2 Group 2 European-like


title: Atrial biopsy, afternoon, Patient 6_PM

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

country: France

institute: Inserm

description: Gene expression in atrial biopsy

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent)
The processed data is available on the Series level and contains the normalized signal intensity values.

source_name: Heart human right atrial tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Absolutely RNA Nanoprep kit (Stratagene).

growth_protocol: Right atrial appendage were processed immediately after collection in ice cold oxygenated buffer to extract RNA

extract_protocol: Extract-All extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Atrial biopsies were flash-frozen and processed later for total RNA extraction

tag: individual

value: Patient 6

value: Right atrial tissue

tag: procedure

value: aortic valve replacement surgery

tag: time of procedure

value: afternoon


title: Atrial biopsy, afternoon, Patient 8_AM

description: Gene expression in atrial biopsy

value: Patient 8


title: GC-2 C

description: DNA methylation proﬁling in GC-2 cells

label_protocol: Affymetrix  Chromatin  Immunoprecipitation  Assay Protocol

value: DMSO


title: 13C starch

description: isotope (starch)

label: 13C starch


title: 13C lipids

description: isotope (lipids

label: 13C lipids


title: ID-003: HFH (High F-hemoglobin)

description:
harvest protocol: Peripheral blood
HFH replicate 2 of 6

value: High F-hemoglobin


title: 7_234_489-6-dpi-SIV_61ECU_81

source_name: Tracheobronchial lymph node, IAV-S 7_234_489-6-dpi-SIV_61ECU_81

tag: breed

value: Cross-bred

value: IAV-S H1N1 OH07


title: Atrial biopsy, afternoon, Patient 5_PM

description: Gene expression in atrial biopsy

value: Patient 5


title: 13C fatty acids

description: isotope (fatty acids)

label: 13C fatty acids


title: Atrial biopsy, afternoon, Patient 4_PM

description: Gene expression in atrial biopsy

value: Patient 4


title: Atrial biopsy, afternoon, Patient 3_PM

description: Gene expression in atrial biopsy

value: Patient 3


title: 7_204_489-14-dpi-PCV2_42RYV_69

source_name: Tracheobronchial lymph node,PCV2 7_204_489-14-dpi-PCV2_42RYV_69


title: 7_201_489-1-dpi-PCV2_42RYU_55

source_name: Tracheobronchial lymph node,PCV2 7_201_489-1-dpi-PCV2_42RYU_55


title: 13C cellobiose

description: isotope (cellobiose)

label: 13C cellobiose

value: surface marine microbes <1 micron


title: 15N amino acids

description: isotope (amino acids)

label: 15N amino acids


title: Atrial biopsy, afternoon, Patient 2_PM

description: Gene expression in atrial biopsy

value: Patient 2


title: Atrial biopsy, afternoon, Patient 7_PM

description: Gene expression in atrial biopsy

value: Patient 7


title: Atrial biopsy, afternoon, Patient 1_PM

description: Gene expression in atrial biopsy

value: Patient 1


title: 6_200_489-14-dpi-Control_42RYU_55

source_name: Tracheobronchial lymph node, control 6_200_489-14-dpi-Control_42RYU_55

value: Sham inoculum from the 3 cell cultures (MARC-145, PK-15, and  385 MDCK cells)


title: 6_203_489-6-dpi-PCV2_42RYV_69

source_name: Tracheobronchial lymph node,PCV2 6_203_489-6-dpi-PCV2_42RYV_69

value: PCV-2 Group 2 European-like


title: Atrial biopsy, morning, Patient 7_AM

description: Gene expression in atrial biopsy

value: Right atrial tissue

value: morning


title: Atrial biopsy, morning, Patient 6_AM

description: Gene expression in atrial biopsy

value: Patient 6

value: aortic valve replacement surgery


title: 4_232_489-1-dpi-SIV_61ECU_81

source_name: Tracheobronchial lymph node, IAV-S 4_232_489-1-dpi-SIV_61ECU_81


title: 13C glucose

description: isotope (glucose)

label: 13C glucose


title: Atrial biopsy, morning, Patient 4_AM

description: Gene expression in atrial biopsy


title: 13C nucleic acid

description: isotope (nucleic acid)

label: 13C nucleic acid


title: Atrial biopsy, morning, Patient 5_AM

description: Gene expression in atrial biopsy


title: 13C cellulose

description: isotope (cellulose)

label: 13C cellulose


title: 15N ammonium

description: isotope (ammonium)

label: 15N ammonium


title: 3_208_489-14-dpi-PRRSV_61ECU_81

source_name: Tracheobronchial lymph node, PRRSV 3_208_489-14-dpi-PRRSV_61ECU_81

value: PRRSV SDSU73


title: 3_198_489-3-dpi-Control_42RYU_55

source_name: Tracheobronchial lymph node, control 3_198_489-3-dpi-Control_42RYU_55


title: 15N protein

description: isotope (protein)

label: 15N protein


title: Atrial biopsy, morning, Patient 3_AM

description: Gene expression in atrial biopsy


title: ammonium_glucose_fluo

description: fluorescence (ammonium and glucose)

data_processing: Isotope ratios extracted using software package LIMAGE (L. Nittle, Carnegie Institute, Washington DC)

label: Alexafluor 532


title: 6_233_489-3-dpi-SIV_61ECU_81

source_name: Tracheobronchial lymph node, IAV-S 6_233_489-3-dpi-SIV_61ECU_81


title: 2_197_489-1-dpi-Control_42RYU_55

source_name: Tracheobronchial lymph node, control 2_197_489-1-dpi-Control_42RYU_55


title: Atrial biopsy, morning, Patient 1_AM

description: Gene expression in atrial biopsy


title: 15N nitrate

description: isotope (nitrate)

label: 15N nitrate


title: nucleic_acids_fluo

description: fluorescence (nucleic acid)


title: 4_199_489-6-dpi-Control_42RYU_55

source_name: Tracheobronchial lymph node, control 4_199_489-6-dpi-Control_42RYU_55


title: T0_fluo

description: no isotope, fluorescence (control)


title: H3K9ac_D+P

status: Public on Mar 02 2018

city: Heidelberg

first: Kersten

middle: Henrik

last: Breuer

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Epigenomics and Cancer Risk Factors

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
Reads were mapped to the GRCh37 reference alignment using the backtrack algorithm of BWA version 0.7.15.
To filter out unmapped reads and alignments with a mapping quality below 20 on the phred scale, samtools view version 1.3.1 was deployed with the parameters "-F 4" and "-q 20".
The MarkDuplicate method of Picard version 2.7.1 was used to eliminate duplicate reads.
Reads were extended to a fragment length of 300 bp and read counts normalized to RPKM were calculated by means of deeptools bamCoverage version 2.3.5 with the parameters  "--extendReads 300" and  "--normalizeUsingRPKM".
To account for global differences in histone acetylation after treatment, H3K9ac and H3K27ac tracks were multiplied by the multiplicative inverse of the mean signal intensity within 1.25 kp up- and downstream of the 100 TSSs with the lowest expression variance across treatments as previously described by Brocks et al. (Nature Genetics, 2017, doi:10.1038/ng.3889).
Genome_build: GRCh37
Supplementary_files_format_and_content: bigWig files contain coverage tracks showing read counts which were normalized to represent RPKM values (files ending with "RPKMnorm") or were corrected according to read counts of 100 TSSs with low expression variance (files ending with "TSSnorm") as discribed above.

source_name: U-937 cells (monocytes)

growth_protocol: Cells were cultured in RPMI 1640 medium, supplemented with 100 U/ml penicillin/streptomycin and 10% FCS at 37°C and 5% CO2 for 92 hours and harvested 72 hours after the first treatment. Medium was changed every 24 hours.

extract_protocol:
Nuclei were extracted by sonication with low power, separated by centrifugation, lysed and chromatin was sheared by sonication with high power. Histone-DNA complexes were immunoprecipitated.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), following the manufacturer's instructions

treatment_protocol: The cells were treated with 50nM DAC (consecutively at 0 hours,24 hours and 48 hours), 8nM Panobinostat (at 48 hours) and 2µM Entinostat (at 48 hours). Cells were harvested after 72 hours and cross-linked with PFA.

value: decitabine + panobinostat

tag: time point

value: 96 hours after seed-out

tag: chip antibody

value: anti H3K9ac, Active Motif, 39917, LOT:23913004


title: Input_E

value: entinostat


title: Input_P

value: panobinostat


title: Input_C

value: untreated control


title: Input_D+P


title: Input_D

value: decitabine


title: H3K9ac_D+E

value: decitabine + entinostat


title: H3K9ac_P


title: H3K9ac_E


title: Input_D+E


title: H3K27ac_E

value: anti H3K27ac, Active Motif, 39133, LOT:31814008


title: H3K9ac_C


title: H3K9ac_D


title: H3K27ac_D+P


title: 2_206_489-3-dpi-PRRSV_61ECU_81

source_name: Tracheobronchial lymph node, PRRSV 2_206_489-3-dpi-PRRSV_61ECU_81

value: Cross-bred


title: H3K27ac_D+E


title: Atrial biopsy, morning, Patient 2_AM

description: Gene expression in atrial biopsy

value: Patient 2

tag: tissue


title: H3K27ac_C


title: H3K27ac_D


title: H3K27ac_P


title: genomic DNA from 200123470035_R06C01

city: Los Angeles

first: Ritz

last: Beate

state: California

address: 650 Charles E Young Dr. South

department: Epidemiology

institute: UCLA Fielding School of Public Health

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing:
R software v3.4.2
GEOsubmit_PEGsaliva_450kMethylationDataBackgroundNormalized.txt contains normalized (background normalization method) data

label: cy3, cy5

extract_protocol: genomic DNA was extracted from saliva samples using the Qiagen Gentra Puregene Cell Kit according to standard instructions

value: Parkinson's disease (PD)

tag: age

tag: gender

value: Female

tag: ethnicity

value: Hispanic

value: saliva


title: genomic DNA from 200123470035_R05C02

tag: disease state

value: PD-free control (Ctrl)

value: Male


title: genomic DNA from 200123470035_R06C02


title: genomic DNA from 200123470035_R04C02


title: genomic DNA from 200123470035_R04C01

value: Caucasian


title: Esophageal mucosae with high risk5

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

institute: National Cancer Center Research Institute

description:
Cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 32

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software V2011.1 (Methylation module 1.9.0), was used.  Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

source_name: biopsy, esophageal mucosa

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.  The same amount of genomic DNA samples from 4 (or 8) individuals were pooled.


title: genomic DNA from 200123470035_R03C02


title: genomic DNA from 200123470035_R05C01


title: Esophageal mucosae with high risk10

description:
Cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 37


title: Esophageal mucosae with high risk4

description:
Cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 31


title: Esophageal mucosae with high risk8

description:
Cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 35


title: Esophageal mucosae with intermediate risk10

description:
Non-cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking
SAMPLE 27