title: Primary medulloblastoma sample_MDT-MB-516 [SNP]


title: Primary medulloblastoma sample_MDT-MB-513 [SNP]

status: Public on Jul 27 2012

type: genomic

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

hyb_protocol: As directed by the manufacturer (Affymetrix)

data_processing: SNP genotyping was performed using the birdseed algorithm (v2) available in Affymetrix Genotyping Console 4.0.  For copy number analysis, CEL files were quantile normalized and signal intensities estimated using the MBEI method in dChip.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary medulloblastoma

extract_protocol: High molecular weight genomic DNA was extracted from primary tissue and cell lines using either the standard SDS/Proteinase K method or Qiagen DNEasy Blood and Tissue Kits.

tag: cell type

value: Primary medulloblastoma

tag: age

tag: gender

value: F

tag: histological subtype

value: Medulloblastoma

tag: subgroup

value: SHH


title: Primary medulloblastoma sample_MDT-MB-517 [SNP]

scan_protocol: As directed by the manufacturer (Affymetrix)

value: M

value: Group 4


title: Primary medulloblastoma sample_MDT-MB-515 [SNP]

label_protocol: As directed by the manufacturer (Affymetrix)


title: Primary medulloblastoma sample_MDT-MB-510 [SNP]


title: Primary medulloblastoma sample_MDT-MB-511 [SNP]

value: Group 3


title: Primary medulloblastoma sample_MDT-MB-514 [SNP]


title: Primary medulloblastoma sample_MDT-MB-522 [SNP]


title: Primary medulloblastoma sample_MDT-MB-507 [SNP]


title: Primary medulloblastoma sample_MDT-MB-498 [SNP]

value: Classic

value: WNT


title: Primary medulloblastoma sample_MDT-MB-521 [SNP]


title: Primary medulloblastoma sample_MDT-MB-504 [SNP]


title: Primary medulloblastoma sample_MDT-MB-506 [SNP]

value: Large Cell/Anaplastic


title: Primary medulloblastoma sample_MDT-MB-508 [SNP]


title: Primary medulloblastoma sample_MDT-MB-501 [SNP]


title: Primary medulloblastoma sample_MDT-MB-503 [SNP]


title: Primary medulloblastoma sample_MDT-MB-512 [SNP]

value: Desmoplastic


title: Primary medulloblastoma sample_MDT-MB-499 [SNP]


title: Primary medulloblastoma sample_MDT-MB-500 [SNP]


title: Primary medulloblastoma sample_MDT-MB-497 [SNP]


title: Primary medulloblastoma sample_MDT-MB-509 [SNP]


title: Primary medulloblastoma sample_MDT-MB-496 [SNP]


title: Primary medulloblastoma sample_MDT-MB-495 [SNP]


title: Primary medulloblastoma sample_MDT-MB-492 [SNP]


title: Primary medulloblastoma sample_MDT-MB-502 [SNP]


title: Primary medulloblastoma sample_MDT-MB-494 [SNP]


title: Primary medulloblastoma sample_MDT-MB-493 [SNP]


title: Primary medulloblastoma sample_MDT-MB-490 [SNP]


title: Primary medulloblastoma sample_MDT-MB-505 [SNP]


title: Primary medulloblastoma sample_MDT-MB-487 [SNP]


title: Primary medulloblastoma sample_MDT-MB-489 [SNP]


title: Primary medulloblastoma sample_MDT-MB-486 [SNP]


title: Primary medulloblastoma sample_MDT-MB-488 [SNP]


title: Primary medulloblastoma sample_MDT-MB-491 [SNP]


title: Primary medulloblastoma sample_MDT-MB-484 [SNP]


title: Primary medulloblastoma sample_MDT-MB-485 [SNP]


title: Primary medulloblastoma sample_MDT-MB-483 [SNP]


title: Primary medulloblastoma sample_MDT-MB-481 [SNP]


title: Primary medulloblastoma sample_MDT-MB-480 [SNP]


title: Primary medulloblastoma sample_MDT-MB-477 [SNP]


title: Primary medulloblastoma sample_MDT-MB-478 [SNP]


title: Primary medulloblastoma sample_MDT-MB-476 [SNP]


title: Primary medulloblastoma sample_MDT-MB-473 [SNP]


title: Primary medulloblastoma sample_MDT-MB-482 [SNP]


title: Primary medulloblastoma sample_MDT-MB-474 [SNP]


title: Primary medulloblastoma sample_MDT-MB-469 [SNP]


title: Primary medulloblastoma sample_MDT-MB-467 [SNP]


title: Primary medulloblastoma sample_MDT-MB-470 [SNP]


title: Primary medulloblastoma sample_MDT-MB-472 [SNP]


title: Primary medulloblastoma sample_MDT-MB-468 [SNP]


title: Primary medulloblastoma sample_MDT-MB-465 [SNP]


title: Primary medulloblastoma sample_MDT-MB-460 [SNP]


title: Primary medulloblastoma sample_MDT-MB-459 [SNP]


title: Primary medulloblastoma sample_MDT-MB-454 [SNP]


title: Primary medulloblastoma sample_MDT-MB-455 [SNP]


title: Primary medulloblastoma sample_MDT-MB-463 [SNP]


title: Primary medulloblastoma sample_MDT-MB-464 [SNP]


title: Primary medulloblastoma sample_MDT-MB-451 [SNP]


title: Primary medulloblastoma sample_MDT-MB-450 [SNP]


title: Primary medulloblastoma sample_MDT-MB-457 [SNP]


title: Primary medulloblastoma sample_MDT-MB-452 [SNP]


title: Primary medulloblastoma sample_MDT-MB-456 [SNP]


title: Primary medulloblastoma sample_MDT-MB-449 [SNP]


title: Primary medulloblastoma sample_MDT-MB-447 [SNP]


title: Primary medulloblastoma sample_MDT-MB-462 [SNP]


title: Primary medulloblastoma sample_MDT-MB-475 [SNP]


title: Primary medulloblastoma sample_MDT-MB-442 [SNP]


title: Primary medulloblastoma sample_MDT-MB-446 [SNP]


title: Primary medulloblastoma sample_MDT-MB-440 [SNP]


title: Primary medulloblastoma sample_MDT-MB-444 [SNP]


title: Primary medulloblastoma sample_MDT-MB-445 [SNP]


title: Primary medulloblastoma sample_MDT-MB-438 [SNP]


title: Primary medulloblastoma sample_MDT-MB-441 [SNP]


title: Primary medulloblastoma sample_MDT-MB-437 [SNP]


title: Primary medulloblastoma sample_MDT-MB-443 [SNP]


title: Primary medulloblastoma sample_MDT-MB-434 [SNP]


title: Primary medulloblastoma sample_MDT-MB-429 [SNP]


title: Primary medulloblastoma sample_MDT-MB-436 [SNP]


title: Primary medulloblastoma sample_MDT-MB-432 [SNP]


title: Primary medulloblastoma sample_MDT-MB-439 [SNP]


title: Primary medulloblastoma sample_MDT-MB-427 [SNP]


title: Primary medulloblastoma sample_MDT-MB-430 [SNP]


title: Primary medulloblastoma sample_MDT-MB-421 [SNP]


title: Primary medulloblastoma sample_MDT-MB-428 [SNP]


title: Primary medulloblastoma sample_MDT-MB-425 [SNP]


title: Primary medulloblastoma sample_MDT-MB-418 [SNP]


title: Primary medulloblastoma sample_MDT-MB-424 [SNP]


title: Primary medulloblastoma sample_MDT-MB-422 [SNP]


title: Primary medulloblastoma sample_MDT-MB-453 [SNP]


title: Primary medulloblastoma sample_MDT-MB-448 [SNP]


title: Primary medulloblastoma sample_MDT-MB-423 [SNP]


title: Primary medulloblastoma sample_MDT-MB-420 [SNP]


title: Primary medulloblastoma sample_MDT-MB-416 [SNP]


title: Primary medulloblastoma sample_MDT-MB-417 [SNP]


title: Primary medulloblastoma sample_MDT-MB-411 [SNP]


title: Primary medulloblastoma sample_MDT-MB-413 [SNP]


title: Primary medulloblastoma sample_MDT-MB-407 [SNP]


title: Primary medulloblastoma sample_MDT-MB-410 [SNP]


title: Primary medulloblastoma sample_MDT-MB-412 [SNP]


title: Primary medulloblastoma sample_MDT-MB-409 [SNP]


title: Primary medulloblastoma sample_MDT-MB-406 [SNP]


title: Primary medulloblastoma sample_MDT-MB-414 [SNP]


title: Primary medulloblastoma sample_MDT-MB-408 [SNP]


title: Primary medulloblastoma sample_MDT-MB-426 [SNP]


title: Primary medulloblastoma sample_MDT-MB-402 [SNP]


title: Primary medulloblastoma sample_MDT-MB-404 [SNP]


title: Primary medulloblastoma sample_MDT-MB-401 [SNP]


title: Primary medulloblastoma sample_MDT-MB-398 [SNP]


title: Primary medulloblastoma sample_MDT-MB-399 [SNP]


title: Primary medulloblastoma sample_MDT-MB-403 [SNP]


title: Primary medulloblastoma sample_MDT-MB-397 [SNP]


title: Primary medulloblastoma sample_MB-1357

type: RNA

hyb_protocol: As directed by Affymetrix.

scan_protocol: As directed by Affymetrix.

data_processing: Signal estimates for Gene Level Analysis were determined using Affymetrix Expression Console (1.1) and default paramters.  Samples were analyzed in three separate batches according to medulloblastoma subgroup affilliation:  SHH, Group 3, and Group 4.

molecule: total RNA

label_protocol: As directed by Affymetrix using 400ng total RNA as starting material.

extract_protocol: Total RNA was extracted from frozen medulloblastoma tissue using the Trizol method (Invitrogen) as directed by the manufacturer.  RNA integrity was assessed using the Agilent 2100 Bioanalyzer prior to processing for the Gene Array.  Samples with RIN values ≥7 were included in the study.

tag: histology


title: Primary medulloblastoma sample_MDT-MB-395 [SNP]


title: Primary medulloblastoma sample_MB-1361


title: Primary medulloblastoma sample_MB-1366


title: Primary medulloblastoma sample_MDT-MB-396 [SNP]


title: Primary medulloblastoma sample_MDT-MB-400 [SNP]


title: Primary medulloblastoma sample_MB-1365


title: Primary medulloblastoma sample_MDT-MB-394 [SNP]


title: Primary medulloblastoma sample_MDT-MB-405 [SNP]


title: Primary medulloblastoma sample_MDT-MB-392 [SNP]


title: Primary medulloblastoma sample_MDT-MB-393 [SNP]


title: Primary medulloblastoma sample_MB-1336


title: Primary medulloblastoma sample_MDT-MB-391 [SNP]


title: Primary medulloblastoma sample_MB-1323


title: Primary medulloblastoma sample_MB-1345


title: Primary medulloblastoma sample_MB-1341


title: Primary medulloblastoma sample_MB-1303


title: Primary medulloblastoma sample_MB-1350


title: Primary medulloblastoma sample_MB-1327


title: Primary medulloblastoma sample_MDT-MB-387 [SNP]


title: Primary medulloblastoma sample_MDT-MB-388 [SNP]


title: Primary medulloblastoma sample_MDT-MB-390 [SNP]


title: Primary medulloblastoma sample_MB-1279


title: Primary medulloblastoma sample_MDT-MB-389 [SNP]


title: Primary medulloblastoma sample_MB-1266


title: Primary medulloblastoma sample_MB-1270


title: Primary medulloblastoma sample_MDT-MB-384 [SNP]


title: Primary medulloblastoma sample_MB-1258


title: Primary medulloblastoma sample_MB-1260


title: Primary medulloblastoma sample_MDT-MB-381 [SNP]


title: Primary medulloblastoma sample_MB-1257


title: Primary medulloblastoma sample_MB-1214


title: Primary medulloblastoma sample_MB-1254


title: Primary medulloblastoma sample_MB-1209


title: Primary medulloblastoma sample_MDT-MB-383 [SNP]


title: Primary medulloblastoma sample_MDT-MB-380 [SNP]


title: Primary medulloblastoma sample_MDT-MB-382 [SNP]


title: Primary medulloblastoma sample_MDT-MB-377 [SNP]


title: Primary medulloblastoma sample_MDT-MB-379 [SNP]


title: Primary medulloblastoma sample_MB-1207


title: Primary medulloblastoma sample_MDT-MB-378 [SNP]


title: Primary medulloblastoma sample_MDT-MB-386 [SNP]


title: Primary medulloblastoma sample_MB-1206


title: Primary medulloblastoma sample_MDT-MB-376 [SNP]


title: Primary medulloblastoma sample_MDT-MB-385 [SNP]


title: Primary medulloblastoma sample_MDT-MB-374 [SNP]


title: Primary medulloblastoma sample_MB-1194


title: Primary medulloblastoma sample_MB-1239


title: Primary medulloblastoma sample_MDT-MB-375 [SNP]


title: Primary medulloblastoma sample_MDT-MB-372 [SNP]


title: Primary medulloblastoma sample_MB-1183


title: Primary medulloblastoma sample_MB-1190

value: LCA


title: Primary medulloblastoma sample_MDT-MB-371 [SNP]


title: Primary medulloblastoma sample_MB-1197


title: Primary medulloblastoma sample_MB-1175


title: Primary medulloblastoma sample_MB-1168


title: Primary medulloblastoma sample_MDT-MB-367 [SNP]


title: Primary medulloblastoma sample_MB-1162


title: Primary medulloblastoma sample_MB-1165


title: Primary medulloblastoma sample_MDT-MB-366 [SNP]


title: Primary medulloblastoma sample_MB-1160


title: Primary medulloblastoma sample_MDT-MB-373 [SNP]


title: Primary medulloblastoma sample_MDT-MB-364 [SNP]


title: Primary medulloblastoma sample_MB-1159


title: Primary medulloblastoma sample_MDT-MB-361 [SNP]


title: Primary medulloblastoma sample_MDT-MB-368 [SNP]


title: Primary medulloblastoma sample_MDT-MB-362 [SNP]


title: Primary medulloblastoma sample_MB-1154

value: MBEN


title: Primary medulloblastoma sample_MDT-MB-359 [SNP]


title: Primary medulloblastoma sample_MB-1153


title: Primary medulloblastoma sample_MB-1146


title: Primary medulloblastoma sample_MB-1164


title: Primary medulloblastoma sample_MDT-MB-363 [SNP]


title: Primary medulloblastoma sample_MDT-MB-360 [SNP]


title: Primary medulloblastoma sample_MB-1145


title: Primary medulloblastoma sample_MB-1141


title: Primary medulloblastoma sample_MB-1138


title: Primary medulloblastoma sample_MDT-MB-354 [SNP]


title: Primary medulloblastoma sample_MB-1136


title: Primary medulloblastoma sample_MDT-MB-353 [SNP]


title: Primary medulloblastoma sample_MDT-MB-350 [SNP]


title: Primary medulloblastoma sample_MDT-MB-358 [SNP]


title: Primary medulloblastoma sample_MDT-MB-351 [SNP]


title: Primary medulloblastoma sample_MDT-MB-347 [SNP]


title: Primary medulloblastoma sample_MDT-MB-349 [SNP]


title: Primary medulloblastoma sample_MDT-MB-357 [SNP]


title: Primary medulloblastoma sample_MB-1134


title: Primary medulloblastoma sample_MB-1135


title: Primary medulloblastoma sample_MDT-MB-348 [SNP]


title: Primary medulloblastoma sample_MB-1131


title: Primary medulloblastoma sample_MB-1128


title: Primary medulloblastoma sample_MDT-MB-344 [SNP]


title: Primary medulloblastoma sample_MDT-MB-342 [SNP]


title: Primary medulloblastoma sample_MDT-MB-343 [SNP]


title: Primary medulloblastoma sample_MB-1125


title: Primary medulloblastoma sample_MB-1126


title: Primary medulloblastoma sample_MB-1121


title: Primary medulloblastoma sample_MDT-MB-355 [SNP]


title: Primary medulloblastoma sample_MDT-MB-346 [SNP]


title: Primary medulloblastoma sample_MDT-MB-338 [SNP]


title: Primary medulloblastoma sample_MDT-MB-341 [SNP]


title: Primary medulloblastoma sample_MDT-MB-340 [SNP]


title: Primary medulloblastoma sample_MDT-MB-370 [SNP]


title: Primary medulloblastoma sample_MB-1114


title: Primary medulloblastoma sample_MDT-MB-369 [SNP]


title: Primary medulloblastoma sample_MDT-MB-339 [SNP]


title: Primary medulloblastoma sample_MDT-MB-337 [SNP]


title: Primary medulloblastoma sample_MDT-MB-334 [SNP]


title: Primary medulloblastoma sample_MDT-MB-345 [SNP]


title: Primary medulloblastoma sample_MB-1104


title: Primary medulloblastoma sample_MB-1105


title: Primary medulloblastoma sample_MB-1111


title: Primary medulloblastoma sample_MDT-MB-365 [SNP]


title: Primary medulloblastoma sample_MDT-MB-335 [SNP]


title: Primary medulloblastoma sample_MDT-MB-333 [SNP]


title: Primary medulloblastoma sample_MB-839


title: Primary medulloblastoma sample_MB-838


title: Primary medulloblastoma sample_MB-831


title: Primary medulloblastoma sample_MB-820


title: Primary medulloblastoma sample_MB-754


title: Primary medulloblastoma sample_MDT-MB-336 [SNP]


title: Primary medulloblastoma sample_MDT-MB-352 [SNP]


title: Primary medulloblastoma sample_MDT-MB-332 [SNP]


title: Primary medulloblastoma sample_MB-734


title: Primary medulloblastoma sample_MDT-MB-331 [SNP]


title: Primary medulloblastoma sample_MDT-MB-329 [SNP]


title: Primary medulloblastoma sample_MDT-MB-325 [SNP]


title: Primary medulloblastoma sample_MDT-MB-322 [SNP]


title: Primary medulloblastoma sample_MDT-MB-356 [SNP]


title: Primary medulloblastoma sample_MDT-MB-321 [SNP]


title: Primary medulloblastoma sample_MDT-MB-323 [SNP]


title: Primary medulloblastoma sample_MDT-MB-324 [SNP]


title: Primary medulloblastoma sample_MDT-MB-314 [SNP]


title: Primary medulloblastoma sample_MDT-MB-320 [SNP]


title: Primary medulloblastoma sample_MDT-MB-309 [SNP]


title: Primary medulloblastoma sample_MDT-MB-317 [SNP]


title: Primary medulloblastoma sample_MDT-MB-327 [SNP]


title: Primary medulloblastoma sample_MDT-MB-310 [SNP]


title: Primary medulloblastoma sample_MDT-MB-313 [SNP]


title: Primary medulloblastoma sample_MDT-MB-308 [SNP]


title: Primary medulloblastoma sample_MDT-MB-318 [SNP]


title: Primary medulloblastoma sample_MDT-MB-306 [SNP]


title: Primary medulloblastoma sample_MDT-MB-303 [SNP]


title: Primary medulloblastoma sample_MDT-MB-307 [SNP]


title: Primary medulloblastoma sample_MB-600


title: Primary medulloblastoma sample_MB-597


title: Primary medulloblastoma sample_MDT-MB-304 [SNP]


title: Primary medulloblastoma sample_MB-596


title: Primary medulloblastoma sample_MB-608


title: Primary medulloblastoma sample_MDT-MB-328 [SNP]


title: Primary medulloblastoma sample_MB-578


title: Primary medulloblastoma sample_MDT-MB-300 [SNP]


title: Primary medulloblastoma sample_MDT-MB-229 [SNP]


title: Primary medulloblastoma sample_MDT-MB-302 [SNP]


title: Primary medulloblastoma sample_MB-577


title: Primary medulloblastoma sample_MB-572


title: Primary medulloblastoma sample_MB-571


title: Primary medulloblastoma sample_MDT-MB-301 [SNP]


title: Primary medulloblastoma sample_MB-570


title: Primary medulloblastoma sample_MB-569


title: Primary medulloblastoma sample_MB-567


title: Primary medulloblastoma sample_MDT-MB-222 [SNP]


title: Primary medulloblastoma sample_MDT-MB-226 [SNP]


title: Primary medulloblastoma sample_MDT-MB-223 [SNP]


title: Primary medulloblastoma sample_MDT-MB-228 [SNP]


title: Primary medulloblastoma sample_MDT-MB-224 [SNP]


title: Primary medulloblastoma sample_MB-563


title: Primary medulloblastoma sample_MDT-MB-319 [SNP]


title: Primary medulloblastoma sample_MB-559


title: Primary medulloblastoma sample_MB-565


title: Primary medulloblastoma sample_MDT-MB-312 [SNP]


title: Primary medulloblastoma sample_MDT-MB-220 [SNP]


title: Primary medulloblastoma sample_MDT-MB-305 [SNP]


title: Primary medulloblastoma sample_MB-555


title: Primary medulloblastoma sample_MDT-MB-311 [SNP]


title: Primary medulloblastoma sample_MB-558


title: Primary medulloblastoma sample_MB-553


title: Primary medulloblastoma sample_MB-554


title: Primary medulloblastoma sample_MDT-MB-225 [SNP]


title: Primary medulloblastoma sample_MB-551


title: Primary medulloblastoma sample_MDT-MB-221 [SNP]


title: Primary medulloblastoma sample_MB-550


title: Primary medulloblastoma sample_MDT-MB-217 [SNP]


title: Primary medulloblastoma sample_MB-547


title: Primary medulloblastoma sample_MDT-MB-216 [SNP]


title: Primary medulloblastoma sample_MDT-MB-215 [SNP]


title: Primary medulloblastoma sample_MDT-MB-208 [SNP]


title: Primary medulloblastoma sample_MB-544


title: Primary medulloblastoma sample_MB-527


title: Primary medulloblastoma sample_MDT-MB-211 [SNP]


title: Primary medulloblastoma sample_MB-540


title: Primary medulloblastoma sample_MDT-MB-210 [SNP]


title: Primary medulloblastoma sample_MB-530


title: Primary medulloblastoma sample_MB-517


title: Primary medulloblastoma sample_MDT-MB-213 [SNP]


title: Primary medulloblastoma sample_MDT-MB-209 [SNP]


title: Primary medulloblastoma sample_MDT-MB-203 [SNP]


title: Primary medulloblastoma sample_MDT-MB-206 [SNP]


title: Primary medulloblastoma sample_MDT-MB-201 [SNP]


title: Primary medulloblastoma sample_MDT-MB-205 [SNP]


title: Primary medulloblastoma sample_MDT-MB-202 [SNP]


title: Primary medulloblastoma sample_MB-447


title: Primary medulloblastoma sample_MDT-MB-219 [SNP]


title: Primary medulloblastoma sample_MB-453


title: Primary medulloblastoma sample_MB-515


title: Primary medulloblastoma sample_MB-437


title: Primary medulloblastoma sample_MB-510


title: Primary medulloblastoma sample_MB-439


title: Primary medulloblastoma sample_MDT-MB-200 [SNP]


title: Primary medulloblastoma sample_MDT-MB-212 [SNP]


title: Primary medulloblastoma sample_MDT-MB-199 [SNP]


title: Primary medulloblastoma sample_MB-414


title: Primary medulloblastoma sample_MDT-MB-207 [SNP]


title: Primary medulloblastoma sample_MB-422


title: Primary medulloblastoma sample_MB-424


title: Primary medulloblastoma sample_MB-403


title: Primary medulloblastoma sample_MB-404


title: Primary medulloblastoma sample_MDT-MB-195 [SNP]


title: Primary medulloblastoma sample_MDT-MB-198 [SNP]


title: Primary medulloblastoma sample_MDT-MB-191 [SNP]


title: Primary medulloblastoma sample_MB-398


title: Primary medulloblastoma sample_MB-397


title: Primary medulloblastoma sample_MB-393


title: Primary medulloblastoma sample_MDT-MB-194 [SNP]


title: Primary medulloblastoma sample_MDT-MB-192 [SNP]


title: Primary medulloblastoma sample_MB-392


title: Primary medulloblastoma sample_MB-395


title: Primary medulloblastoma sample_MDT-MB-189 [SNP]


title: Primary medulloblastoma sample_MB-386


title: Primary medulloblastoma sample_MB-384


title: Primary medulloblastoma sample_MDT-MB-187 [SNP]


title: Primary medulloblastoma sample_MDT-MB-193 [SNP]


title: Primary medulloblastoma sample_MB-390


title: Primary medulloblastoma sample_MDT-MB-182 [SNP]


title: Primary medulloblastoma sample_MDT-MB-188 [SNP]


title: Primary medulloblastoma sample_MB-402


title: Primary medulloblastoma sample_MB-382


title: Primary medulloblastoma sample_MDT-MB-179 [SNP]


title: Primary medulloblastoma sample_MDT-MB-196 [SNP]


title: Primary medulloblastoma sample_MDT-MB-185 [SNP]


title: Primary medulloblastoma sample_MB-380


title: Primary medulloblastoma sample_MDT-MB-186 [SNP]


title: Primary medulloblastoma sample_MDT-MB-176 [SNP]


title: Primary medulloblastoma sample_MB-379


title: Primary medulloblastoma sample_MB-381


title: Primary medulloblastoma sample_MB-376


title: Primary medulloblastoma sample_MB-377


title: Primary medulloblastoma sample_MDT-MB-180 [SNP]


title: Primary medulloblastoma sample_MB-374


title: Primary medulloblastoma sample_MDT-MB-178 [SNP]


title: Primary medulloblastoma sample_MDT-MB-175 [SNP]


title: Primary medulloblastoma sample_MB-366


title: Primary medulloblastoma sample_MB-372


title: Primary medulloblastoma sample_MDT-MB-190 [SNP]


title: Primary medulloblastoma sample_MDT-MB-184 [SNP]


title: Primary medulloblastoma sample_MB-362


title: Primary medulloblastoma sample_MB-365


title: Primary medulloblastoma sample_MDT-MB-174 [SNP]


title: Primary medulloblastoma sample_MDT-MB-169 [SNP]


title: Primary medulloblastoma sample_MB-364


title: Primary medulloblastoma sample_MDT-MB-173 [SNP]


title: Primary medulloblastoma sample_MDT-MB-170 [SNP]


title: Primary medulloblastoma sample_MDT-MB-166 [SNP]


title: Primary medulloblastoma sample_MB-357


title: Primary medulloblastoma sample_MDT-MB-177 [SNP]


title: Primary medulloblastoma sample_MDT-MB-165 [SNP]


title: Primary medulloblastoma sample_MB-354


title: Primary medulloblastoma sample_MB-358


title: Primary medulloblastoma sample_MB-353


title: Primary medulloblastoma sample_MB-350


title: Primary medulloblastoma sample_MB-343


title: Primary medulloblastoma sample_MDT-MB-163 [SNP]


title: Primary medulloblastoma sample_MB-344


title: Primary medulloblastoma sample_MDT-MB-164 [SNP]


title: Primary medulloblastoma sample_MB-342


title: Primary medulloblastoma sample_MB-346


title: Primary medulloblastoma sample_MDT-MB-154 [SNP]


title: Primary medulloblastoma sample_MDT-MB-181 [SNP]


title: Primary medulloblastoma sample_MB-223


title: Primary medulloblastoma sample_MDT-MB-158 [SNP]


title: Primary medulloblastoma sample_MDT-MB-160 [SNP]


title: Primary medulloblastoma sample_MDT-MB-153 [SNP]


title: Primary medulloblastoma sample_MB-208


title: Primary medulloblastoma sample_MB-222


title: Primary medulloblastoma sample_MDT-MB-162 [SNP]


title: Primary medulloblastoma sample_MDT-MB-167 [SNP]


title: Primary medulloblastoma sample_MDT-MB-183 [SNP]


title: Primary medulloblastoma sample_MB-196


title: Primary medulloblastoma sample_MDT-MB-151 [SNP]


title: Primary medulloblastoma sample_MDT-MB-155 [SNP]


title: Primary medulloblastoma sample_MB-189


title: Primary medulloblastoma sample_MDT-MB-156 [SNP]


title: Primary medulloblastoma sample_MDT-MB-150 [SNP]


title: Primary medulloblastoma sample_MB-177


title: Primary medulloblastoma sample_MB-179


title: Primary medulloblastoma sample_MDT-MB-152 [SNP]


title: Primary medulloblastoma sample_MDT-MB-147 [SNP]


title: Primary medulloblastoma sample_MB-174


title: Primary medulloblastoma sample_MB-180


title: Primary medulloblastoma sample_MDT-MB-145 [SNP]


title: Primary medulloblastoma sample_MDT-MB-148 [SNP]


title: Primary medulloblastoma sample_MB-340


title: Primary medulloblastoma sample_MB-153


title: Primary medulloblastoma sample_MDT-MB-141 [SNP]


title: Primary medulloblastoma sample_MB-139


title: Primary medulloblastoma sample_MDT-MB-142 [SNP]


title: Primary medulloblastoma sample_MDT-MB-146 [SNP]


title: Primary medulloblastoma sample_MB-135


title: Primary medulloblastoma sample_MDT-MB-136 [SNP]


title: Primary medulloblastoma sample_MDT-MB-140 [SNP]


title: Primary medulloblastoma sample_MB-141


title: Primary medulloblastoma sample_MDT-MB-138 [SNP]


title: Primary medulloblastoma sample_MDT-MB-139 [SNP]


title: Primary medulloblastoma sample_MB-156


title: Primary medulloblastoma sample_MB-162


title: Primary medulloblastoma sample_MB-134


title: Primary medulloblastoma sample_MDT-MB-135 [SNP]


title: Primary medulloblastoma sample_MB-130


title: Primary medulloblastoma sample_MB-127


title: Primary medulloblastoma sample_MDT-MB-134 [SNP]


title: Primary medulloblastoma sample_MDT-MB-132 [SNP]


title: Primary medulloblastoma sample_MDT-MB-133 [SNP]


title: Primary medulloblastoma sample_MDT-MB-130 [SNP]


title: Primary medulloblastoma sample_MDT-MB-128 [SNP]


title: Primary medulloblastoma sample_MDT-MB-129 [SNP]


title: Primary medulloblastoma sample_MB-123


title: Primary medulloblastoma sample_MB-50


title: Primary medulloblastoma sample_MB-117


title: Primary medulloblastoma sample_MB-38


title: Primary medulloblastoma sample_MDT-MB-131 [SNP]


title: Primary medulloblastoma sample_MB-121


title: Primary medulloblastoma sample_MB-9


title: Primary medulloblastoma sample_MB-29


title: Primary medulloblastoma sample_MB-49


title: Primary medulloblastoma sample_MDT-MB-144 [SNP]


title: Primary medulloblastoma sample_MDT-MB-125 [SNP]


title: Primary medulloblastoma sample_MDT-MB-123 [SNP]


title: Primary medulloblastoma sample_MB-5


title: Primary medulloblastoma sample_MB-4


title: Primary medulloblastoma sample_MB-1362


title: Primary medulloblastoma sample_MDT-MB-122 [SNP]


title: Primary medulloblastoma sample_MB-1261


title: Primary medulloblastoma sample_MDT-MB-118 [SNP]


title: Primary medulloblastoma sample_MB-1245


title: Primary medulloblastoma sample_MB-3


title: Primary medulloblastoma sample_MDT-MB-124 [SNP]


title: Primary medulloblastoma sample_MDT-MB-119 [SNP]


title: Primary medulloblastoma sample_MDT-MB-116 [SNP]


title: Primary medulloblastoma sample_MB-1189


title: Primary medulloblastoma sample_MDT-MB-121 [SNP]


title: Primary medulloblastoma sample_MDT-MB-117 [SNP]


title: Primary medulloblastoma sample_MDT-MB-115 [SNP]


title: Primary medulloblastoma sample_MB-1240


title: Primary medulloblastoma sample_MB-591


title: Primary medulloblastoma sample_MDT-MB-127 [SNP]


title: Primary medulloblastoma sample_MB-543


title: Primary medulloblastoma sample_MDT-MB-109 [SNP]


title: Primary medulloblastoma sample_MB-576


title: Primary medulloblastoma sample_MB-575


title: Primary medulloblastoma sample_MDT-MB-108 [SNP]


title: Primary medulloblastoma sample_MDT-MB-126 [SNP]


title: Primary medulloblastoma sample_MDT-MB-111 [SNP]


title: Primary medulloblastoma sample_MB-535


title: Primary medulloblastoma sample_MDT-MB-105 [SNP]


title: Primary medulloblastoma sample_MB-514


title: Primary medulloblastoma sample_MDT-MB-112 [SNP]


title: Primary medulloblastoma sample_MB-448


title: Primary medulloblastoma sample_MDT-MB-103 [SNP]


title: Primary medulloblastoma sample_MB-511


title: Primary medulloblastoma sample_MDT-MB-110 [SNP]


title: Primary medulloblastoma sample_MB-445


title: Primary medulloblastoma sample_MDT-MB-106 [SNP]


title: Primary medulloblastoma sample_MB-442


title: Primary medulloblastoma sample_MDT-MB-100 [SNP]


title: Primary medulloblastoma sample_MDT-MB-102 [SNP]


title: Primary medulloblastoma sample_MB-426


title: Primary medulloblastoma sample_MDT-MB-114 [SNP]


title: Primary medulloblastoma sample_MDT-MB-107 [SNP]


title: Primary medulloblastoma sample_MDT-MB-101 [SNP]


title: Primary medulloblastoma sample_MB-421


title: Primary medulloblastoma sample_MB-399


title: Primary medulloblastoma sample_MB-400


title: Primary medulloblastoma sample_MB-396


title: Primary medulloblastoma sample_MB-412


title: Primary medulloblastoma sample_MB-423


title: Primary medulloblastoma sample_MDT-MB-75 [SNP]


title: Primary medulloblastoma sample_MDT-MB-113 [SNP]


title: Primary medulloblastoma sample_MDT-MB-76 [SNP]


title: Primary medulloblastoma sample_MB-360


title: Primary medulloblastoma sample_MDT-MB-68 [SNP]


title: Primary medulloblastoma sample_MB-373


title: Primary medulloblastoma sample_MDT-MB-71 [SNP]


title: Primary medulloblastoma sample_MDT-MB-70 [SNP]


title: Primary medulloblastoma sample_MB-355


title: Primary medulloblastoma sample_MDT-MB-79 [SNP]


title: Primary medulloblastoma sample_MDT-MB-67 [SNP]


title: Primary medulloblastoma sample_MB-337


title: Primary medulloblastoma sample_MDT-MB-74 [SNP]


title: Primary medulloblastoma sample_MDT-MB-73 [SNP]


title: Primary medulloblastoma sample_MDT-MB-80 [SNP]


title: Primary medulloblastoma sample_MDT-MB-66 [SNP]


title: Primary medulloblastoma sample_MB-334


title: Primary medulloblastoma sample_MB-333


title: Primary medulloblastoma sample_MDT-MB-62 [SNP]


title: Primary medulloblastoma sample_MB-359


title: Primary medulloblastoma sample_MDT-MB-58 [SNP]


title: Primary medulloblastoma sample_MB-331


title: Primary medulloblastoma sample_MDT-MB-72 [SNP]


title: Primary medulloblastoma sample_MB-325


title: Primary medulloblastoma sample_MB-329


title: root_alaAT-ox 3/8_biological rep3

city: Edmonton

first: Perrin

middle: Hudson

last: Beatty

state: Alberta

address: G425 Biological Sciences

department: Biological Sciences

country: Canada

institute: University of Alberta

description: Transcriptome data from hydroponically grown rice plants, using 5 mM NH4+ as the nitrogen source

hyb_protocol: All biologically replicated RNA samples were labelled and hybridized in parallel using the protocol suggested by the manufacturer (Syngenta Biotechnology).

scan_protocol: cDNA target synthesis quality was assessed by examination of the 3' and 5' probesets of the reference gene controls on the Affymetrix genechip and scanned using GCOS software.

data_processing: dCHIP was used to normalize and model the data. The raw microarray signals were normalized using the invarient set normalization method. The model-based expression values were calculated using the fifth percentile, perfect match only model with outlier detection.

label: biotin

organism: Oryza sativa

source_name: transgenic Oryza sativa over-expressing HvAlaAT with the root-specific promoter OsANT1, 3/8 line, root tissue

growth_protocol: 5mM NH4+ as the nitrogen source, hydroponic growth, 28 degrees C, 70% relative humidity, 14 hr day length/10 hr night length, light intensity 750 uE.

extract_protocol:
Tissue samples were taken, weighed and flash frozen in liquid nitrogen until they were ground and the RNA extracted.
Total RNA was extracted using the TRI reagent protocol according to manufacturers instructions (Applied Biosystems). RNA samples were cleaned of phenol contamination using Rneasy plant mini kit.

tag: tissue

value: root


title: root_alaAT-ox 3/8_biological rep4

label_protocol: All biologically replicated RNA samples were labelled and hybridized in parallel using the protocol suggested by the manufacturer (Syngenta Biotechnology).


title: Primary medulloblastoma sample_MDT-MB-56 [SNP]


title: Primary medulloblastoma sample_MDT-MB-63 [SNP]


title: Primary medulloblastoma sample_MB-182


title: Primary medulloblastoma sample_MDT-MB-55 [SNP]


title: Primary medulloblastoma sample_MB-205


title: root_alaAT-ox 3/8_biological rep1


title: Primary medulloblastoma sample_MB-152


title: Primary medulloblastoma sample_MB-167


title: root_alaAT-ox 1/8_biological rep4

source_name: transgenic Oryza sativa over-expressing HvAlaAT with the root-specific promoter OsANT1, 1/8 line, root tissue


title: Primary medulloblastoma sample_MB-151


title: Primary medulloblastoma sample_MB-146


title: Primary medulloblastoma sample_MDT-MB-54 [SNP]


title: Primary medulloblastoma sample_MB-100


title: Primary medulloblastoma sample_MDT-MB-45 [SNP]


title: Primary medulloblastoma sample_MB-1374


title: root_alaAT-ox 1/8_biological rep3


title: Primary medulloblastoma sample_MDT-MB-53 [SNP]


title: root_alaAT-ox 1/8_biological rep2


title: Primary medulloblastoma sample_MDT-MB-50 [SNP]


title: Primary medulloblastoma sample_MB-26


title: Primary medulloblastoma sample_MB-1360


title: Primary medulloblastoma sample_MB-1264


title: root_alaAT-ox 3/8_biological rep2


title: root_alaAT-ox 1/7_biological rep4

source_name: transgenic Oryza sativa over-expressing HvAlaAT with the root-specific promoter OsANT1, 1/7 line, root tissue


title: Primary medulloblastoma sample_MDT-MB-52 [SNP]


title: Primary medulloblastoma sample_MB-1236


title: root_alaAT-ox 1/8_biological rep1


title: Primary medulloblastoma sample_MDT-MB-46 [SNP]


title: Primary medulloblastoma sample_MDT-MB-49 [SNP]


title: Primary medulloblastoma sample_MB-1218


title: root_alaAT-ox 1/7_biological rep3


title: Primary medulloblastoma sample_MB-1185


title: Primary medulloblastoma sample_MDT-MB-43 [SNP]


title: Primary medulloblastoma sample_MB-1133


title: root_alaAT-ox 1/7_biological rep1


title: root_alaAT-ox 1/7_biological rep2


title: Primary medulloblastoma sample_MB-1113


title: root_wildtype NB_biological rep4

source_name: Wildtype Oryza sativa cv. Nipponbare, root tissue


title: Primary medulloblastoma sample_MB-1106


title: root_wildtype NB_biological rep3


title: Primary medulloblastoma sample_MDT-MB-41 [SNP]


title: Primary medulloblastoma sample_MDT-MB-42 [SNP]


title: Primary medulloblastoma sample_MB-749


title: root_wildtype NB_biological rep1


title: Primary medulloblastoma sample_MB-732


title: Primary medulloblastoma sample_MB-707


title: Primary medulloblastoma sample_MB-817


title: root_wildtype NB_biological rep2


title: Primary medulloblastoma sample_MDT-MB-39 [SNP]


title: Primary medulloblastoma sample_MB-606


title: shoot_alaAT-ox 3/8_biological rep4

source_name: transgenic Oryza sativa over-expressing HvAlaAT with the root-specific promoter OsANT1, 3/8 line, shoot tissue

value: shoot


title: Primary medulloblastoma sample_MDT-MB-38 [SNP]


title: Primary medulloblastoma sample_MDT-MB-36 [SNP]


title: Primary medulloblastoma sample_MB-1211


title: Primary medulloblastoma sample_MB-592


title: Primary medulloblastoma sample_MB-599


title: Primary medulloblastoma sample_MB-593


title: Primary medulloblastoma sample_MDT-MB-37 [SNP]


title: Primary medulloblastoma sample_MDT-MB-40 [SNP]


title: Primary medulloblastoma sample_MDT-MB-44 [SNP]


title: Primary medulloblastoma sample_MDT-MB-57 [SNP]


title: Primary medulloblastoma sample_MDT-MB-35 [SNP]


title: Primary medulloblastoma sample_MDT-MB-34 [SNP]


title: Primary medulloblastoma sample_MB-526


title: Primary medulloblastoma sample_MB-541


title: Primary medulloblastoma sample_MB-545


title: Primary medulloblastoma sample_MB-460


title: Primary medulloblastoma sample_MDT-MB-47 [SNP]


title: Primary medulloblastoma sample_MDT-MB-28 [SNP]


title: shoot_alaAT-ox 1/8_biological rep4

source_name: transgenic Oryza sativa over-expressing HvAlaAT with the root-specific promoter OsANT1, 1/8 line, shoot tissue


title: Primary medulloblastoma sample_MB-375


title: shoot_alaAT-ox 1/8_biological rep3


title: Primary medulloblastoma sample_MB-438


title: Primary medulloblastoma sample_MB-332


title: Primary medulloblastoma sample_MDT-MB-29 [SNP]


title: shoot_alaAT-ox 3/8_biological rep1


title: shoot_alaAT-ox 1/8_biological rep2


title: shoot_alaAT-ox 3/8_biological rep3


title: shoot_alaAT-ox 1/7_biological rep4

source_name: transgenic Oryza sativa over-expressing HvAlaAT with the root-specific promoter OsANT1, 1/7 line, shoot tissue


title: Primary medulloblastoma sample_MDT-MB-30 [SNP]


title: Primary medulloblastoma sample_MDT-MB-24 [SNP]


title: Primary medulloblastoma sample_MDT-MB-21 [SNP]


title: Primary medulloblastoma sample_MB-224


title: Primary medulloblastoma sample_MDT-MB-26 [SNP]


title: shoot_alaAT-ox 3/8_biological rep2


title: Primary medulloblastoma sample_MB-184


title: Primary medulloblastoma sample_MB-158


title: Primary medulloblastoma sample_MB-165


title: Primary medulloblastoma sample_MDT-MB-23 [SNP]


title: Primary medulloblastoma sample_MDT-MB-25 [SNP]


title: shoot_alaAT-ox 1/7_biological rep2


title: Primary medulloblastoma sample_MB-118


title: shoot_alaAT-ox 1/7_biological rep1


title: shoot_wildtype NB_biological rep4

source_name: Wildtype Oryza sativa cv. Nipponbare, shoot tissue


title: Primary medulloblastoma sample_MDT-MB-22 [SNP]


title: Primary medulloblastoma sample_MB-138


title: Primary medulloblastoma sample_MDT-MB-20 [SNP]


title: Primary medulloblastoma sample_MB-198


title: shoot_alaAT-ox 1/8_biological rep1


title: Primary medulloblastoma sample_MB-428


title: shoot_wildtype NB_biological rep3


title: Primary medulloblastoma sample_MDT-MB-15 [SNP]


title: Primary medulloblastoma sample_MB-110


title: shoot_alaAT-ox 1/7_biological rep3


title: Primary medulloblastoma sample_MB-107


title: Primary medulloblastoma sample_MDT-MB-16 [SNP]


title: shoot_wildtype NB_biological rep2


title: Primary medulloblastoma sample_MDT-MB-18 [SNP]


title: Primary medulloblastoma sample_MDT-MB-11 [SNP]


title: Primary medulloblastoma sample_MB-108


title: Primary medulloblastoma sample_MB-14


title: LK-wildtype-3

city: Melbourne

first: Chris

last: Slape

address: 99 Commercial Rd

department: ACBD

country: Australia

institute: Monash University

description: Pool of bone marrow from 3 3-month old wild type mice

hyb_protocol: Illumina Mouse WG-6 v2.0 beadchip

scan_protocol: Illumina iScan

data_processing: GeneSpring v11.5.1 [quantile_bkgd]

organism: Mus musculus

source_name: LK-Sorted primary bone marrow

label_protocol: RNA was reverse transcribed using a T7-promoter-oligo(dT) primer. An in vitro transcription reaction with biotin labeled nucleotides was then performed.

extract_protocol: Total RNA was isolated from FACS-sorted LK cells from the pooled BM from three mice of each genotype using the Trizol method

value: 3 months old

tag: genotype/variation

value: wild type

value: Lineage negative Kit positive (LK) cells


title: LK-transgenic-3

description: Pool of bone marrow from 3 3-month old NHD13 mice

value: NHD13 transgenic


title: Tet2KD_C10_24h_2

city: Barcelona

first: Eric

middle: M.

last: Kallin

state: Barcelona

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

country: Spain

institute: Center for Genomic Regulation

description:
Gene expression in 24 hour induced C10 cells expressing shRNA targeting Tet2 mRNA
No primary cells were used in this study - only derivatives of an established cell line called HAFTL

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and1  min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 110%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples. Data were normalized using the limma package in Bioconductor version 2.8.

source_name: C10 Tet2 knockdown cells, 24hour induced, rep2

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany).

growth_protocol: C10 cells were maintained in RPMI media supplemented with 10% FBS, 20mM L-glutamine, 20μM 2-mercaptoethanol & 1μg/ml puromycin.

extract_protocol: RNA was prepared using RNeasy spin columns (Qiagen catalogue number 74104) 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: Induction was carried out in the growth media supplemented with 100 nM bEstradiol, 10 ng/ml IL-3 and 10 ng/ml M-CSF.

tag: induction time (hours)

tag: shRNA

tag: cell line origin

value: HAFTL


title: Tet2KD_C10_0h_1

description:
Gene expression in uninduced C10 cells expressing shRNA targeting Tet2 mRNA
No primary cells were used in this study - only derivatives of an established cell line called HAFTL

source_name: C10 Tet2 knockdown cells, uninduced, rep1


title: Primary medulloblastoma sample_MB-16

value: F

value: SHH


title: Tet2KD_C10_24h_1

source_name: C10 Tet2 knockdown cells, 24hour induced, rep1


title: LK-transgenic-2


title: Primary medulloblastoma sample_MB-105


title: Tet2KD_C10_0h_2

source_name: C10 Tet2 knockdown cells, uninduced, rep2


title: Primary medulloblastoma sample_MDT-MB-31 [SNP]

value: Primary medulloblastoma


title: Primary medulloblastoma sample_MB-7

value: M


title: Primary medulloblastoma sample_MDT-MB-9 [SNP]

value: Classic

value: Group 4


title: Primary medulloblastoma sample_MDT-MB-10 [SNP]


title: shoot_wildtype NB_biological rep1


title: LK-wildtype-2


title: Primary medulloblastoma sample_MDT-MB-8 [SNP]

value: Large Cell/Anaplastic

value: Group 3


title: Control_C10_24h_2

description:
Gene expression in 24 hour induced C10 cells expressing a control shRNA
No primary cells were used in this study - only derivatives of an established cell line called HAFTL

source_name: C10 control cells, 24hour induced, rep2

value: Control


title: BH14_MC_rep3 vs BH14_Control_rep3

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

hyb_protocol: Labeled products were pooled and served as a final Master Mix for the array, The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybridization master for a given source and biological replicate.

scan_protocol: Axon GenePix 4200 Professional, 5 micron resolution.

data_processing: Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.

organism: Daphnia pulex

label_protocol: cDNA labeling using 1 O.D. Cy-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA.

growth_protocol: 24 hour juveniles were isolated from synchronized cultures of brood mothers. Mothers were fed a control diet of the non toxic green algae at an optimal diet ratio under constat light and temperature conditions

extract_protocol: Tissue was homogenized using Trizol reagent (Invitrogen), and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

treatment_protocol: Animals were exposed for 16 days to a control diet or a diet containing 50% of the toxic Microcystis aeruginosa. Animals were fed daily and experimental jars were changed out three times a week. After 16 days RNA was extracted.

tag: Sex

value: female

tag: developmental stage

value: adult

value: whole body


title: LK-wildtype-1

value: 3 months old


title: Primary medulloblastoma sample_MDT-MB-13 [SNP]

value: Desmoplastic


title: Control_C10_0h_1

description:
Gene expression in uninduced C10 cells expressing a control shRNA
No primary cells were used in this study - only derivatives of an established cell line called HAFTL

source_name: C10 control cells, uninduced, rep1


title: UCSD CLL patient #129

status: Public on Jul 26 2012

city: La Jolla

first: andrew

last: greaves

state: ca

address: 3855 Health Sciences Dr

department: Cancer Center

country: USA

institute: UCSD

description: Gene expression data from UCSD CLL patient #129

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133plus2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GCRMA using Affymetrix default analysis settings and quantile normalization as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: UCSD CLL patient #129

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression AnalysisTechnical Manual, 2001, Affymetrix).

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

value: PBMC

tag: sampling time to first treatment (years)

tag: treatment event (1


title: Control_C10_24h_1

source_name: C10 control cells, 24hour induced, rep1


title: UCSD CLL patient #130

description: Gene expression data from UCSD CLL patient #130

source_name: UCSD CLL patient #130


title: Control_C10_0h_2

source_name: C10 control cells, uninduced, rep2


title: UCSD CLL patient #128

description: Gene expression data from UCSD CLL patient #128

source_name: UCSD CLL patient #128


title: Primary medulloblastoma sample_MDT-MB-14 [SNP]

source_name: Primary medulloblastoma


title: LK-transgenic-1

value: NHD13 transgenic

value: Lineage negative Kit positive (LK) cells


title: TaxN

city: Xinxiang

first: Hui

last: Wang

state: Henan Province

address: eastern section of Jinsui road

department: Research Center for Immunology

country: China

institute: Xinxiang Medical University

hyb_protocol: standard Phalanx protocol (See http://www.phalanxbiotech.com/)

data_processing: The data were analyzed by GenePix Pro 6.0

source_name: Stably transfected Jurkat_pCMV-control

growth_protocol: These cells were maintained in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum, glutamine, G418 and antibiotics at 37 °C in 5% CO2.

extract_protocol: Total RNA from the TaxN cell was isolated using the Trizol (Invitrogen life technologies) according to the supplier's protocols.

treatment_protocol: Jurkat cells were transfected with pCMV-Bam plasmids, and selected by G418. cells stably integrated pCMV-Bam were selected and maintained in the presence of G418.

tag: cell line

value: Jurkat (CD4 T cell)

tag: treatment

value: stably integrated with pCMV


title: TaxP

scan_protocol: standard Phalanx protocol (See http://www.phalanxbiotech.com/)

source_name: Stably transfected Jurkat_pCMV-Tax

extract_protocol: Total RNA from the TaxP cell was isolated using the Trizol (Invitrogen life technologies) according to the supplier's protocols.

treatment_protocol: Jurkat cells were transfected with pCMV-Bam-Tax plasmids, and selected by G418. cells stably expresse Tax were selected and maintained in the presence of G418.

value: stably integrated with pCMV-Tax


title: BH14_MC_rep2 vs BH14_Control_rep2


title: UCSD CLL patient #126

description: Gene expression data from UCSD CLL patient #126

source_name: UCSD CLL patient #126

tag: cell type


title: UCSD CLL patient #125

description: Gene expression data from UCSD CLL patient #125

source_name: UCSD CLL patient #125


title: UCSD CLL patient #123

description: Gene expression data from UCSD CLL patient #123

source_name: UCSD CLL patient #123


title: UCSD CLL patient #124

description: Gene expression data from UCSD CLL patient #124

source_name: UCSD CLL patient #124


title: BH14_Control_rep1 vs BH14_MC_rep1


title: BH14_Control_rep4 vs BH14_MC_rep4


title: UCSD CLL patient #117

description: Gene expression data from UCSD CLL patient #117

source_name: UCSD CLL patient #117


title: UCSD CLL patient #114

description: Gene expression data from UCSD CLL patient #114

source_name: UCSD CLL patient #114


title: Primary medulloblastoma sample_MDT-MB-7 [SNP]

value: Primary medulloblastoma

tag: age

value: M

value: SHH


title: UCSD CLL patient #118

description: Gene expression data from UCSD CLL patient #118

source_name: UCSD CLL patient #118


title: UCSD CLL patient #111

description: Gene expression data from UCSD CLL patient #111

source_name: UCSD CLL patient #111


title: UCSD CLL patient #116

description: Gene expression data from UCSD CLL patient #116

source_name: UCSD CLL patient #116


title: Primary medulloblastoma sample_MDT-MB-4 [SNP]

tag: gender

value: F

value: Classic

value: Group 4


title: UCSD CLL patient #105

description: Gene expression data from UCSD CLL patient #105

source_name: UCSD CLL patient #105


title: UCSD CLL patient #101

description: Gene expression data from UCSD CLL patient #101

source_name: UCSD CLL patient #101


title: UCSD CLL patient #104

description: Gene expression data from UCSD CLL patient #104

source_name: UCSD CLL patient #104


title: UCSD CLL patient #112

description: Gene expression data from UCSD CLL patient #112

source_name: UCSD CLL patient #112


title: UCSD CLL patient #102

description: Gene expression data from UCSD CLL patient #102

source_name: UCSD CLL patient #102


title: Primary medulloblastoma sample_MDT-MB-6 [SNP]

source_name: Primary medulloblastoma

tag: histological subtype


title: UCSD CLL patient #100

description: Gene expression data from UCSD CLL patient #100

source_name: UCSD CLL patient #100


title: UCSD CLL patient #120

description: Gene expression data from UCSD CLL patient #120

source_name: UCSD CLL patient #120


title: UCSD CLL patient #110

description: Gene expression data from UCSD CLL patient #110

source_name: UCSD CLL patient #110


title: UCSD CLL patient #109

description: Gene expression data from UCSD CLL patient #109

source_name: UCSD CLL patient #109


title: UCSD CLL patient #121

description: Gene expression data from UCSD CLL patient #121

source_name: UCSD CLL patient #121


title: UCSD CLL patient #106

description: Gene expression data from UCSD CLL patient #106

source_name: UCSD CLL patient #106


title: UCSD CLL patient #107

description: Gene expression data from UCSD CLL patient #107

source_name: UCSD CLL patient #107


title: UCSD CLL patient #119

description: Gene expression data from UCSD CLL patient #119

source_name: UCSD CLL patient #119


title: UCSD CLL patient #127

description: Gene expression data from UCSD CLL patient #127

source_name: UCSD CLL patient #127


title: UCSD CLL patient #115

description: Gene expression data from UCSD CLL patient #115

source_name: UCSD CLL patient #115


title: UCSD CLL patient #113

description: Gene expression data from UCSD CLL patient #113

source_name: UCSD CLL patient #113


title: UCSD CLL patient #99

description: Gene expression data from UCSD CLL patient #99

source_name: UCSD CLL patient #99


title: UCSD CLL patient #103

description: Gene expression data from UCSD CLL patient #103

source_name: UCSD CLL patient #103


title: Primary medulloblastoma sample_MDT-MB-5 [SNP]

tag: subgroup


title: UCSD CLL patient #122

description: Gene expression data from UCSD CLL patient #122

source_name: UCSD CLL patient #122


title: Primary medulloblastoma sample_MDT-MB-1 [SNP]


title: UCSD CLL patient #108

description: Gene expression data from UCSD CLL patient #108

source_name: UCSD CLL patient #108


title: Primary medulloblastoma sample_MDT-MB-2 [SNP]

value: Group 3


title: UCSD CLL patient #98

description: Gene expression data from UCSD CLL patient #98

source_name: UCSD CLL patient #98


title: UCSD CLL patient #96

description: Gene expression data from UCSD CLL patient #96

source_name: UCSD CLL patient #96


title: UCSD CLL patient #97

description: Gene expression data from UCSD CLL patient #97

source_name: UCSD CLL patient #97


title: UCSD CLL patient #93

description: Gene expression data from UCSD CLL patient #93

source_name: UCSD CLL patient #93


title: UCSD CLL patient #94

description: Gene expression data from UCSD CLL patient #94

source_name: UCSD CLL patient #94


title: UCSD CLL patient #95

description: Gene expression data from UCSD CLL patient #95

source_name: UCSD CLL patient #95


title: UCSD CLL patient #90

description: Gene expression data from UCSD CLL patient #90

source_name: UCSD CLL patient #90


title: UCSD CLL patient #92

description: Gene expression data from UCSD CLL patient #92

source_name: UCSD CLL patient #92


title: UCSD CLL patient #89

description: Gene expression data from UCSD CLL patient #89

source_name: UCSD CLL patient #89


title: UCSD CLL patient #88

description: Gene expression data from UCSD CLL patient #88

source_name: UCSD CLL patient #88


title: UCSD CLL patient #80

description: Gene expression data from UCSD CLL patient #80

source_name: UCSD CLL patient #80


title: UCSD CLL patient #85

description: Gene expression data from UCSD CLL patient #85

source_name: UCSD CLL patient #85


title: UCSD CLL patient #91

description: Gene expression data from UCSD CLL patient #91

source_name: UCSD CLL patient #91


title: Primary medulloblastoma sample_MDT-MB-3 [SNP]

source_name: Primary medulloblastoma


title: UCSD CLL patient #79

description: Gene expression data from UCSD CLL patient #79

source_name: UCSD CLL patient #79


title: UCSD CLL patient #86

description: Gene expression data from UCSD CLL patient #86

source_name: UCSD CLL patient #86


title: UCSD CLL patient #78

description: Gene expression data from UCSD CLL patient #78

source_name: UCSD CLL patient #78


title: UCSD CLL patient #74

description: Gene expression data from UCSD CLL patient #74

source_name: UCSD CLL patient #74


title: UCSD CLL patient #84

description: Gene expression data from UCSD CLL patient #84

source_name: UCSD CLL patient #84


title: UCSD CLL patient #82

description: Gene expression data from UCSD CLL patient #82

source_name: UCSD CLL patient #82


title: UCSD CLL patient #76

description: Gene expression data from UCSD CLL patient #76

source_name: UCSD CLL patient #76


title: UCSD CLL patient #72

description: Gene expression data from UCSD CLL patient #72

source_name: UCSD CLL patient #72


title: UCSD CLL patient #87

description: Gene expression data from UCSD CLL patient #87

source_name: UCSD CLL patient #87


title: UCSD CLL patient #71

description: Gene expression data from UCSD CLL patient #71

source_name: UCSD CLL patient #71


title: UCSD CLL patient #81

description: Gene expression data from UCSD CLL patient #81

source_name: UCSD CLL patient #81


title: UCSD CLL patient #69

description: Gene expression data from UCSD CLL patient #69

source_name: UCSD CLL patient #69


title: UCSD CLL patient #73

description: Gene expression data from UCSD CLL patient #73

source_name: UCSD CLL patient #73


title: UCSD CLL patient #77

description: Gene expression data from UCSD CLL patient #77

source_name: UCSD CLL patient #77


title: UCSD CLL patient #68

description: Gene expression data from UCSD CLL patient #68

source_name: UCSD CLL patient #68


title: UCSD CLL patient #75

description: Gene expression data from UCSD CLL patient #75

source_name: UCSD CLL patient #75


title: UCSD CLL patient #83

description: Gene expression data from UCSD CLL patient #83

source_name: UCSD CLL patient #83


title: UCSD CLL patient #66

description: Gene expression data from UCSD CLL patient #66

source_name: UCSD CLL patient #66


title: UCSD CLL patient #67

description: Gene expression data from UCSD CLL patient #67

source_name: UCSD CLL patient #67


title: UCSD CLL patient #65

description: Gene expression data from UCSD CLL patient #65

source_name: UCSD CLL patient #65


title: UCSD CLL patient #70

description: Gene expression data from UCSD CLL patient #70

source_name: UCSD CLL patient #70


title: UCSD CLL patient #62

description: Gene expression data from UCSD CLL patient #62

source_name: UCSD CLL patient #62


title: UCSD CLL patient #64

description: Gene expression data from UCSD CLL patient #64

source_name: UCSD CLL patient #64


title: UCSD CLL patient #61

description: Gene expression data from UCSD CLL patient #61

source_name: UCSD CLL patient #61


title: UCSD CLL patient #60

description: Gene expression data from UCSD CLL patient #60

source_name: UCSD CLL patient #60


title: UCSD CLL patient #55

description: Gene expression data from UCSD CLL patient #55

source_name: UCSD CLL patient #55


title: UCSD CLL patient #50

description: Gene expression data from UCSD CLL patient #50

source_name: UCSD CLL patient #50


title: UCSD CLL patient #63

description: Gene expression data from UCSD CLL patient #63

source_name: UCSD CLL patient #63


title: UCSD CLL patient #45

description: Gene expression data from UCSD CLL patient #45

source_name: UCSD CLL patient #45


title: UCSD CLL patient #48

description: Gene expression data from UCSD CLL patient #48

source_name: UCSD CLL patient #48


title: UCSD CLL patient #42

description: Gene expression data from UCSD CLL patient #42

source_name: UCSD CLL patient #42


title: UCSD CLL patient #43

description: Gene expression data from UCSD CLL patient #43

source_name: UCSD CLL patient #43


title: UCSD CLL patient #53

description: Gene expression data from UCSD CLL patient #53

source_name: UCSD CLL patient #53


title: UCSD CLL patient #58

description: Gene expression data from UCSD CLL patient #58

source_name: UCSD CLL patient #58


title: UCSD CLL patient #39

description: Gene expression data from UCSD CLL patient #39

source_name: UCSD CLL patient #39


title: UCSD CLL patient #44

description: Gene expression data from UCSD CLL patient #44

source_name: UCSD CLL patient #44


title: UCSD CLL patient #49

description: Gene expression data from UCSD CLL patient #49

source_name: UCSD CLL patient #49


title: UCSD CLL patient #54

description: Gene expression data from UCSD CLL patient #54

source_name: UCSD CLL patient #54


title: UCSD CLL patient #41

description: Gene expression data from UCSD CLL patient #41

source_name: UCSD CLL patient #41


title: UCSD CLL patient #40

description: Gene expression data from UCSD CLL patient #40

source_name: UCSD CLL patient #40


title: UCSD CLL patient #59

description: Gene expression data from UCSD CLL patient #59

source_name: UCSD CLL patient #59


title: UCSD CLL patient #36

description: Gene expression data from UCSD CLL patient #36

source_name: UCSD CLL patient #36


title: UCSD CLL patient #51

description: Gene expression data from UCSD CLL patient #51

source_name: UCSD CLL patient #51


title: UCSD CLL patient #35

description: Gene expression data from UCSD CLL patient #35

source_name: UCSD CLL patient #35


title: UCSD CLL patient #32

description: Gene expression data from UCSD CLL patient #32

source_name: UCSD CLL patient #32


title: UCSD CLL patient #46

description: Gene expression data from UCSD CLL patient #46

source_name: UCSD CLL patient #46


title: UCSD CLL patient #38

description: Gene expression data from UCSD CLL patient #38

source_name: UCSD CLL patient #38


title: UCSD CLL patient #33

description: Gene expression data from UCSD CLL patient #33

source_name: UCSD CLL patient #33


title: UCSD CLL patient #56

description: Gene expression data from UCSD CLL patient #56

source_name: UCSD CLL patient #56


title: UCSD CLL patient #37

description: Gene expression data from UCSD CLL patient #37

source_name: UCSD CLL patient #37


title: UCSD CLL patient #31

description: Gene expression data from UCSD CLL patient #31

source_name: UCSD CLL patient #31


title: UCSD CLL patient #30

description: Gene expression data from UCSD CLL patient #30

source_name: UCSD CLL patient #30


title: UCSD CLL patient #47

description: Gene expression data from UCSD CLL patient #47

source_name: UCSD CLL patient #47


title: UCSD CLL patient #52

description: Gene expression data from UCSD CLL patient #52

source_name: UCSD CLL patient #52


title: UCSD CLL patient #27

description: Gene expression data from UCSD CLL patient #27

source_name: UCSD CLL patient #27


title: UCSD CLL patient #28

description: Gene expression data from UCSD CLL patient #28

source_name: UCSD CLL patient #28


title: UCSD CLL patient #29

description: Gene expression data from UCSD CLL patient #29

source_name: UCSD CLL patient #29


title: UCSD CLL patient #26

description: Gene expression data from UCSD CLL patient #26

source_name: UCSD CLL patient #26


title: UCSD CLL patient #20

description: Gene expression data from UCSD CLL patient #20

source_name: UCSD CLL patient #20


title: UCSD CLL patient #25

description: Gene expression data from UCSD CLL patient #25

source_name: UCSD CLL patient #25


title: UCSD CLL patient #23

description: Gene expression data from UCSD CLL patient #23

source_name: UCSD CLL patient #23


title: UCSD CLL patient #19

description: Gene expression data from UCSD CLL patient #19

source_name: UCSD CLL patient #19


title: UCSD CLL patient #16

description: Gene expression data from UCSD CLL patient #16

source_name: UCSD CLL patient #16


title: UCSD CLL patient #18

description: Gene expression data from UCSD CLL patient #18

source_name: UCSD CLL patient #18


title: UCSD CLL patient #21

description: Gene expression data from UCSD CLL patient #21

source_name: UCSD CLL patient #21


title: UCSD CLL patient #24

description: Gene expression data from UCSD CLL patient #24

source_name: UCSD CLL patient #24


title: UCSD CLL patient #22

description: Gene expression data from UCSD CLL patient #22

source_name: UCSD CLL patient #22


title: UCSD CLL patient #17

description: Gene expression data from UCSD CLL patient #17

source_name: UCSD CLL patient #17


title: UCSD CLL patient #12

description: Gene expression data from UCSD CLL patient #12

source_name: UCSD CLL patient #12


title: UCSD CLL patient #11

description: Gene expression data from UCSD CLL patient #11

source_name: UCSD CLL patient #11


title: UCSD CLL patient #14

description: Gene expression data from UCSD CLL patient #14

source_name: UCSD CLL patient #14


title: UCSD CLL patient #15

description: Gene expression data from UCSD CLL patient #15

source_name: UCSD CLL patient #15


title: UCSD CLL patient #10

description: Gene expression data from UCSD CLL patient #10

source_name: UCSD CLL patient #10


title: UCSD CLL patient #5

description: Gene expression data from UCSD CLL patient #5

source_name: UCSD CLL patient #5


title: UCSD CLL patient #8

description: Gene expression data from UCSD CLL patient #8

source_name: UCSD CLL patient #8


title: UCSD CLL patient #13

description: Gene expression data from UCSD CLL patient #13

source_name: UCSD CLL patient #13


title: UCSD CLL patient #7

description: Gene expression data from UCSD CLL patient #7

source_name: UCSD CLL patient #7


title: UCSD CLL patient #9

description: Gene expression data from UCSD CLL patient #9

source_name: UCSD CLL patient #9


title: UCSD CLL patient #4

description: Gene expression data from UCSD CLL patient #4

source_name: UCSD CLL patient #4


title: 1005-00009_LS

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

hyb_protocol: Following fragmentation, 11 microg of cRNA were hybridized for 16 hr at 45oC on a GeneChip HG U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data was normalized by GCRMA.

source_name: skin biopsy, LS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

treatment_protocol: For each patient, one 4-mm skin punch biopsy was collected from a lesion located on the trunk or extremities, with approximately 0.5 mm or more of induration and approximately 5 mm from the edge of the plaque, and another from a macroscopically normal non-lesion on a similar body area to the biopsy plaque (i.e. arm, arm or leg, leg).  Biopsies were kept frozen at -80oC until RNA preparation.

tag: subject

tag: disease state

value: moderate-to-severe psoriasis

value: skin

tag: biopsy type

value: psoriasis lesion (LS)


title: 1022-00006_NL

source_name: skin biopsy, NL

tag: tissue

value: non-lesion (NL)


title: 1022-00006_LS


title: UCSD CLL patient #3

description: Gene expression data from UCSD CLL patient #3

source_name: UCSD CLL patient #3

value: PBMC


title: UCSD CLL patient #57

description: Gene expression data from UCSD CLL patient #57

source_name: UCSD CLL patient #57


title: UCSD CLL patient #6

description: Gene expression data from UCSD CLL patient #6

source_name: UCSD CLL patient #6


title: 1016-00010_LS


title: UCSD CLL patient #1

description: Gene expression data from UCSD CLL patient #1

source_name: UCSD CLL patient #1


title: UCSD CLL patient #2

description: Gene expression data from UCSD CLL patient #2

source_name: UCSD CLL patient #2


title: 1022-00008_NL


title: 2016-00037_LS


title: 1019-00014_LS


title: 2016-00037_NL


title: 1022-00008_LS


title: 1016-00010_NL


title: 1019-00005_NL


title: 1019-00005_LS


title: 1019-00014_NL


title: MLN CD103+ DC from Cre+ mice 2

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

description: RMA expression values derived from GeneSpring software; gene-level analysis

hyb_protocol: Samples were hybridized with Affymetrix Mouse Exon 1.0 ST Arrays and scanned at the U of A Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed at the gene-level with the GeneSpring (Agilent) software package using default data workflow, normalized to control samples (from Cre- mice)

source_name: Pooled from four Cre+ mice

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Splenic CD11c+ Dc were isolated by magetic cell sorting. MLN CD11c+CD103+ DC were flow sorted

extract_protocol: RNA was isolated using RNAqueous®-Micro kit (Ambion), according to the manufacturer’s instructions.

treatment_protocol: Cell were not treated but used immediately for RNA isolation

tag: genetic background

value: mesenteric lymph node CD103+ DC from Cre- mice

tag: cell phenotype

tag: genotype

value: Cre+ TGFBR2 deletion


title: 1005-00009_NL


title: MLN CD103+ DC from Cre- mice 2

source_name: Pooled from four Cre- healthy mice

value: Cre- control


title: MLN CD103+ DC from Cre+ mice 3


title: MLN CD103+ DC from Cre- mice 1


title: Splenic CD11c+ DC from Cre- mice 3

source_name: Cre- healthy mouse

value: Splenic CD11c+ DC from Cre- mice


title: MLN CD103+ DC from Cre- mice 3


title: Splenic CD11c+ DC from Cre+ mice 3

source_name: Cre+ mouse

value: Splenic CD11c+ DC from Cre+ mice


title: Splenic CD11c+ DC from Cre+ mice 1


title: Splenic CD11c+ DC from Cre- mice 1


title: Splenic CD11c+ DC from Cre- mice 2


title: MS miRNA subject-8

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

description: nCounter Human miRNA Expression Assay Kit detected miRNAs in sorted CD14+/CD16- blood-derived monocytes (miRNA transcriptomes per 100 ng total RNA)

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString.com) with 5 µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions.  For each assay, a high-density scan (600 fields of view) was performed

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using vsn normalization

source_name: CD14+CD16- monocytes

label_protocol: 100 ng of total RNA was used in 5 µl with specific miRNA tag probes from Nanostring using nCounter Human miRNA Expression Assay Kit

extract_protocol: Blood monocytes were sorted and total RNA was extracted using mirVana miRNA isolation kit (Ambion) according to the manufacturer’s protocol

value: CD14+CD16- monocytes

value: 67 years

tag: Sex

value: Male

value: multiple sclerosis

tag: ethnicity

value: Non-hispanic

tag: onset site

tag: fvc

tag: alsfrs


title: MS miRNA subject-7

tag: cell type

value: 51 years


title: UCSD CLL patient #34

description: Gene expression data from UCSD CLL patient #34

source_name: UCSD CLL patient #34

tag: sampling time to first treatment (years)

tag: treatment event (1


title: MS miRNA subject-6

tag: age

value: Female


title: Splenic CD11c+ DC from Cre+ mice 2


title: MS miRNA subject-4

value: 71 years


title: hippocampus at P7, Nex-Cre mediated CTCF deletion mutant, biological rep1

city: suita

first: teruyoshi

last: hirayama

state: osaka

address: 1-3 yamadaoka

department: graduate school of frontier biosciences

country: Japan

institute: osaka university

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The array data were analyzed using the Affymetrix GeneChip Expression Console and Partek Genomics Suite Version 6.4 (Partek). The Probeset intensities were normalized using the RMA algorithm.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: hippocampus_P7_Nex-Cre mediated CTCF deletion mutant

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mouse cerebral cortex and hippocampus from postnatal day 7

extract_protocol: Mouse cerebral cortex and hippocampus were removed as quickly as possible, then snap frozen in liquid N2 and genotyped. Total RNA was extracted using TRIzol (Invitrogen), then purified with an RNeasy mini column (Qiagen). Hybridization cocktail preparation and hybridization to the array were performed according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual.

tag: strain background

tag: genotype/variation

value: CTCF; Nex-Cre (fl/fl; +/Cre)

value: conditional knockout (cKO) of CTCF

tag: gender

value: male

value: postnatal day (P) 7

value: hippocampus


title: hippocampus at P7, biological rep3

value: CTCF; Nex-Cre (fl/fl; +/+)

value: control


title: hippocampus at P7, Nex-Cre mediated CTCF deletion mutant, biological rep2


title: MS miRNA subject-3

value: 68 years

tag: disease state


title: MS miRNA subject-2

value: 63 years


title: 1022-00018_NL

tag: subject

value: moderate-to-severe psoriasis

tag: tissue

value: skin

tag: biopsy type

value: non-lesion (NL)


title: hippocampus at P7, biological rep1


title: hippocampus at P7, biological rep2


title: 1016-00019_NL


title: hippocampus at P7, Nex-Cre mediated CTCF deletion mutant, biological rep3


title: 1016-00016_LS

value: psoriasis lesion (LS)


title: MS miRNA subject-1

value: CD14+CD16- monocytes

value: 61 years

value: Male

value: multiple sclerosis

value: Non-hispanic


title: 2016-00007_LS


title: cerebral cortex at P7, Nex-Cre mediated CTCF deletion mutant, biological rep3

source_name: cerebral cortex_P7_Nex-Cre mediated CTCF deletion mutant

value: CTCF; Nex-Cre (fl/fl; +/Cre)

value: conditional knockout (cKO) of CTCF

value: cerebral cortex


title: cerebral cortex at P7, biological rep2

source_name: cerebral cortex_P7

value: male

value: postnatal day (P) 7


title: MS miRNA subject-5

value: 49 years


title: 1016-00019_LS


title: sALS miRNA subject-6

value: 36 years

value: Female

value: Sporadic amyotrophic lateral sclerosis (SALS)

value: limb


title: cerebral cortex at P7, biological rep3

value: CTCF; Nex-Cre (fl/fl; +/+)

value: control


title: sALS miRNA subject-7

value: CD14+CD16- monocytes

value: 69 years


title: cerebral cortex at P7, Nex-Cre mediated CTCF deletion mutant, biological rep4


title: cerebral cortex at P7, biological rep4


title: cerebral cortex at P7, Nex-Cre mediated CTCF deletion mutant, biological rep2


title: cerebral cortex at P7, Nex-Cre mediated CTCF deletion mutant, biological rep1


title: 1016-00016_NL

value: moderate-to-severe psoriasis

value: skin

value: non-lesion (NL)


title: 1022-00019_NL


title: sALS miRNA subject-8

value: 61 years

value: Male

value: Non-hispanic


title: sALS miRNA subject-4

value: 42 years


title: sALS miRNA subject-5


title: cerebral cortex at P7, biological rep1

value: male

value: postnatal day (P) 7

value: cerebral cortex


title: sALS miRNA subject-3

value: 67 years

value: Female

value: both limbs


title: sALS miRNA subject-1

value: 59 years

value: Sporadic amyotrophic lateral sclerosis (SALS)

value: limb


title: HC miRNA subject-8

value: CD14+CD16- monocytes

value: healthy control


title: sALS miRNA subject-2

value: 78 years


title: Faah-/- Blastocyst rep1

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Faah-/- Blastocyst

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 8 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: Faah-/- Blastocyst

label_protocol: 2-round linear amplification was used with Agilent Low RNA Input Fluorescent Linear Amplification Kit. The procedure is described in detail in Sharov AA, Piao Y, Ko MS. Methods Enzymol. 2010;477:511-41. PMID:20699157

extract_protocol: About 50 blastocysts were collected and pooled together for RNA extraction and cDNA was generated as previously described by us. Total RNA from TS cells was extracted by Trizol reagents (Invitrogen). Quantitative PCR using the cDNA from the embryos or TS cells was performed as described in Robins JC, Heizer A, Hardiman A, Hubert M,Handwerger S (2007) Oxygen Tension Directs the Differentiation Pathway of Human Cytotrophoblast Cells. Placenta 28(11-12):1141-1146.

treatment_protocol: Female mice were mated with fertile males and checked for vaginal plug at 0900h to confirm successful mating (day 1 of pregnancy=vaginal plug). To collect embryos, mice were scarified at 1500h on day 4 of pregnancy. The blastocysts were snap frozen in  minimum volumes of  M2 medium in 1.5 ml tube and stored in -80C until RNA isolation. The four group of blastocyst/morula samples are collected from both uteri and oviduct from WT or KO mice respectively on day 4 of pregnancy. Blastocysts are separated from morula by visual identification. There is no more treatment before we freeze down the samples.

value: Faah-/-

tag: strain

tag: development stage

value: Blastocyst

tag: individual identifier

source_name: Universal Mouse Reference + 129ES Cell RNA

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

tag: sample type

value: reference


title: HC miRNA subject-7

value: 51 years

tag: Sex

value: Male

tag: ethnicity

value: Non-hispanic

tag: onset site

tag: fvc


title: HC miRNA subject-6

tag: cell type

tag: alsfrs


title: HC miRNA subject-4

tag: age

value: 71 years


title: Cnr1-/- Morula rep2

description: Cnr1-/- Morula

source_name: Cnr1-/- Morula

tag: genotype/variation

value: Morula


title: HC miRNA subject-5

value: 49 years


title: Cnr1-/- Morula rep1

description: Cnr1-/- Morula


title: Cnr1-/- Blastcyst rep2

description: Cnr1-/- Blastcyst

source_name: Cnr1-/- Blastcyst


title: Faah-/- Blastocyst rep2

description: Faah-/- Blastocyst


title: HC miRNA subject-3

value: 58 years


title: HC miRNA subject-2

value: 69 years

value: Female


title: Wild Type Blastcyst rep2

description: Wild Type Blastcyst

source_name: Wild Type Blastcyst

value: Wild Type


title: Cnr1-/- Blastcyst rep1

description: Cnr1-/- Blastcyst


title: HC miRNA subject-1

value: 48 years


title: Wild Type Blastcyst rep1

description: Wild Type Blastcyst


title: Patient 8_CL_CD8

city: Seattle

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

department: Medicine

institute: University of Washington

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using CubicSpline with background subtraction using Illumina Genome Studio (V2010.3)

source_name: CD8 cells laser captured from dermal-epidermal junction and dermal area from contra-lateral biopsy at 8 weeks post healed

label_protocol: cDNA were synthesized  using NuGEN pico kits from the extracted total RNA and biotinylated cDNA were prepared using a NuGEN labeling kit for Illumina arrays (Ref8_v3)

extract_protocol: RNA from laser captured cells was extracted with Arturus PicoPure RNA isolation kits in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: illumina chip bar code

value: dermal-epidermal junction skin

value: Laser captured CD8 cells


title: Patient 9_JC_CD8

source_name: CD8 cells laser captured from dermal-epidermal junction from 8 weeks post healed biopsy


title: Patient 5_arm_CD8

source_name: CD8 cells laser captured from dermal-epidermal junction and dermal area from arm biopsy at 8 weeks post healed


title: Patient 4_arm_CD8


title: Patient 8_JC_CD8


title: Patient 3_arm_CD8


title: Patient 9_CL_CD8


title: 2012-00034_LS

source_name: skin biopsy, LS

tag: disease state

value: moderate-to-severe psoriasis

value: skin

value: psoriasis lesion (LS)


title: 2012-00034_NL

source_name: skin biopsy, NL

tag: subject

value: non-lesion (NL)


title: Patient 7_JC_CD8

tag: tissue


title: Patient 7_CL_CD8


title: Patient 6_CL_CD8


title: Patient 5_CL_CD8


title: +/+ hippocampus 1

city: Martinsried

first: Stephan

last: Direnberger

address: Grosshaderner Str. 2

institute: Ludwig-Maximilians University

hyb_protocol: Following fragmentation, 15 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip MoGene-1.0-st-v1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner with GCOS 1.4.

data_processing: The data were analysed using Bioconductor package 'xps' under R-2.10.0. Background correction, normalization and probe summarization was performed with RMA for each tissue separately using the core transcript annotation.

source_name: hippocampus, transgenic

label_protocol: Biotinylated cDNA was prepared according to the Affymetrix Whole Transkript Sense Labelling protocol from100 ng total RNA according to the manufacturer

extract_protocol: RNA  was extracted by using RNeasy Midi Kit (Qiagen) following manufacturers instructions for animal tissues.

tag: genotype

value: transgenic

value: hippocampus


title: 1022-00026_LS

tag: biopsy type


title: +/+ hippocampus 3

tag: strain


title: wt hippocampus 2

source_name: hippocampus, wild type

value: wild type


title: wt hippocampus 3


title: +/+ heart 2

source_name: heart muscle, transgenic

value: heart muscle


title: 1022-00026_NL


title: +/+ heart 1


title: MLN CD103+ DC from Cre+ mice 1

source_name: Pooled from four Cre+ mice

tag: genetic background

value: mesenteric lymph node CD103+ DC from Cre- mice

tag: cell phenotype

value: Cre+ TGFBR2 deletion


title: +/+ heart 3


title: 1022-00014_NL


title: Patient 5_JC_CD8


title: Patient 4_JC_CD8


title: +/+ hippocampus 2


title: wt hippocampus 1


title: Patient 1_CL_CD8


title: 1022-00014_LS


title: Patient 3_JC_CD8


title: Patient 2_CL_CD8


title: Patient 4_CL_CD8


title: +/+ skeletal muscle 3

source_name: skeletal muscle, transgenic

value: skeletal muscle


title: wt heart 1

source_name: heart muscle, wild type


title: wt heart 3


title: Patient 2_JC_CD8


title: wt heart 2


title: Patient 6_JC_CD8


title: 1025-00006_LS


title: Patient 3_CL_CD8


title: 1025-00006_NL


title: wt skeletal muscle 2

source_name: skeletal muscle, wild type


title: Patient 1_JC_CD8


title: +/+ skeletal muscle 2


title: wt skeletal muscle 1


title: 1012-00006_NL


title: 1019-00004_LS


title: wt skeletal muscle 3


title: Positive_LPS_4

city: Bethesda

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

hyb_protocol: Labeled cRNA were hybridized to Affymetrix Rat Gene 1.0 ST Array (Affymetrix, Inc) in blinded interleaved fashion.  Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate probe-level measurements for each hybridized cRNA.

scan_protocol: Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.

data_processing: The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 29,215 RMA normalized gene fragment expression values for each hybridized cRNA.

organism: Rattus norvegicus

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Rat Gene 1.0 ST Array (Affymetrix, Inc).   300 ng of total RNA was used per samples and the arrays stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Briefly, 200ul chloroform was added to homogenized tissue and centrifuged for 15 min. Aqueous solution was transfered to a new Eppendorf tube and 100ul ETOH was added.  Solution was transfered to a Qiagen Column and underwent two centrifuge cycles. Liquid was discarded and 750ul RW1 buffer was added to the column and centrifuged for 10 min. Liquid was discarded and 500 ul RPE buffer was added and centrifuged for 10 min. The step was repeated twice.  Column was transfered to a fresh tube and centrifuged at max speed for 1 min. to remove excess liquid. 30ul DEPC-treated water was added and centrifuged 5 min. RNA was quantitated on a spectrophotometer (NanoDrop, Thermo Scientific, USA).

treatment_protocol: LPS (0.25mg/kg) or saline vehicle was administered to pregnant dams on gestation day 15. 4 h post injection pregnant dams were anesthetized and a midline incision was made into the peritoneal cavity to expose the embryos.  Embryos were removed and placed in cold PBS. Fetal brains were removed and placed in Eppendorf tubes filled with 1ml TRIzol reagent (Invitrogen, USA) and stored at -80 until processing.

value: Sprague-Dawley

value: gestation (embryonic) day 15

value: fetal brain

tag: class


title: 1016-00013_LS


title: Positive_LPS_3


title: +/+ skeletal muscle 1


title: Positive_LPS_9


title: Positive_LPS_1


title: Positive_LPS_2


title: HC-88

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

data_processing: Data were quantile normalized using Matlab software

label: biotin / SA-Cy3

source_name: PBMC

label_protocol: 300 ng of total RNA from each sample was labeled using the Illumina Total Prep RNA Amplification Kit following manufacturer's directions (Ambion)

extract_protocol: Total RNA was isolated from frozen PBMCs using QIAshredder columns for cell homogenization followed by use of the RNeasy Micro Kit.  DNA was eliminated through on-column DNase I treatment according to the manufacturer’s directions (Qiagen).

treatment_protocol: Whole blood was drawn into BD Vacutainer K2EDTA tubes. PBMCs were isolated over a Ficoll-paque Plus density gradient.  PBMCs were frozen in FBS and 10% DMSO and stored in liquid nitrogen.

tag: disease

value: healthy control

value: PBMC


title: Positive_LPS_7


title: Negative_LPS_10


title: HC-279


title: Positive_LPS_5


title: Positive_LPS_8


title: MDD-433

value: major depressive disorder


title: MDD-566


title: HC-569


title: BD1-568

value: bipolar disorder


title: Negative_LPS_8


title: Negative_LPS_6


title: HC-115


title: HC-204


title: Negative_LPS_9


title: Negative_LPS_5


title: MDD-402


title: Negative_LPS_7


title: 1025-00009_NL

value: moderate-to-severe psoriasis

value: skin


title: Negative_LPS_4


title: BD2-338


title: 1025-00009_LS

value: psoriasis lesion (LS)


title: Positive_LPS_6


title: Negative_LPS_1


title: MDD-573


title: MDD-407


title: HC-262


title: diX for DNA extraction

city: Beijing

first: Jing

last: Zhang

address: Room 224, Old Building of Life Sciences, No.5 Yiheyuan Road, Haidian District,

department: College of Life Sciences

institute: Peking University

description: DNA hybridazation to produce new CDF file.

hyb_protocol: A standard Affymetrix one-cycle Eukaryotic protocol  was employed as described in Affymetrix Technical Analysis Manual.15 ug randomly fragmented labelled cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Whole Genome Array. GeneChip arrays were then washed  and stained with Streptavidin Phycoerythrin (SAPE) solution.

scan_protocol: GeneChip arrays were scanned with a G2500A GeneArray Scanner (Affymetrix).

data_processing: Custom CDF files were generated from gDNA hybridization at intensity thresholds increasing stepwise from 20 to 300 by using a parser written in Perl and the optimal gDNA hybridization intensity threshold (80) was determined empirically and corresponding CDF file was applied for further analysis. Data were further normalized by Invariant Set Normalization method with dChip.

organism: Populus tomentosa

source_name: differentiating xylem from two trees

label_protocol: Biotinylated cRNA were obtained  with a GeneChip IVT Labeling Kit (Affymetrix) while biotinylated DNA was generated by the Bioprime DNA labelling System (Invitrogen).

growth_protocol: Four-year-old single clonal plantation of healthy Populus tomentosa trees were grown in Renqiu, Hebei province in northern China (38° 50´N, 116°10´E).

extract_protocol: Total RNA was extracted with TRIzol Reagent from cryo-sections. Linear acrylamide (LPA, 0.5 mg/ml) was added as a carrier to aid RNA precipitation. Extracted total RNA was then purified with RNeasy Micro columns (QIAGEN).Genomic DNA was isolated with a modified CTAB method.

treatment_protocol: Populus trees were girdled in early June, a 1.2-m strip of bark was peeled from trees and exposed tissue was wrapped with a transparent plastic sheet. Sample blocks were collected within 2 weeks after girdling and immediately frozen in liquid nitrogen and then stored at –70C. Samples were obtained by cryo-sectioning.

value: differentiating xylem

tag: regenerating stage

value: Stage 0

tag: tree

value: tree4 and tree5


title: 1025-00004_LS


title: HC-253


title: 2016-00031_LS


title: MDD-580


title: Negative_LPS_3


title: HC-350


title: BD2-244


title: MDD-398


title: 2016-00027_NL

value: non-lesion (NL)


title: Negative_LPS_2


title: rC, biological rep1

description:
Transcriptome profiling data of regenerated cambium
Populus_rC_1

source_name: regenerated cambium at stage III

value: regenerated cambium

value: Stage III


title: rC, biological rep2

description:
Transcriptome profiling data of regenerated cambium
Populus_rC_2


title: 1016-00013_NL


title: MDD-286


title: diC, biological rep1

description:
Transcriptome profiling data of differentiating regenerated cambium
Populus_diC_1

source_name: differentiating regenerated cambium at stage II

value: differentiating regenerated cambium

value: Stage II


title: 2016-00013_LS


title: MDD-369


title: 2016-00013_NL


title: rPh, biological rep2

description:
Transcriptome profiling data of regenerated phloem
Populus_rPh_2

source_name: regenerated phloem at stage II

value: regenerated phloem


title: rPh, biological rep1

description:
Transcriptome profiling data of regenerated phloem
Populus_rPh_1


title: diC, biological rep2

description:
Transcriptome profiling data of differentiating regenerated cambium
Populus_diC_2


title: fALS mRNA subject-4

description: Nanostring  GX Human Immunology and Nanostring Human Inflammation assays detected RNAs in sorted CD14+/CD16- blood-derived monocytes (RNA transcriptom per 100 ng total RNA)

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString.com) with 5 µl of the sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h

source_name: CD14+CD16- monocytes

label_protocol: 100 ng of total RNA was used in 5 µl with specific mRNA tag probes from Nanostring using the Nanostring  GX Human Immunology and Nanostring Human Inflammation assays

extract_protocol: Blood monocytes were sorted and total RNA was extracted using mirVana RNA isolation kit (Ambion) according to the manufacturer’s protocol

tag: cell type

value: CD14+CD16- monocytes

value: 53 yeasr

tag: Sex

value: Male

value: familial amyotrophic lateral sclerosis fALS SOD1 L113T

tag: ethnicity

value: Non-hispanic

tag: onset site

value: limb

tag: fvc

value: U


title: HC-285

value: healthy control

value: PBMC


title: fALS mRNA subject-3

tag: age

value: 69 years

value: Female

tag: disease state

value: familial amyotrophic lateral sclerosis fALS SOD1 A10G

tag: alsfrs


title: deX, biological rep1

description:
Transcriptome profiling data of dedifferentiating xylem
Populus_deX_1

source_name: dedifferentiating xylem at regenerating stage I

tag: tissue

value: dedifferentiating xylem

value: Stage I


title: MDD-347

value: major depressive disorder


title: diX, biological rep1

description:
Transcriptome profiling data of differentiating xylem
Populus_diX_1

source_name: differentiating xylem residue on the trunk after girdling

value: differentiating xylem

value: Stage 0


title: diX, biological rep2

description:
Transcriptome profiling data of differentiating xylem
Populus_diX_2


title: HC-216


title: MDD-343


title: HC-321


title: fALS mRNA subject-2

value: CD14+CD16- monocytes

value: 72 years

value: familial amyotrophic lateral sclerosis fALS SOD1 A4V


title: HC-172


title: BD1-362

value: bipolar disorder


title: MDD-328


title: fALS mRNA subject-1

value: 61 years

value: Male

value: Non-hispanic


title: deX, biological rep2

description:
Transcriptome profiling data of dedifferentiating xylem
Populus_deX_2


title: HC mRNA subject-10

value: 70 years

value: Healthy control


title: HC-296

value: healthy control

value: PBMC


title: HC mRNA subject-9

value: 68 years

value: Female


title: HC mRNA subject-8

value: 60 years


title: HC-84


title: MDD-341

value: major depressive disorder


title: Retina from NeuroD1 cKO mouse at ZT20, biological rep 2

first: Margaret

last: Ochocinska

address: 49 Convent Dr. Rm.6A71

department: NICHD/PDEGEN

institute: National Institutes of Health

description:
TR_N2
Gene expression from the retina of a NeuroD1 cKO mouse at ZT20.

hyb_protocol: GeneChip® One-Cycle Target Labeling from Affymetrix. Fluidics script EukGE_Ws2v5 was used with GeneChip® Fluidics Station 450.

scan_protocol: Affymetrix GCOS default settings and GeneChip Scanner 3000.

data_processing: GCOS software statistical algorithm (Affymetrix).

source_name: NeuroD1 cKO at ZT20, retina

label_protocol: Nugen Ovation RNA amplification system V2 and FL-Ovation cDNA Biotin Module V2.

growth_protocol: NeuroD1 conditional knockout (cKO) mice were generated by crossing NeuroD1flox/flox mice with NeuroD1+/flox::Crx-cre+/- mice to produce NeuroD1flox/flox/Crx-cre+/- (cKO) mice and  NeuroD1flox/flox::Crx-cre-/- (CON) mice. CON and cKO mice (both genders, 2 months of age) were bred and housed in LD 12:12 light cycles with food and water ad libitum.

extract_protocol: Total mouse pineal and retina RNA was isolated using the RNeasy Micro RNA isolation kit (Qiagen).

treatment_protocol: Pineal glands and retinas were collected during the day (ZT6) and night (ZT20). 6 pineal glands or retinas were pooled per sample. ZT20 samples were collected under dim red lighting conditions.

value: C57BL/6J; NeuroD1flox::Crx-Cre+/-

tag: genotype

value: NeuroD1 cKO

value: 2 months

value: retina

tag: time


title: HC mRNA subject-7

value: CD14+CD16- monocytes


title: HC-418


title: R30_leaf_detip-retip-30d-rep1

city: Pullman

first: Glenn

middle: W

last: Turner

address: PO Box 646340, Washington State University

department: Institute of Biological Chemistry

institute: Washington State University

description: mature leaf from a day 30 detip-retip plant after 15 days of regrowth

hyb_protocol: 15ug biotinylated cRNA hybridized for 16 hr at 45C in Affymetrix 640 hybridization oven at 50rpm

scan_protocol: Standard Affymetrix Scan on Affymetrix 7G scanner

data_processing: The data were analyzed using GeneChip Operating Software with affymetrix default  settings utilizing global scaling for normalization and a target intensity value of 125.

organism: Glycine max

source_name: mature leaf

label_protocol: Standard Affymetrix one cycle labeling and fragmentation protocol

growth_protocol: Plants were grown in growth chambers, in 4-L pots, with a minimum ligh intensity of 360-400 umol m2/s, with 16h daylengths, and day/night temperatures of 25/18oC.

extract_protocol: RNA was extracted from leaf samples using a method developed for tissues containing abundant polysaccharides and polyphenols (Gehrig et al., 2000).  In addition, the extracted RNA was further purified using the RNeasy kit (Qiagen, Valencia, CA).

treatment_protocol: Soybean plants were cultivated in growth chambers for 30 days.  Experimental plants were then subjected to a daily removal of all axillary and terminal buds for a period of 15 days (designated D1-15; “Detip” period), while controls were left untreated (C0-15) through the same time period.  Following the Detip period, shoot tips on experimental plants were allowed to regrow for another 15 days (R16-30; “Retip” period) while control plants continued to be grown without treatment (C16-30).  Samples were collected at 5 day intervals, frozen in liquid nitrogen immediately after harvest, and stored at -80oC until further analysis.

tag: sample type

value: bud removal and regrowth

value: mature leaf


title: HC mRNA subject-6

value: 63 years

value: Male


title: BD1-588

value: bipolar disorder


title: C30_leaf_control-30d-rep2

description: mature leaf from a day 30 control plant

value: control


title: Retina from NeuroD1 cKO mouse at ZT20, biological rep 3

description:
TR_N3
Gene expression from the retina of a NeuroD1 cKO mouse at ZT20.

tag: strain


title: C30_leaf_control-30d-rep3

description: mature leaf from a day 30 control plant


title: R30_leaf_detip-retip-30d-rep2


title: Retina from NeuroD1 cKO mouse at ZT20, biological rep 1

description:
TR_N1
Gene expression from the retina of a NeuroD1 cKO mouse at ZT20.


title: HC mRNA subject-5

value: 59 years

value: Healthy control

value: Non-hispanic


title: C30_leaf_control-30d-rep1

description: mature leaf from a day 30 control plant


title: HC-592

value: healthy control

value: PBMC


title: R20_leaf_detip-retip-20d-rep2

description: mature leaf from a detip-retip plant after 5 days of regrowth


title: R20_leaf_detip-retip-20d-rep1


title: R20_leaf_detip-retip-20d-rep3


title: Retina from NeuroD1 cKO mouse at ZT6, biological rep 3

description:
TR_D3
Gene expression from the retina of a NeuroD1 cKO mouse at ZT6.

source_name: NeuroD1 cKO at ZT6, retina


title: Retina from NeuroD1 cKO mouse at ZT6, biological rep 1

description:
TR_D1
Gene expression from the retina of a NeuroD1 cKO mouse at ZT6.


title: HC-209


title: R30_leaf_detip-retip-30d-rep3


title: HC mRNA subject-4

value: 36 years

value: Female


title: Retina from NeuroD1 cKO mouse at ZT6, biological rep 2

description:
TR_D2
Gene expression from the retina of a NeuroD1 cKO mouse at ZT6.

value: C57BL/6J; NeuroD1flox::Crx-Cre+/-

value: NeuroD1 cKO


title: Retina from control mouse at ZT20, biological rep 2

description:
CR_N2
Gene expression from the retina of a control mouse at ZT20.

source_name: Control at ZT20, retina

value: C57BL/6J; NeuroD1flox::Crx-Cre-/-

value: 2 months

value: retina


title: Retina from control mouse at ZT20, biological rep 3

description:
CR_N3
Gene expression from the retina of a control mouse at ZT20.


title: HC mRNA subject-2

value: CD14+CD16- monocytes

value: 42 years


title: MDD-305

value: major depressive disorder


title: HC mRNA subject-1

value: 61 years