title: Sample_586 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_585 CD_1_Terminal Ileum

status: Public on Aug 10 2016

type: RNA

city: Boston

first: Ramnik

middle: J

last: Xavier

state: MA

address: 185 Cambridge Street

country: USA

institute: Massachusetts General Hospital

description: CD_1_Terminal Ileum

hyb_protocol: according to the manufacturer’s protocol

data_processing:
Data from each version of probeset (lot) was first independently normalized and samples were analyzed for quality controls using following steps.
Background noise was estimated using mean expression levels of spiked-in negative controls
Estimated noise value was subtracted from raw counts data for each sample. Negative count values were reset to 1
Count values of spike-in positive controls were summed per sample and the average value was used to estimate a scaling factor for each sample. Expression value of each sample was adjusted using the sample specific normalization factor
Samples with higher than acceptable background noise and positive control based scaling factor <0.3 or >3.0 were identified as outliers and removed from analysis
Next, geometric mean of housekeeping genes was computed for each sample and the average value was used to compute the normalization factor. Data was adjusted in a similar fashion as was done previously with spiked-in positive controls
Finally, samples with housekeeping-genes based normalization factor <0.2 or >5.0 were removed as outliers.
Data Lots 2 & 3 were independently calibrated to Lot 1 using following steps.
The average of medians of calibration samples, for a given pair of lots, was computed and used to estimate normalization factor for each sample.
Each lot was scaled with the normalization factor computed in the previous step.
Geometric means of counts per gene between repeated samples was computed within a lot and a calibration factor was estimated per gene.
Calibration per gene was applied for the non-reference lot. All computations were performed in MATLAB. Nine hundred and eighty-nine samples passed data normalization and quality control.

molecule: polyA RNA

organism: Homo sapiens

source_name: Terminal Ileum

label_protocol: Extracted RNA (100ng) was used as input for expression profiling on the NanoString platform according to manufacturer's specifications.

extract_protocol: Using a combined Trizol (Life Technologies)-chloroform extraction and the RNeasy Midi Kit (Qiagen) for RNA extraction, total RNA was extracted by manufacturer’s protocol and RNA purity and quantity was measured by NanoDrop spectrophotometer (Promega).

treatment_protocol: At the time of endoscopy, mucosal biopsies were collected in RNA-later (Qiagen) and stored at -80°C ahead of downstream processing. If samples were collected at the time of surgery, mucosal tissue sample obtained from bowel resection specimens with colonoscopic biopsy forceps were processed immediately or stored at 4°C for processing within 12 hours. Intestinal source location and inflammation status was indicated as “uninflamed” or “inflamed” based on the endoscopic or gross appearance of the tissue by the endoscopist or investigator at time of surgical specimen collection.

tag: patient id

tag: disease

value: CD

tag: inflamed (0=no, 1=yes)

tag: nanostring codeset


title: Sample_584 CD_1_Cecum

scan_protocol: according to the manufacturer’s protocol

source_name: Cecum


title: Sample_582 CD_0_Descending Colon

description: CD_0_Descending Colon

source_name: Descending Colon


title: Sample_590 CD_0_Transverse Colon

description: CD_0_Transverse Colon

source_name: Transverse Colon


title: Sample_583 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_595 CD_1_Descending Colon

description: CD_1_Descending Colon


title: Sample_579 UC_1_Descending Colon

description: UC_1_Descending Colon

value: UC


title: Sample_592 CD_0_Rectum

source_name: Rectum


title: Sample_578 UC_0_Ascending Colon

description: UC_0_Ascending Colon

source_name: Ascending Colon


title: Sample_577 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_589 CD_1_Cecum


title: Sample_576 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_572 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_575 CD_1_Rectum


title: Sample_574 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_580 UC_0_Cecum


title: Sample_570 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_568 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_569 CD_1_Ascending Colon

description: CD_1_Ascending Colon


title: Sample_567 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_565 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_573 UC_1_Rectum


title: Sample_581 CD_1_Rectum


title: Sample_564 UC_1_Rectum


title: Sample_566 CD_0_Rectum


title: Sample_561 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_562 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_560 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_558 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_559 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon

source_name: Sigmoid Colon


title: Sample_556 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_555 CD_1_Descending Colon

description: CD_1_Descending Colon


title: Sample_571 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_553 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_552 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_551 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_554 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_550 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_557 CD_1_Ascending Colon

description: CD_1_Ascending Colon


title: Sample_549 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_546 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_563 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_547 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_545 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_544 UC_0_Cecum


title: Sample_542 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_543 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_540 CD_1_Ascending Colon

description: CD_1_Ascending Colon


title: Sample_537 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_539 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_536 CD_1_Descending Colon

description: CD_1_Descending Colon


title: Sample_541 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_538 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_534 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_533 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_531 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_530 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_532 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_535 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_528 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_529 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_527 CD_1_Descending Colon

description: CD_1_Descending Colon


title: Sample_548 UC_1_Rectum


title: Sample_524 UC_1_Rectum


title: Sample_525 UC_1_Rectum


title: Sample_523 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_522 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_519 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_521 CD_1_Rectum


title: Sample_520 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_517 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_516 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_518 CD_1_Descending Colon

description: CD_1_Descending Colon


title: Sample_513 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_515 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_512 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_511 CD_0_Colon

source_name: Colon


title: Sample_508 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_507 CD_0_Rectum

value: QQ


title: Sample_510 CD_0_Colon


title: Sample_505 UC_0_Ascending Colon

description: UC_0_Ascending Colon

value: OO


title: Sample_509 CD_0_Colon


title: Sample_503 UC_0_Descending Colon

description: UC_0_Descending Colon

value: NN


title: Sample_526 UC_0_Transverse Colon

description: UC_0_Transverse Colon


title: Sample_502 UC_0_Descending Colon

description: UC_0_Descending Colon

value: MM


title: Sample_504 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_501 CD_1_Rectum

value: LL


title: Sample_498 UC_1_Rectum


title: Sample_499 Indeterminate_0_Rectum

value: KK

value: Indeterminate


title: Sample_497 UC_0_Cecum


title: Sample_500 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_496 UC_1_Efferent Limb

description: UC_1_Efferent Limb

source_name: Efferent Limb


title: Sample_494 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_493 UC_0_Cecum


title: Sample_492 UC_1_Rectum


title: Sample_514 CD_0_Cecum


title: Sample_490 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_495 UC_1_Pouch

source_name: Pouch


title: Sample_487 UC_NA_Rectum


title: Sample_486 UC_NA_Cecum


title: Sample_488 UC_NA_Terminal Ileum

description: UC_NA_Terminal Ileum


title: Sample_506 UC_0_Rectum

value: PP


title: Sample_491 UC_1_Cecum


title: Sample_489 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_484 UC_1_Rectum


title: Sample_485 UC_NA_Terminal Ileum

description: UC_NA_Terminal Ileum


title: Sample_482 UC_1_Rectum


title: Sample_481 UC_0_Cecum


title: Sample_483 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_479 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_478 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_477 UC_1_Cecum


title: Sample_476 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_471 CD_1_Cecum


title: Sample_475 UC_1_Cecum


title: Sample_474 UC_0_Cecum


title: Sample_473 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_472 UC_1_Rectum


title: Sample_470 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_467 UC_0_Rectum


title: Sample_466 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_464 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_469 UC_0_Terminal Ileum

description: UC_0_Terminal Ileum


title: Sample_480 UC_1_Rectum


title: Sample_463 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_461 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_459 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_462 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_460 CD_0_Rectum


title: Sample_458 CD_0_Cecum


title: Sample_455 CD_1_Rectum


title: Sample_454 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_448 CD_NA_Terminal Ileum

description: CD_NA_Terminal Ileum


title: Sample_452 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_451 CD_1_Rectum


title: Sample_449 CD_1_Pouch


title: Sample_468 UC_0_Rectum


title: Sample_447 CD_NA_Terminal Ileum

description: CD_NA_Terminal Ileum


title: Sample_443 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_444 CD_0_Cecum


title: Sample_445 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_456 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_441 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_442 CD_1_Rectum


title: Sample_446 CD_0_Pouch


title: Sample_457 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_440 CD_0_Cecum


title: Sample_439 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_453 CD_1_Cecum


title: Sample_438 CD_1_Pouch


title: Sample_434 CD_0_Afferent Limb

description: CD_0_Afferent Limb

source_name: Afferent Limb


title: Sample_436 CD_0_Cecum


title: Sample_437 CD_0_Efferent Limb

description: CD_0_Efferent Limb


title: Sample_430 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon


title: Sample_431 CD_1_Rectum


title: Sample_432 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_433 CD_1_Rectum


title: Sample_435 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_429 CD_0_Cecum


title: Sample_426 CD_0_Descending Colon

description: CD_0_Descending Colon

value: AS


title: Sample_450 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_424 CD_0_Descending Colon

description: CD_0_Descending Colon

value: AQ


title: Sample_428 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_422 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon

value: AP


title: Sample_423 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_427 CD_1_Descending Colon

description: CD_1_Descending Colon


title: Sample_425 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: AR


title: Sample_415 UC_1_Ascending Colon

description: UC_1_Ascending Colon

value: AK


title: Sample_417 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: AL


title: Sample_421 UC_0_Rectum

value: AO


title: Sample_419 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon

value: AM


title: Sample_414 CD_0_Rectum

value: AJ

value: CD


title: Sample_416 UC_0_Transverse Colon

description: UC_0_Transverse Colon

value: UC


title: Sample_413 UC_1_Rectum

value: AI


title: Sample_412 UC_0_Rectum


title: Sample_418 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_410 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon

value: AG


title: Sample_411 CD_0_Ascending Colon

description: CD_0_Ascending Colon

value: AH


title: Sample_409 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_465 UC_0_Cecum


title: Sample_408 CD_0_Cecum

value: AF


title: Sample_407 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon

value: AE


title: Sample_405 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum

value: AD


title: Sample_406 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_404 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon

value: AC


title: Sample_402 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon

value: ZZZ


title: Sample_401 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_399 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon

value: YYY


title: Sample_400 UC_1_Rectum


title: Sample_396 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon

value: WWW


title: Sample_395 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon

value: VVV


title: Sample_398 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: XXX


title: Sample_394 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_393 UC_0_Rectum

value: UUU


title: Sample_420 UC_0_Descending Colon

description: UC_0_Descending Colon

value: AN


title: Sample_392 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: TTT


title: Sample_391 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum

value: CD


title: Sample_389 CD_1_ileocolonic anastomosis

description: CD_1_ileocolonic anastomosis

source_name: ileocolonic anastomosis

value: RRR


title: Sample_403 UC_0_Rectum

value: AB

value: UC


title: Sample_386 CD_0_Rectum

value: PPP


title: Sample_388 Indeterminate_1_Sigmoid Colon

description: Indeterminate_1_Sigmoid Colon

value: OOO

value: Indeterminate


title: Sample_387 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum

value: QQQ


title: Sample_384 UC_1_Transverse Colon

description: UC_1_Transverse Colon

value: LLL


title: Sample_382 UC_0_Descending Colon

description: UC_0_Descending Colon

value: KKK


title: Sample_390 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_381 UC_1_Descending Colon

description: UC_1_Descending Colon


title: Sample_383 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon

value: NNN


title: Sample_378 CD_0_Ascending Colon

description: CD_0_Ascending Colon

value: III


title: Sample_397 UC_1_Rectum

value: WWW


title: Sample_380 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum

value: JJJ


title: Sample_377 CD_1_Ascending Colon

description: CD_1_Ascending Colon


title: Sample_376 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: HHH


title: Sample_379 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_375 UC_1_Rectum

value: GGG


title: Sample_374 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_372 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon

value: EEE


title: Sample_370 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum

value: DDD

value: CD


title: Sample_385 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon

value: MMM


title: Sample_369 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_366 CD_0_Rectum

value: BBB


title: Sample_368 UC_1_Rectum

value: CCC

value: UC


title: Sample_365 CD_0_Rectum

value: AAA


title: Sample_364 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon

value: ZZ


title: Sample_362 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum

value: YY


title: Sample_363 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_360 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon

value: WW


title: Sample_373 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: FFF


title: Sample_356 CD_0_Rectum

value: TT


title: Sample_357 UC_1_Ascending Colon

description: UC_1_Ascending Colon

value: UU


title: Sample_358 UC_0_Transverse Colon

description: UC_0_Transverse Colon


title: Sample_359 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: VV


title: Sample_371 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_353 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon

value: RR


title: Sample_348 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: K


title: Sample_354 UC_1_Rectum

value: SS


title: Sample_347 CD_0_Cecum

value: E


title: Sample_346 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: D

value: CD


title: Sample_345 UC_0_Descending Colon

description: UC_0_Descending Colon

value: A


title: Sample_344 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_351 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_367 UC_0_Descending Colon

description: UC_0_Descending Colon

value: CCC


title: Sample_349 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_343 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_341 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_342 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_339 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_355 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_340 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_350 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_338 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_336 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_335 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: C


title: Sample_352 UC_1_Ascending Colon

description: UC_1_Ascending Colon

value: BB

value: UC


title: Sample_333 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_328 Non-IBD Control_0_Colon

description: Non-IBD Control_0_Colon

value: Non-IBD Control


title: Sample_332 Sigmoid Cancer_0_Terminal Ileum

description: Sigmoid Cancer_0_Terminal Ileum

value: Sigmoid Cancer


title: Sample_330 Non-IBD Control_0_Colon

description: Non-IBD Control_0_Colon


title: Sample_334 UC_0_Descending Colon

description: UC_0_Descending Colon


title: Sample_326 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_325 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon

value: W


title: Sample_324 UC_1_Transverse Colon

description: UC_1_Transverse Colon


title: Sample_331 Non-IBD Control_0_Colon

description: Non-IBD Control_0_Colon


title: Sample_329 Non-IBD Control_0_Colon

description: Non-IBD Control_0_Colon


title: Sample_323 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_327 UC_0_Colon


title: Sample_321 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_337 CD_0_Cecum


title: Sample_319 CD_0_ileocolonic anastomosis

description: CD_0_ileocolonic anastomosis


title: Sample_322 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_361 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: XX


title: Sample_320 CD_0_ileocolonic anastomosis

description: CD_0_ileocolonic anastomosis


title: Sample_316 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_317 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_315 UC_0_Rectum

value: JJ


title: Sample_314 CD_0_Cecum

value: II


title: Sample_312 CD_0_Rectum

value: GG


title: Sample_311 CD_0_Ascending Colon

description: CD_0_Ascending Colon

value: FF


title: Sample_318 CD_1_Colon


title: Sample_310 UC_0_Cecum

value: DD


title: Sample_308 UC_0_Descending Colon

description: UC_0_Descending Colon

value: CC


title: Sample_313 UC_0_Transverse Colon

description: UC_0_Transverse Colon

value: HH


title: Sample_305 UC_0_Rectum

value: Y


title: Sample_307 UC_0_Rectum

value: AA


title: Sample_306 CD_0_Ascending Colon

description: CD_0_Ascending Colon

value: Z

value: CD


title: Sample_302 UC_0_Colon


title: Sample_304 CD_0_Descending Colon

description: CD_0_Descending Colon

value: X


title: Sample_303 UC_1_Colon

value: UC


title: Sample_301 UC_1_Colon


title: Sample_299 Indeterminate_1_Colon

value: Indeterminate


title: Sample_298 CD_1_Colon


title: Sample_290 UC_0_Colon


title: Sample_300 Indeterminate_0_Colon


title: Sample_291 Indeterminate_1_Colon


title: Sample_296 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_293 UC_0_Colon


title: Sample_295 UC_0_Colon


title: Sample_294 UC_1_Colon


title: Sample_288 UC_0_Colon


title: Sample_287 UC_1_Colon


title: Sample_292 UC_1_Colon


title: Sample_289 UC_1_Colon


title: Sample_297 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_286 UC_0_Colon


title: Sample_309 UC_1_Terminal Ileum

description: UC_1_Terminal Ileum


title: Sample_284 UC_1_Ascending Colon

description: UC_1_Ascending Colon


title: Sample_283 UC_1_Colon


title: Sample_279 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_280 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_282 CD_1_Colon


title: Sample_285 UC_1_Colon


title: Sample_276 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_274 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_277 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_273 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_278 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_269 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_270 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_271 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_263 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_281 CD_1_Colon


title: Sample_259 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_260 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_264 CD_1_Rectum


title: Sample_262 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_261 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_272 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_268 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_256 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_257 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_258 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_252 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_251 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_254 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_253 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_275 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_267 CD_0_Rectum

value: V


title: Sample_266 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon

value: U


title: Sample_265 CD_0_Rectum


title: Sample_248 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_250 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_255 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_247 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_249 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_244 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_241 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_243 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_240 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_242 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_230 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_237 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_238 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_232 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_231 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_235 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_236 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_228 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_246 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_234 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_233 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_223 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_226 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_227 CD_0_Cecum


title: Sample_225 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_218 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_217 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_222 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_219 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_221 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_229 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_220 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_215 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_216 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_214 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_245 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_239 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_213 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_211 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: C


title: Sample_209 UC_1_Ascending Colon

description: UC_1_Ascending Colon

value: B


title: Sample_210 UC_0_Transverse Colon

description: UC_0_Transverse Colon


title: Sample_212 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: D


title: Sample_208 UC_0_Descending Colon

description: UC_0_Descending Colon

value: A


title: Sample_207 UC_1_Sigmoid Colon

description: UC_1_Sigmoid Colon


title: Sample_203 CD_1_Colon


title: Sample_202 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_195 CD_0_Colon


title: Sample_205 CD_0_Colon


title: Sample_204 CD_0_Colon


title: Sample_193 CD_0_Colon


title: Sample_194 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_196 CD_0_Colon


title: Sample_198 UC_0_Colon


title: Sample_200 CD_0_Colon


title: Sample_190 UC_1_Rectum


title: Sample_189 UC_0_Cecum


title: Sample_191 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_201 CD_1_Colon


title: Sample_187 UC_0_Cecum


title: Sample_192 CD_0_Colon


title: Sample_199 CD_1_Colon


title: Sample_188 UC_0_Rectum


title: Sample_197 UC_1_Colon


title: Sample_206 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_186 UC_0_Rectum


title: Sample_183 CD_0_Cecum


title: Sample_184 CD_0_Rectum


title: Sample_185 UC_0_Cecum


title: Sample_182 CD_0_Rectum


title: Sample_180 CD_1_Rectum

value: T


title: Sample_179 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon

value: S


title: Sample_178 CD_1_Sigmoid Colon

description: CD_1_Sigmoid Colon

value: R


title: Sample_177 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_175 CD_0_Descending Colon

description: CD_0_Descending Colon

value: P


title: Sample_171 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: M


title: Sample_172 CD_0_Rectum

value: N


title: Sample_173 UC_0_Rectum

value: O


title: Sample_181 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon

value: CD


title: Sample_170 CD_1_Rectum

value: L


title: Sample_174 CD_1_Cecum


title: Sample_167 UC_1_Transverse Colon

description: UC_1_Transverse Colon

value: J

value: UC


title: Sample_165 UC_1_Rectum

value: I


title: Sample_164 UC_0_Sigmoid Colon

description: UC_0_Sigmoid Colon


title: Sample_162 CD_0_Transverse Colon

description: CD_0_Transverse Colon

value: G


title: Sample_159 CD_0_Cecum

value: E


title: Sample_169 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon


title: Sample_161 CD_1_Cecum


title: Sample_168 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: K


title: Sample_163 CD_0_Sigmoid Colon

description: CD_0_Sigmoid Colon

value: H


title: Sample_160 CD_0_Ascending Colon

description: CD_0_Ascending Colon

value: F


title: Sample_166 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_158 CD_1_ileocolonic anastomosis

description: CD_1_ileocolonic anastomosis


title: Sample_155 CD_0_Colon


title: Sample_156 UC_1_Colon


title: Sample_154 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_153 CD_1_Descending Colon

description: CD_1_Descending Colon


title: Sample_176 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

value: Q


title: Sample_157 UC_0_Ascending Colon

description: UC_0_Ascending Colon


title: Sample_151 Indeterminate_0_Colon

value: Indeterminate


title: Sample_150 CD_0_Colon


title: Sample_148 UC_0_Cecum


title: Sample_224 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_149 UC_1_Cecum


title: Sample_146 CD_0_Colon


title: Sample_147 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_152 Indeterminate_1_Terminal Ileum

description: Indeterminate_1_Terminal Ileum


title: Sample_144 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_145 CD_1_Colon


title: Sample_143 CD_0_Cecum


title: Sample_139 CD_0_Colon


title: Sample_140 UC_1_Colon


title: Sample_141 UC_0_Colon


title: Sample_135 Non-IBD Control_0_Descending Colon

description: Non-IBD Control_0_Descending Colon

value: Non-IBD Control


title: Sample_136 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: Sample_134 Non-IBD Control_0_Descending Colon

description: Non-IBD Control_0_Descending Colon


title: Sample_137 CD_1_Colon


title: Sample_129 Non-IBD Control_0_Descending Colon

description: Non-IBD Control_0_Descending Colon


title: Sample_130 Non-IBD Control_0_Descending Colon

description: Non-IBD Control_0_Descending Colon


title: Sample_125 Non-IBD Control_0_Descending Colon

description: Non-IBD Control_0_Descending Colon


title: Sample_126 Non-IBD Control_0_Descending Colon

description: Non-IBD Control_0_Descending Colon


title: Sample_132 Non-IBD Control_0_Descending Colon

description: Non-IBD Control_0_Descending Colon


title: Sample_124 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: Sample_127 Non-IBD Control_0_Descending Colon

description: Non-IBD Control_0_Descending Colon


title: Sample_123 Non-IBD Control_0_Ascending Colon

description: Non-IBD Control_0_Ascending Colon


title: Sample_142 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_122 Non-IBD Control_0_Ascending Colon

description: Non-IBD Control_0_Ascending Colon


title: Sample_131 Non-IBD Control_0_Descending Colon

description: Non-IBD Control_0_Descending Colon


title: Sample_121 Non-IBD Control_0_Ascending Colon

description: Non-IBD Control_0_Ascending Colon


title: Sample_118 Non-IBD Control_0_Ascending Colon

description: Non-IBD Control_0_Ascending Colon


title: Sample_133 Non-IBD Control_0_Descending Colon

description: Non-IBD Control_0_Descending Colon


title: Sample_119 Non-IBD Control_0_Ascending Colon

description: Non-IBD Control_0_Ascending Colon


title: Sample_117 Non-IBD Control_0_Ascending Colon

description: Non-IBD Control_0_Ascending Colon


title: Sample_116 Non-IBD Control_0_Ascending Colon

description: Non-IBD Control_0_Ascending Colon


title: Sample_120 Non-IBD Control_0_Ascending Colon

description: Non-IBD Control_0_Ascending Colon


title: Sample_138 CD_1_Colon


title: Sample_115 Non-IBD Control_0_Ascending Colon

description: Non-IBD Control_0_Ascending Colon


title: Sample_128 Non-IBD Control_0_Descending Colon

description: Non-IBD Control_0_Descending Colon


title: Sample_113 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_114 Non-IBD Control_0_Ascending Colon

description: Non-IBD Control_0_Ascending Colon


title: Sample_112 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_109 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_111 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_107 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_110 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_108 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_106 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_105 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_104 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_102 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_103 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_100 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_101 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_99 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_98 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_97 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_96 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_95 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_94 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_93 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_88 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_86 CD_1_Jejunum

source_name: Jejunum


title: Sample_87 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_89 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_90 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_92 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_91 CD_0_Cecum


title: Sample_84 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_85 CD_0_Jejunum


title: Sample_83 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_81 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_82 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_80 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_78 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_79 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_77 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_75 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_76 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_74 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_72 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_71 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_73 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_69 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: Sample_68 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: Sample_70 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: Sample_66 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: Sample_67 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: Sample_65 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: RPE/choroid/sclera_5XFAD TG_rep2

city: Seoul

first: Sung Wook

last: Park

address: 101, Daehak-ro

department: Biomedical sciences

country: South Korea

institute: Seoul National University

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the Affymetrix GeneChip® Mouse Gene 2.0 ST Array for 16 hours at 45C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained using SAPE (Streptavidin Phycoerythrin) and washed in a Genechip Fluidics Station 450 (Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix). the image data was extracted through Affymetrix Command Console software1.1.

data_processing: The raw .cel file generated through above procedure meant expression intensity data and was used for the next step.  Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: RPE/choroid/sclera_5XFAD TG

label_protocol: Per RNA sample, 300 ng were used as input into the Affymetrix procedure as recommended by protocol (http://www.affymetrix.com). Briefly, 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA (cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: All animal experiments in this study were in strict agreement with the Association for Research in Vision and Ophthalmology Statement for the Use of Animals in Ophthalmic and Vision Research and the guidelines of the Gwangju Institute of Science and Technology Animal Care and Use Committee.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, USA). RNA quality was assessed by Agilent 2100 bioanalyser (Agilent Technologies, USA), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, USA).

treatment_protocol: No experimental treatment was performed.

tag: genotype/variation

value: 5XFAD hetero

tag: age

value: 12 months old

tag: tissue

value: RPE/choroid/scleral complex


title: RPE/choroid/sclera_littermate WT_rep3

description: WT littermate

source_name: RPE/choroid/sclera_littermate WT

value: wild type


title: Sample_64 Non-IBD Control_0_Ascending Colon

description: Non-IBD Control_0_Ascending Colon


title: Sample_63 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: Sample_61 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: RPE/choroid/sclera_5XFAD TG_rep3


title: Sample_62 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: RPE/choroid/sclera_littermate WT_rep2

description: WT littermate


title: RPE/choroid/sclera_littermate WT_rep1

description: WT littermate


title: iTreg_rep3

city: Montreal

first: Bruce

middle: David

last: Mazer

state: Quebec

address: 1001 boul. Décarie

department: RESP

country: Canada

institute: RI-MUHC

description: Gene expression data of IVIg-generated induced Treg from allergen-exposed IVIg-treated animals

hyb_protocol: Following fragmentation, target ss-DNA was hybridized for 16 hours at 45°C to Affymetrix Mouse Gene 2.0 ST arrays. Arrays were stained and washed using the GeneChips Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G. Images were processed using GeneChip Command Console (AGCC) software to generate CEL files.

data_processing: Raw data was read using the Bioconductor oligo package. Probe intensities were normalized across all arrays by the robust multi-array average (RMA) algorithm.

source_name: Treg, IVIg-induced

label_protocol: 2 ng of total RNA were subjected to two rounds of amplification using Affymetrix GeneChip Pico WT two-cycle target labeling and control reagents according to the manufacturer's protocols

growth_protocol: DEREG mice were sensitized and challenged with ovalbumin (OVA) to induce allergic airways disease. Endogenous Treg were depleted with injection of 40 ng/g diptheria toxin before IVIg or HSA treatment (2 g/kg).

extract_protocol: RNA was extracted with TRIzol reagent (Life Technologies) and cleaned with RNeasy Mini silica-gel membrane columns (Qiagen).

treatment_protocol: Spleens were dissected, lymphocytes were prepared, and Treg were isolated by flow cytometric sorting.

value: spleen

tag: cell type

value: T lymphocyte


title: Sample_60 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: iTreg_rep1


title: iTreg_rep2


title: e_iTreg_rep4

description: Gene expression data of all Treg from allergen-exposed IVIg-treated animals

source_name: Treg, mixed endogenous and IVIg-induced


title: Sample_58 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum

source_name: Terminal Ileum

value: CD


title: e_iTreg_rep2


title: eTreg_rep4

description: Gene expression data of endogenous Treg from allergen-exposed animals

source_name: Treg, endogenous


title: e_iTreg_rep3


title: iTreg_rep4


title: e_iTreg_rep1


title: RPE/choroid/sclera_5XFAD TG_rep1


title: eTreg_rep2


title: eTreg_rep1


title: Sample_56 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_59 Non-IBD Control_0_Terminal Ileum

description: Non-IBD Control_0_Terminal Ileum


title: Sample_54 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_55 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: eTreg_rep3


title: Sample_52 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_51 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_57 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: KOC2

city: Sendai

first: Keiko

last: Taguchi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba

department: Tohoku Medical Megabank Organization

country: Japan

institute: Tohoku University

description: Gene expression in CDDO-Im-treated Nrf2 knockout (delta7/delta7) rat

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: Data was obtained using the Agilent Feature Extraction software (v10.1), using default for all parameters.  The data were analyzed using GeneSpring GX software (v11.5) (Agilent).

organism: Rattus norvegicus

source_name: Nrf2 knockout (delta7/delta7) /CDDO-Im

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from whole livers using Sepazol-RNA I Suger G (Nacalai Tesque).

treatment_protocol: gavage of CDDO-Im (30 umol/kg body weight, 6 hours)

tag: strain

value: Nrf2 knockout (delta7/delta7)

value: liver

tag: treatment

value: CDDO-Im


title: Sample_50 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: KOC3


title: KOC1


title: KOV3

description: Gene expression in Vehicle-treated Nrf2 knockout (delta7/delta7) rat

source_name: Nrf2 knockout (delta7/delta7) /Vehicle

value: Vehicle


title: KOV2


title: KOV1


title: Sample_49 CD_0_Descending Colon

description: CD_0_Descending Colon

source_name: Descending Colon


title: WC1

description: Gene expression in CDDO-Im-treated Wildtype rat

source_name: Wildtype for delta7 line /CDDO-Im

value: Wildtype for delta7


title: Sample_47 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_53 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: WC2


title: Sample_46 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_42 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_41 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_43 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_40 CD_0_Transverse Colon

description: CD_0_Transverse Colon

source_name: Transverse Colon


title: Sample_45 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: 1007

description: Gene expression in CDDO-Im-treated Nrf2 knockout (+1/+1) rat

source_name: Nrf2 knockout (+1/+1) /CDDO-Im

treatment_protocol: Gavage of CDDO-Im (30 umol/kg body weight, 6 hours)

value: Nrf2 knockout (+1/+1)


title: 1002


title: 1009

source_name: Wildtype for +1 line /CDDO-Im

value: Wildtype for +1


title: Sample_39 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: 1005


title: 1051

description: Gene expression in Vehicle-treated Nrf2 knockout (+1+1) rat

source_name: Nrf2 knockout (+1/+1) /Vehicle


title: Sample_38 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_37 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: WV3

description: Gene expression in Vehicle-treated Wildtype rat

source_name: Wildtype for delta7 line /Vehicle


title: WC3


title: 1050

description: Gene expression in Vehicle-treated Nrf2 knockout (+1/+1) rat


title: Sample_36 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_44 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: WV1


title: Sample_35 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: WV2


title: Sample_48 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: 1052


title: 1049

source_name: Wildtype for +1 line /Vehicle


title: 982


title: Sample_32 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_34 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_33 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: 1025


title: DEN Cholic Acid Diet

city: Kansas City

first: Udayan

last: Apte

state: KS

address: 3901 Rainbow Blvd

department: Pharmacology, Toxicology and Therapeutics

institute: University of Kansas Med Center

description: Gene expression data from Livers of mice treated with DEN and then fed 0.2% chloic acid containing diet

hyb_protocol: Using the GeneChip 645 Hybridization Oven, labeled target RNA is hybridized overnight  to interrogating oligo probes contained in the GeneChip miRNA 4.0 expression cartridge array (Affymetrix #902017). Hybridized Genechips undergo low and high stringency washing and R-Phycoerythrin-Streptavidin staining procedures using the GeneChip fluidics station 450. After washing, GeneChips undergo a single scan using a GeneChip scanner 3000 7G with autoloader. Fluidics and scan functions are controlled by Affymetrix GeneChip Command Console software (AGCC).

scan_protocol: Single Scan; Affymetrix GeneChip Scanner 3000 7G with Autoloader; Affymetrix GeneChip Command Console (AGCC) ver. 1.1

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 (RMA) using RMA default analysis settings: RMA Background Correction; Quantile Normalization; Median Polish probeset summarization.

label_protocol: 1ug of Total RNA is labeled using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix #901910). The FlashTag labeling system employs the 3DNA dendrimer signal amplification technology. 3DNA dendrimer is a branched structure of single and double stranded DNA conjugates which incorporates numerous biotin labels for ultrasensitive expression detection.

extract_protocol: Total RNAs were isolated using the trizol reagent (invitrogen, CA, USA).

treatment_protocol: 4 groups- ND, 0.2%CA, DEN+ND and DEN+0.2%CA

value: Liver

value: 10 months


title: 1024


title: 985


title: DEN Control Diet

description: Gene expression data from Livers of mice treated with DEN and then fed control diet


title: Sample_31 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_28 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_30 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_29 CD_0_Transverse Colon

description: CD_0_Transverse Colon


title: Sample_27 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: No DEN Control Diet

description: Gene expression data from Livers of mice fed control diet

source_name: Livers of mice fed control diet


title: shSMAD3_NC

city: Guangzhou

first: Mengfeng

last: Li

state: Guangdong

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

country: China

institute: Sun Yat-sen University

description: A549 Cells transduced with pSuper Retro Puro shSMAD3 treated with vehicle for 12hr

hyb_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Data normalization and transformation was performed on Genespring GX 11 (Agilent) in shanghai biochip corporation.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: A549 cells were cultured in complete DMEM medium and supplied with 10% FBS.

extract_protocol: Total RNA was isolated using RNeasy RNA isolation kit (Qiagen) following supplier’s protocol.

treatment_protocol: Retro-viral vector was co-transfected with the pIK packaging plasmid in 293FT cells by using standard calcium phosphate transfection method. Thirty-six hours after the co-transfection, supernatants were collected and incubated with cells to be infected for 24 hours in the presence of polybrene (2.5 μg/mL).  Following infection, puromycin (1.5μg/mL) was used to select stably transduced cells for 10 days.

tag: cell line


title: Vector_TGF

description: A549 Cells transduced with pSin EF2 Puro Vector treated with TGF-β1 for 12hr


title: CCT6A_NC

description: A549 Cells transduced with pSin EF2 Puro CCT6A treated with vehicle for 12hr


title: Sample_25 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: No DEN Cholic Acid Diet

description: Gene expression data from Livers of mice fed 0.2% cholic acid containing diet


title: shSMAD2_TGF

description: A549 Cells transduced with pSuper Retro Puro shSMAD2 treated with TGF-β1 for 12hr


title: shSMAD3_TGF

description: A549 Cells transduced with pSuper Retro Puro shSMAD3 treated with TGF-β1 for 12hr


title: shSMAD2_NC

description: A549 Cells transduced with pSuper Retro Puro shSMAD2 treated with vehicle for 12hr


title: shVector_TGF

description: A549 Cells transduced with pSuper Retro Puro Vector treated with TGF-β1 for 12hr


title: CCT6A_TGF

description: A549 Cells transduced with pSin EF2 Puro CCT6A treated with TGF-β1 for 12hr


title: Huh1_siControl_4

city: Daejeon

first: Yang

last: Suk-Jin

address: 125 Gwahak-ro, Yuseong-gu

institute: KRIBB (Korea Research Institute of Bioscience and Biotechnology)

description: Gene expression analysis of Huh1 cell line under transfected with control siRNA. At 48hrs after the control siRNA trasfection to Huh-1 cells, the cells were incubated in 1% O2 for 24 hrs. Biological replication #2, Technical replicatipon #2

hyb_protocol: Labeled cRNA (750ng) was hybridized to HumanHT-12 v4 chips at 58℃ for 18 hours.

scan_protocol: After hybridizing procedures, chips were scanned using a BeadArray Reader and BeadScan software (Illumina).

data_processing: Data extraction and normalization were elevated by BeadStudio software (v. 3.1.1.0, Illumina); content Descriptor; HumanHT-12_V4_0_R2_15002873_B.bgx

label: Biotin

source_name: Huh1_siControl_1% O2 for 24hrs

label_protocol: Illumina TotalPrep RNA Amplification kit (Applied Biosystem/Ambion, Austin, TX, USA) was used to generate biotin-UTP labeled cRNA according to manufacturer’s instructions

growth_protocol: Huh-1 cells were maintained in Dulbecco’s modified Eagle medium (DMEM; Gibco BRL, Grand Island, NY). Media was supplemented with heat-inactivated 10% fetal bovine serum (GIBCO BRL) and 1× Antibiotic-Antimycotic (GIBCO BRL). Cells were cultured at 37℃ in a humidified incubator under 5% CO2. Hypoxic culture conditions were constructed with O2/CO2 incubator (1%O2, 5% CO2 and 92%-94% N2, MCO-5M, Sanyo, Japan)

extract_protocol: Total RNA extraction was perforemd using QIAGEN RNeasy mini kit according to manufacturer's instruction. Total RNA integrity was determined with ExperionTM RNA StdSens (BIO-RAD).

treatment_protocol: Using RNAiMAX (Invitrogen) reagents, Huh-1 cells were reverse-transfected with control siRNA or siLSD1. After 48hrs, cells were incubated under 1% O2 for 24hrs.

value: Hepatocellular Carcinoma Cells

tag: transfected with

value: control siRNA


title: Sample_20 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_21 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_23 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_22 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_24 CD_0_Descending Colon

description: CD_0_Descending Colon


title: Sample_19 CD_0_Ascending Colon

description: CD_0_Ascending Colon

source_name: Ascending Colon


title: Sample_26 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Huh1_siLSD1_4

description: Gene expression analysis of Huh1 cell line under transfected with siLSD1. At 48hrs after the control siRNA trasfection to Huh-1 cells, the cells were incubated in 1% O2 for 24 hrs. Biological replication #2, Technical replicatipon #2

source_name: Huh1_siLSD1_1% O2 for 24hrs


title: Huh1_siLSD1_1

description: Gene expression analysis of Huh1 cell line under transfected with siLSD1. At 48hrs after the control siRNA trasfection to Huh-1 cells, the cells were incubated in 1% O2 for 24 hrs. Biological replication #1, Technical replicatipon #1


title: Huh1_siControl_2

description: Gene expression analysis of Huh1 cell line under transfected with control siRNA. At 48hrs after the control siRNA trasfection to Huh-1 cells, the cells were incubated in 1% O2 for 24 hrs. Biological replication #1, Technical replicatipon #2


title: Huh1_siLSD1_3

description: Gene expression analysis of Huh1 cell line under transfected with siLSD1. At 48hrs after the control siRNA trasfection to Huh-1 cells, the cells were incubated in 1% O2 for 24 hrs. Biological replication #2, Technical replicatipon #1


title: Huh1_siLSD1_2

description: Gene expression analysis of Huh1 cell line under transfected with siLSD1. At 48hrs after the control siRNA trasfection to Huh-1 cells, the cells were incubated in 1% O2 for 24 hrs. Biological replication #1, Technical replicatipon #2


title: Huh1_siControl_3

description: Gene expression analysis of Huh1 cell line under transfected with control siRNA. At 48hrs after the control siRNA trasfection to Huh-1 cells, the cells were incubated in 1% O2 for 24 hrs. Biological replication #2, Technical replicatipon #1


title: Huh1_siControl_1

description: Gene expression analysis of Huh1 cell line under transfected with control siRNA. At 48hrs after the control siRNA trasfection to Huh-1 cells, the cells were incubated in 1% O2 for 24 hrs. Biological replication #1, Technical replicatipon #1


title: shVector_NC

description: A549 Cells transduced with pSuper Retro Puro Vector treated with vehicle for 12hr


title: Vector_NC

description: A549 Cells transduced with pSin EF2 Puro Vector treated with vehicle for 12hr


title: Sample_17 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: Sample_18 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_16 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_12 CD_0_Rectum

source_name: Rectum


title: Sample_11 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum

source_name: Terminal Ileum


title: Sample_13 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_14 CD_0_Terminal Ileum

description: CD_0_Terminal Ileum


title: Sample_15 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: 5991878040_H

city: Indianapolis

first: Guanglong

last: Jiang

state: IN

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

description: MCF7 AKT2 shRNA E2 3hrs

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Genes that showed statistically insignificant signals in majority of samples were removed from the microarray data, and only those probes that showed statistically significant signal in at least half of samples of at least one group were retained. The probe level data was then collapsed to gene level data by retaining only the probes, which showed a maximal coefficient of variation across all samples. The data was imported into partek genomics suite for differential expression analysis. ANOVA analysis was performed to identify genes differentially expressed between AKT1KD vs. pLKO, AKT2KD vs. pLKO, and AKT1KD vs. AKT2KD groups.

source_name: 8 MCF7 AKT2 shRNA E2 3hrs

label_protocol: Microarray with biological triplicates was performed using Illumina HumanHT-12 V4 expression beadchip. Standard Illumina label protocol was used.

growth_protocol: Cells were maintained in phenol red free MEM with 5% charcoal dextran treated fetal calf serum for four days and then treated with ethanol or 0.1 nM estradiol for three hours.

extract_protocol: RNA was prepared using RNeasy kit (Qiagen, Valencia, CA, USA) and cDNA from two μgs of RNA was synthesized using the cDNA Synthesis kit (Bio- Rad, Hercules, CA, USA). qRT-PCR was performed using SyberGreen on a TaqMan 7900HT instrument (Applied Biosystems, Carlsbad, CA, USA).

treatment_protocol: Cells were treated with ethanol or estradiol dissolved in ethanol.

value: AKT2 shRNA

value: 0.1 nM estradiol


title: 5991878014_G

description: MCF7 AKT2 shRNA E2 3hrs

source_name: 5 MCF7 AKT2 shRNA E2 3hrs


title: Sample_10 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: 5991878014_K

description: MCF7 AKT2 shRNA E2 3hrs

source_name: 7 MCF7 AKT2 shRNA E2 3hrs


title: 5991878014_L

description: MCF7 AKT2 shRNA E2 3hrs

source_name: 7-rep MCF7 AKT2 shRNA E2 3hrs


title: 5991878040_F

description: MCF7 AKT2 shRNA E2 3hrs

source_name: 6 MCF7 AKT2 shRNA E2 3hrs


title: KO_BCL11b_F/F_PLZF-Cre_Vα14_transgenic_Cy5_WT_BCL11b_F/F_ Vα14_transgenic_Cy3

city: Albany

first: Dorina

last: Avram

state: NY

address: 43 New Scotland Avenue

department: Center for Immunology and Microbial Disease

institute: Albany Medical Center

hyb_protocol: Samples were hybridized to Mouse Whole Genome, 4x44k (AMADID 026655) arraysincubated in SureHyb chambers for 17hrs at 10rpm in a 65C incubator

scan_protocol: Slides were scanned on an Agilent C scanner and the data extracted using Feature Extraction 10.10.1.1.

data_processing: Data processing using Agilent GeneSpring 11

source_name: PloxPlzfCre Va14 KO2 8456

label_protocol: Amplified cRNA was generated from total RNA using Agilent QuickAmp Labeling Kit, No Dye (Cat. No. 5190-0424).  aRNA was labeled with cyanine dyes using Kreatech ULS aRNA Fluorescent Labeling Kit (Cat. No. EA-006).Concentration, purity and dye-incorporation levels were determined using a Nanodrop ND-1000. Total RNA fidelity was measured using a Bioanalyzer 2100. Cy3 and Cy5 labeled components were normalized to 825ng each and were fragmented at 60C for 30 minutes prior to hybridization.

growth_protocol: Total cells were collected from mouse spleen and liver and processed according to standard protocol.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Intraperitoneal treatment with 4 μg of  α-Galactosylceramide for 1 hour.

value: Invariant natural killer T (iNKT) cells

value: Bcl11b wild-type

source_name: PloxPlzfCre Va14 WT2 8455

value: Bcl11b knock-out


title: 5991878040_E

description: MCF7 AKT2 shRNA

source_name: 2 MCF7 AKT2 shRNA

value: ethanol


title: 5991878040_K

description: MCF7 AKT1 shRNA E2 3hrs

source_name: 16-rep MCF7 AKT1 shRNA E2 3hrs

value: AKT1 shRNA


title: 5991878040_B

description: MCF7 PLKO E2 3 hrs

source_name: 22 MCF7 PLKO E2 3 hrs

value: PLKO


title: 5991878040_J

description: MCF7 AKT1 shRNA E2 3hrs

source_name: 13-rep MCF7 AKT1 shRNA E2 3hrs


title: Sample_9 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum

value: CD


title: 5991878040_C

description: MCF7 AKT1 shRNA

source_name: 11 MCF7 AKT1 shRNA


title: 5991878014_F

description: MCF7 AKT2 shRNA

source_name: 1 MCF7 AKT2 shRNA


title: 5991878014_I

description: MCF7 AKT1 shRNA

source_name: 12 MCF7 AKT1 shRNA


title: 5991878014_J

description: MCF7 AKT2 shRNA

source_name: 3 MCF7 AKT2 shRNA


title: 5991878040_D

description: MCF7 AKT1 shRNA E2 3hrs

source_name: 16 MCF7 AKT1 shRNA E2 3hrs


title: 5991878014_H

description: MCF7 PLKO E2 3 hrs

source_name: 24 MCF7 PLKO E2 3 hrs


title: 5991878014_C

description: MCF7 PLKO E2 3 hrs

source_name: 21 MCF7 PLKO E2 3 hrs


title: 5991878040_G

description: MCF7 AKT2 shRNA

source_name: 4 MCF7 AKT2 shRNA


title: 5991878040_L

description: Stratagene Universal Human Reference RNA (Illumina Catalog # 740000)

tag: reference


title: 5991878014_E

description: MCF7 AKT1 shRNA E2 3hrs

source_name: 13 MCF7 AKT1 shRNA E2 3hrs


title: 5991878014_D

description: MCF7 AKT1 shRNA

source_name: 10 MCF7 AKT1 shRNA


title: Sample_8 CD_0_Ascending Colon

description: CD_0_Ascending Colon

source_name: Ascending Colon


title: Sample_7 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum

source_name: Terminal Ileum


title: Sample_5 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_4 CD_0_Descending Colon

description: CD_0_Descending Colon

source_name: Descending Colon


title: Sample_2 CD_0_Ascending Colon

description: CD_0_Ascending Colon


title: WT Input

type: genomic

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

hyb_protocol: Samples were hybridized to Affymetrix S. cerevisiae Tiling 1.0R arrays according to Affymetrix specifications.

scan_protocol: Samples were scanned on Affymetrix S. cerevisiae Tiling 1.0R arrays according to Affymetrix specifications.

data_processing:
Signal intensity data was analyzed using Affymetrix Tiling Analysis Software (TAS, version 1.1), using default settings, except for a bandwidth of 60 and target intensities were scaled to 500. Normalization is described in the Description column under Samples.
Wig files were generated using a custom Perl script to convert the text output to a wig output. Note, data is Log2(IP/input)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Formaldehyde crosslinked and sonicated DNA from wild-type yeast

label_protocol: IP and Input samples were end-repaired using T4 DNA polymerase, ligated to adaptors, and PCR amplifed (Ligation Mediated-PCR). The resulting PCR products were fragmented and labeled using the GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix), according to the the manufacturer’s instructions.

growth_protocol: Yeast cultures (60 ml) were grown in YPD medium to mid-log phase

extract_protocol: Yeast cells were lysed with glass beads in a multi-tube vortexer for 2 hours at 4˚C . The extracts were sonicated, yielding DNA fragments ~400 bp in size on average. ChIP was performed using an anti-histone H2B polyclonal antibody.

treatment_protocol: Yeast cell cultures were cross-linked with 1% formaldehyde at room temperature for 15-20 minutes, and then the cells were pelleted and snap-frozen in liquid nitrogen.

value: sonication

tag: genotype

value: WT

tag: antibody


title: HBR∆ H2B IP - replicate 2

description: Quantile Normalized Within Groups (TAS software)

source_name: Formaldehyde crosslinked and sonicated DNA from HBR∆ (htb1-∆30-37) mutant yeast

value: sonication + anti-H2B antiboty for ChIP


title: HBR∆ H2B IP - replicate 1

description: Quantile Normalized Between Groups (TAS software)


title: Sample_1 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: WT H2B IP - replicate 1


title: WT H2B IP - replicate 2


title: Sample_3 CD_1_Terminal Ileum

description: CD_1_Terminal Ileum


title: Sample_6 CD_0_Transverse Colon

description: CD_0_Transverse Colon

source_name: Transverse Colon


title: 5991878040_I

description: MCF7 PLKO

source_name: 17-rep MCF7 PLKO


title: mouse liver, DeltaKlf6, 12h after PHx_3

city: Essen

first: Lars

middle: P

last: Bechmann

address: Hufelandstr. 55

department: Gastroenterology and Hepatology

country: Germany

institute: University Hospital Essen

description: KO 470

hyb_protocol: Samples were hybridized on a GeneChip HT MG-430 PM 16-Array Plate using the GeneTitan MC Instrument (Affymetrix) and the GeneTitan Hybridization, Wash, and Stain Kit (Affymetrix)

scan_protocol: Hybridization signals were detected with Affymetrix Gene Chip Scanner 3000

data_processing: CEL files were processed for further data analysis by the GeneChip Command Console Software (AGCC, version 3.2.4, Affymetrix). Robust multiarray average (RMA) normalization was carried out with the Expression Console Software (version 1.2.1, Affymetrix).

source_name: mouse liver tissue of DeltaKlf6 mice 12h after PHx

label_protocol: RNA samples were preprocessed with the 3' IVT Express Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer's instructions

extract_protocol: TRIzol® (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions. RNA was purified utilizing RNeasy Mini Kit (Qiagen).

value: liver


title: mouse liver, DeltaKlf6, 12h after PHx_1

description: KO 440


title: HBR∆ Input


title: mouse liver, wt, 12h after PHx_2

description: wt 460

source_name: mouse liver tissue of C57Bl/6 mice 12h after PHx

value: wildtype


title: mouse liver, DeltaKlf6, 12h after PHx_2

description: KO 453


title: 5991878014_B

description: MCF7 PLKO

source_name: 17 MCF7 PLKO


title: M2c-2

city: Chui-ku,Kobe

first: Kyoko

last: Yamashiro

address: 6-4-3, inatojima-Minamimachi,

institute: Asubio pharma co.,LTD.

description: CD14+ monocytes were cultured with M-CSF for seven days, and then stimulated for 24 h with IL-10

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity > 21pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Whole Genome Ver. 2.0 arrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green  PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters

source_name: Macrophage

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: Human Macrophages were cultured in RPMI1640 medium under 5% CO2 condition.

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen), quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: CD14+ monocytes from human peripheral blood mononuclear cells were cultured with GM-CSF or M-CSF for seven days, and then stimulated for 24 h with LPS+ IFN-γ, IFN-γ, IL-4, IL-1β, and IL-10.

tag: cell population

value: CD14+ monocytes

tag: macrophage subtype


title: M2a-2

description: CD14+ monocytes were cultured with M-CSF for seven days, and then stimulated for 24 h with IL-4


title: mouse liver, wt, 12h after PHx_1

description: wt 445


title: 5991878040_A

description: MCF7 PLKO

source_name: 19 MCF7 PLKO


title: 5991878014_A

source_name: Stratagene Universal Human Reference RNA (Illumina Catalog # 740000)


title: M2b-2

description: CD14+ monocytes were cultured with M-CSF for seven days, and then stimulated for 24 h with IL-1β


title: M1-2

description: CD14+ monocytes were cultured with M-CSF for seven days, and then stimulated for 24 h with LPS and IFN-γ


title: M1(-)-2

description: CD14+ monocytes were cultured with M-CSF for seven days, and then stimulated for 24 h with IFN-γ


title: M2b-1


title: mouse liver, wt, 12h after PHx_3

description: wt 437


title: AT-II_WT_tumor

city: Shanghai

first: Liu

last: Yanfang

address: 800 Xiangyin Road

department: Immunology

institute: Second Military Medical University

description: Gene expression in AT-II cells from WT mouse with tumor cell inoculation subcutaneously

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent technologies, Santa Clara, CA, US)with default settings.

source_name: alveolar type II lung epithelial cells, WT, tumor inoculation

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Lewis lung carcinoma (LLC) was subcutaneously inoculated in Tlr3-/- and WT mice. Two weeks later, lung tissues from Tlr3-/- and WT mice with or without tumor inoculation were dissociated and AT-II cells were sorted using a MoFlo XDP flow cytometer.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: lung

tag: gander

value: female

value: wild type

tag: condition

value: with tumor inoculation


title: M1-1


title: AT-II_Tlr3 deficient_tumor

description: Gene expression in AT-II cells from TLR3 deficient mouse with tumor cell inoculation subcutaneously

source_name: alveolar type II lung epithelial cells, Tlr3 deficient, tumor inoculation

value: Tlr3 deficient,


title: M2a-1


title: M0-2

description: CD14+ monocytes were cultured with M-CSF for seven days, and then incubated for 24 h without additional factors


title: M1(-)-1


title: AT-II_WT_normal

description: Gene expression in AT-II cells from WT mouse without tumor cell inoculation

source_name: alveolar type II lung epithelial cells, WT, without tumor inoculation

value: without tumor inoculation


title: M2c-1


title: AT-II_Tlr3 deficient_normal

description: Gene expression in AT-II cells from TLR3 deficient mouse without tumor cell inoculation

source_name: alveolar type II lung epithelial cells, Tlr3 deficient, without tumor inoculation


title: M0-1


title: N2_5FU_B

city: Houston

first: Natalia

middle: V

last: Kirienko

state: TX

address: 6100 Main St. MS140

department: BioSciences

institute: Rice University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data were analyzed with GC-RMA in the R programming language, using the Bioconductor package gcrma. Analysis was performed using default settings.

organism: Caenorhabditis elegans

label_protocol: Affymetrix standard protocol

growth_protocol: N2 worms were synchronized by hypochlorite treatment. Arrested L1s were plated on 10 cm NGM plates seeded with E. coli OP50 and grown at 15°C overnight then shifted to 25°C for 44h until they reached sterile young adult stage.

extract_protocol: RNA was extracted using TRI Reagent (Molecular Research Center) according to manufacturer's instructions and purified using an RNeasy column (Qiagen).

treatment_protocol: Animals were grown until young adult stage. Afterward, worms were incubated for 8 hours at 25°C in 6-well plates with liquid S basal media + E. coli with DMSO or 5-fluorouracil

tag: media

value: S basal, E. coli OP50

value: Whole organism


title: N2_5FU_A


title: N2_DMSO_C

source_name: N2, DMSO, 8h

value: DMSO


title: N2_5FU_C


title: CCIC/shG9a

city: TAIPEI

first: SHIH-TING

last: CHA

address: 6F., No.2, Syu-jhou Road,

country: Taiwan

institute: National Taiwan University

description: total RNA

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (MS105019) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: •Data analysis by GeneSpring 7.3.1 (Agilent Technologies)

label_protocol: Agilent customer Human R16 miRNA array, total 1205 human miRNAs and 142 human viral miRNAs represented

growth_protocol: 37°C incubator with humidified atmosphere of 5% CO2

extract_protocol: RNA was prepared using TRIZOL RNA isolation protocol following the manufacturer's recommendations (invitrogen).

treatment_protocol: transfection reagent by LIPOFETAMINE2000

tag: ID


title: N2_DMSO_A


title: MCF10CA1a cells treated with 15 µM  RSV (resveratrol) for 9 days, biological replicate 3

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

institute: The University of British Columbia

description:
human highly invasive breast cancer cell line
Sample 12

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: MCF10CA1a cells treated with RSV

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from human breast cancer cell lines using standard phenol:chloroform extraction protocol

value: RSV tested sample

value: breast cancer cells

tag: disease state

value: cancer


title: MCF10CA1a cells treated with 15 µM  RSV (resveratrol) for 9 days, biological replicate 2

description:
human highly invasive breast cancer cell line
Sample 11


title: N2_DMSO_B


title: MCF10CA1a cells treated with vehicle control (ethanol), biological replicate 3

description:
human highly invasive breast cancer cell line
Sample 9

value: Ethanol vehicle control


title: nonCCICs/DNG9A

description: total RNA

tag: age


title: MCF10CA1h cells treated with 15 µM  RSV (resveratrol) for 9 days, biological replicate 1

description:
human lowly invasive breast cancer cell line
Sample 4

source_name: MCF10CA1h cells treated with RSV


title: CCIC/GIPZ

description: total RNA

source_name: CCIC/GIPZ


title: MCF10CA1h cells treated with 15 µM  RSV (resveratrol) for 9 days, biological replicate 2

description:
human lowly invasive breast cancer cell line
Sample 5


title: MCF10CA1a cells treated with vehicle control (ethanol), biological replicate 1

description:
human highly invasive breast cancer cell line
Sample 7


title: MCF10CA1a cells treated with vehicle control (ethanol), biological replicate 2

description:
human highly invasive breast cancer cell line
Sample 8


title: MCF10CA1a cells treated with 15 µM  RSV (resveratrol) for 9 days, biological replicate 1

description:
human highly invasive breast cancer cell line
Sample 10


title: MCF10CA1h cells treated with 15 µM  RSV (resveratrol) for 9 days, biological replicate 3

description:
human lowly invasive breast cancer cell line
Sample 6


title: nonCCIC/pcDNA3

description: total RNA


title: CYJ8_RTOV2

status: Public on Aug 09 2016

first: Je-Keun

last: Rhee

address: 222 Banpo-daero, Seocho-Gu

institute: Catholic Univ. of Korea

hyb_protocol: Genomic DNA from tumor and matched normal samples were simultaneously hybridized onto the array

scan_protocol: the Agilent array was scanned using Agilent Feature Extraction Software

data_processing: The intensity for each probe was corrected for background information and the array CGH data was produced by probe-level summarization.

label_protocol: Labeling was carried out according to the manufacturer’s protocols for Agilent SurePrint G3.

extract_protocol: For genomic DNA extraction, we used the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendation

tag: gender

tag: tissue

value: Right ovary

tag: Stage

value: IVB

value: ovarian serous adenocarcinoma

tag: individual id

source_name: CYJ8 normal

value: blood normal


title: MCF10CA1h cells treated with vehicle control (ethanol), biological replicate 3

description:
human lowly invasive breast cancer cell line
Sample 3

tag: cell line

tag: treatment

tag: cell type


title: CYJ8_D-pouch

value: Peritoneum


title: CYJ8_OM2

value: female

value: Omentum


title: CYJ6_RTOV2

value: IIIC

source_name: CYJ6 normal


title: CYJ8_OM1-2


title: CYJ8_asc

value: ascites


title: CYJ6_DP1


title: CYJ6_RTOV1


title: CYJ6_OM


title: MCF10CA1h cells treated with vehicle control (ethanol), biological replicate 2

description:
human lowly invasive breast cancer cell line
Sample 2


title: CYJ4_RTOV

source_name: CYJ4 normal


title: CYJ6_LTOV2

value: Left ovary


title: CYJ6_LTOV4


title: CYJ6_DP2


title: CYJ6_LTOV1


title: Aspergillus nidulans (sirAdelta) 48 h

city: tsukuba

first: Eriko

last: Itoh

address: 1-1-1 tennodai

institute: university of tsukuba

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

scan_protocol: Genechips were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with GCOS program (version 1.4, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Aspergillus nidulans

source_name: Aspergillus nidulans (sirAdelta) grown  for 48 h

label_protocol: Biotinylated cRNA were prepared from 250 ng total RNA using GeneChip 3' IVT Express Kit.

growth_protocol: Conidia were incubated for 24, 48, and 72 h at 30oC and 120 rpm in 500-ml Erlenmeyer flasks containing 200 ml of MM medium (1% glucose, 0.6% NaNO3, 10 mM KH2PO4, 7 mM KCl, 2 mM MgSO4, 0.25 mg l-1 biotin and 0.2% Hutner's trace metals (v/v)) (Barratt et al. 1965).

extract_protocol: Mycelia were immediately frozen in liquid nitrogen and powdered to prepare total RNA using the RNeasy plant mini kit (Qiagen, Venlo, Netherlands).

treatment_protocol: Mycelia were harvested by filtration and washed by ddH2O.

tag: strain

value: SirAd (biA1; argB2; sirA::argB)

tag: growth time


title: Aspergillus nidulans 24 h

source_name: Aspergillus nidulans grown  for 24 h

value: FGSCA26 (biA1)


title: MCF10CA1h cells treated with vehicle control (ethanol), biological replicate 1

description:
human lowly invasive breast cancer cell line
Sample 1


title: Aspergillus nidulans 48 h

source_name: Aspergillus nidulans grown  for 48 h


title: Aspergillus nidulans 72 h

source_name: Aspergillus nidulans grown  for 72 h


title: CYJ4_LTOV4


title: CYJ6_RTOV3-1


title: Aspergillus nidulans(sirAdelta) 72 h

source_name: Aspergillus nidulans (sirAdelta) grown  for 72 h


title: CYJ4_OM3


title: CYJ4_LTOV3


title: FAP_83_post_Taf_Female

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

hyb_protocol: The Gene Titan Hybridization, Wash and Stain Kit for WT Array Plates (Affymetrix) is used to hybridize 3ug of the labeled cDNA to a multi peg Gene 1.1 ST Array Plate. The hybridization cocktail also contains Control Oligo B2 and 20X Eukaryotic Hybridization Controls as recommended by Affymetrix. Hybridization is carried out for 17 hours at 48C in the Gene Titan MC (Multichannel) Instrument ( Affymetrix). After hybridization the peg array plate is automatically washed and stained and moved to the scanner.

scan_protocol: The peg array plate is automatically moved to the Xenon laser scanner of the Titan MC instrument and scanned at default settings recommended for the peg array.

data_processing:
Probes to Import: Interrogating Probes and Control Probes, Probe filtering: skip, Algorithm: RMA, Background Correction: RMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish
HuGene-1_1-st-v1.r4.pgf
HuGene-1_1-st-v1.r4.mps

source_name: Tafamidis Treated Female

label_protocol: The cDNA generated from the WT Expression Kit is fragmented and biotin labeled with the Affymetrix GeneChip WT Terminal Labeling Kit ( Affymetrix). The cDNA is fragmented with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonucleaseI (APE I). The fragmented cDNA is then labeled with terminal deoxynucleotidyl transferase (TdT) and a biotin reagent.

extract_protocol: RNA Extraction from PAXgene Blood Tubes: Total RNA including small and miRNA is extracted with the PreAnalytiX  PAXgene Blood miRNA kit ( QIAGEN). A semi automated method using the QIAcube (QIAGEN) is used following manufacturer’s instructions. The quantity and quality of the RNA is assessed on a nanodrop and Agilent Bioanalyzer. miRNAeasy kit PN 217004 (Qiagen)

value: Peripheral Whole Blood


title: Aspergillus nidulans (sirAdelta) 24 h

source_name: Aspergillus nidulans (sirAdelta) grown  for 24 h


title: CYJ1_UT2

city: Seoul


title: CYJ4_LTOV1


title: CYJ1_OM2

source_name: CYJ1 normal


title: FAP_8_post_Taf_Male

source_name: Tafamidis Treated Male


title: CYJ1_RTOV


title: CYJ1_asc


title: CYJ4_OM2


title: CYJ4_asc


title: CYJ4_LTOV2


title: CYJ4_OM1


title: FAP_78_post_Taf_Female


title: FAP_71_post_Taf_Female


title: FAP_7_post_Taf_Female


title: FAP_61_post_Taf_Male


title: FAP_5_post_Taf_Male


title: FAP_54_post_Taf_Female


title: FAP_55_post_Taf_Female


title: FAP_44_post_Taf_Male


title: FAP_42_post_Taf_Male


title: FAP_41_post_Taf_Male


title: FAP_43_post_Taf_Male


title: FAP_40_post_Taf_Female


title: FAP_58_post_Taf_Female


title: FAP_53_post_Taf_Female


title: FAP_6_post_Taf_Female


title: FAP_48_post_Taf_Male


title: FAP_49_post_Taf_Female


title: FAP_50_post_Taf_Female


title: FAP_45_post_Taf_Male


title: FAP_47_post_Taf_Male


title: FAP_52_post_Taf_Female


title: CYJ1_PT2-1


title: FAP_38_post_Taf_Male


title: FAP_37_post_Taf_Male


title: FAP_39_post_Taf_Female


title: FAP_33_post_Taf_Male


title: FAP_3_post_Taf_Female


title: FAP_30_post_Taf_Male


title: FAP_31_post_Taf_Female


title: FAP_36_post_Taf_Male


title: FAP_25_post_Taf_Male


title: FAP_26_post_Taf_Male


title: FAP_17_post_Taf_Male


title: FAP_23_post_Taf_Female


title: FAP_18_post_Taf_Female


title: FAP_27_post_Taf_Female


title: FAP_11_post_Taf_Male


title: FAP_13_post_Taf_Female


title: FAP_10_post_Taf_Male


title: FAP_267

source_name: Asymptomatic Male


title: FAP_265


title: FAP_268


title: FAP_269


title: FAP_24_post_Taf_Female


title: FAP_22_post_Taf_Male


title: FAP_260

source_name: Asymptomatic Female


title: FAP_262


title: FAP_264


title: FAP_257


title: FAP_1_post_Taf_Male


title: FAP_256


title: FAP_16_post_Taf_Female


title: FAP_263


title: FAP_259


title: FAP_270


title: FAP_266


title: FAP_14_post_Taf_Female


title: FAP_255_rpt


title: FAP_258


title: CYJ6_asc


title: FAP_253


title: FAP_248


title: FAP_254


title: FAP_255


title: FAP_250


title: FAP_251


title: FAP_252


title: FAP_245


title: FAP_243


title: FAP_242

source_name: Symptomatic Male


title: FAP_247


title: FAP_249


title: FAP_244


title: FAP_241


title: FAP_240


title: FAP_239


title: FAP_9_post_Taf_Male


title: FAP_237


title: FAP_236


title: FAP_235


title: FAP_233

source_name: Symptomatic Female


title: FAP_234


title: FAP_238


title: FAP_232


title: FAP_228


title: FAP_230


title: FAP_226


title: FAP_231


title: FAP_229


title: FAP_221


title: FAP_227


title: FAP_222


title: FAP_217


title: FAP_220


title: FAP_224


title: FAP_225


title: FAP_210


title: FAP_223


title: FAP_214


title: FAP_216


title: FAP_215


title: FAP_213


title: FAP_209


title: FAP_219


title: FAP_211


title: FAP_208


title: FAP_204


title: FAP_205


title: FAP_203


title: FAP_197


title: FAP_207


title: FAP_206


title: FAP_195


title: FAP_201


title: FAP_202


title: FAP_196


title: FAP_200


title: FAP_199


title: FAP_198


title: FAP_190


title: FAP_184


title: FAP_193


title: FAP_191


title: FAP_188


title: FAP_178


title: FAP_180


title: FAP_176


title: FAP_183


title: FAP_181


title: FAP_175


title: FAP_172


title: FAP_170


title: FAP_167


title: FAP_174


title: FAP_141b


title: FAP_189


title: FAP_173


title: FAP_177


title: FAP_169


title: FAP_135b


title: FAP_179


title: FAP_185


title: FAP_168


title: FAP_182


title: FAP_114b


title: FAP_102b


title: FAP_171


title: FAP_096b


title: FAP_187


title: FAP_091b


title: FAP_088b


title: FAP_090b


title: FAP_087b


title: FAP_086b


title: FAP_082b


title: FAP_083b


title: FAP_079b


title: FAP_076b


title: FAP_073b


title: FAP_071b


title: FAP_081b


title: FAP_085b


title: FAP_078b


title: FAP_075b


title: FAP_084b


title: FAP_077b


title: FAP_080b


title: FAP_072b


title: FAP_089b


title: FAP_066b


title: FAP_068b


title: FAP_063b


title: FAP_065b


title: FAP_060b


title: FAP_067b


title: HS_VN_B_19710898 replicate 2

city: London

first: Paolo

last: Salomoni

address: 72 Huntley St

department: Cancer Institute

country: United Kingdom

institute: University College London

description: Biological repeat 2 of 2

hyb_protocol: Hybridization of Cy3 and Cy5 labeled cDNA probe onto coated slide spotted with samples was performed as described in detail in Dvorkina et al.

scan_protocol: Slides were scanned using Inno Scan 700 (Innopsys) using autocalibration to obtain optimized non-saturating images for each fluorophore

data_processing: Image analysis was done with BlueFuse for Microarrays, BlueGnome. The data underwent Cross Channel Correction, followed by Lowess Normalisation. After normalising the data, the mean fold ratio value was derived and a cyber-T test was performed to generate a p-value. The software BASE was used to carry out the normalization. The resulting dataset contained expression ratios of 35065 genes.

source_name: IMR32 PML-I-OE

label_protocol: Labeling protocol described in Dvorkina et al.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit according to the manufacturers’ instructions

treatment_protocol: Neuroblastoma cell line overexpressing PML-I. IMR32 cells were infected with retroviral vector expressing PML-I isoform. Also described in Dvorkina et al.

value: Neuroblastoma cell line

tag: genotype/variation

value: overexpressing PML-I

source_name: IMR32 pBpuro

treatment_protocol: Neuroblastoma cell line transduced with an empty retroviral vector

value: vector control


title: FAP_059b


title: FAP_070b


title: FAP_061b


title: Mature melanosomes_RNase treated_rep2

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

description:
RNA from RNase treated mature melanosomes replicate 2
MMELT 2

hyb_protocol: Hybridization was performed in a SureHyb chamber at 55°C for 20h.

scan_protocol: Microarray scanning was performed using the Agilent Scanner G2505C.

data_processing: The data were quantile normalized and fold-changes were calculated using R/Bioconductor scripts.

source_name: MNT-1 melanosomes

label_protocol: Samples were labeled according to the Agilent miRNA Complete Labeling and Hyb kit protocol.

growth_protocol: MNT-1 cells were cultured in DMEM medium supplemented with 10% FBS, 1% penicillin-streptomycin, and 1% L-glutamine.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Melanosomes were treated with RNase A for 10 min at 37 °C, followed by the addition of RNase inhibitor.

tag: sample type

value: Mature melanosomes

value: RNase


title: FAP_069b


title: FAP_056b


title: HS_VN_A_19710897 replicate 1

description: Biological repeat 1 of 2


title: FAP_055b


title: FAP_057b


title: FAP_053b


title: Mature melanosomes_RNase treated_rep1

description:
RNA from RNase treated mature melanosomes replicate 1
MMELT 1


title: Pre-mature melanosomes_RNase treated_rep1

description:
RNA from RNase treated pre-mature melanosomes replicate 1
PMMELT 1

value: Pre-mature melanosomes


title: FAP_052b


title: FAP_062b

source_name: Male Control


title: FAP_051b


title: Mature melanosomes_untreated.rep1

description:
RNA from untreated mature melanosomes
MMEL 1

value: untreated


title: MNT-1 cells_rep2

description:
Cellular RNA replicate 2
MNT-1 2

source_name: MNT-1 melanoma cells

value: MNT-1 cells


title: MNT-1 cells_rep1

description:
Cellular RNA replicate 1
MNT-1 1


title: Pre-mature melanosomes_RNase treated_rep2

description:
RNA from RNase treated pre-mature melanosomes replicate 2
PMMELT 2


title: Pre-mature melanosomes_untreated.rep1

description:
RNA from untreated pre-mature melanosomes
PMMEL 1


title: FAP_047b


title: FAP_044b


title: FAP_046b


title: FAP_042b


title: FAP_041b


title: FAP_040b


title: FAP_050b


title: FAP_038b


title: FAP_036b


title: FAP_032b


title: FAP_037b


title: FAP_039b


title: FAP_033b


title: FAP_035b


title: FAP_031b


title: FAP_030b


title: FAP_028b


title: FAP_034b


title: FAP_029b


title: FAP_026b


title: FAP_023b


title: FAP_025b


title: FAP_022b


title: FAP_020b


title: FAP_021b


title: FAP_017b


title: FAP_015b


title: FAP_019b


title: FAP_027b


title: FAP_014b


title: FAP_013b


title: Liver, AIN 93W (control) diet, age 24 months, replicate 2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1)

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Mice arrived at the age of 7 weeks and received AIN-93G for 2 weeks acclimatization period. At the age of 9 weeks, dietary intervention was started and the diets were maintained until sacrifice time points at the age of 6, 12, 24 and 28 months.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Prior to sacrifice each mouse was first fasted for 4 hours after which they received an intragastric gavage of 400ul of 0.5% carboxymethyl cellulose, then fasted again for another 6 hours. The animals in CR diet group were fed with half of the portion they normally received 15 min before the first fasting. During the sacrifice, after sedation with a mixture of isoflurane (1.5%), nitrous oxide (70%) and oxygen (30%), liver tissue was snap-frozen and stored at -80C until further analysis.

tag: strain/background

value: male

value: 24 months

value: AIN-93W (control)

tag: nafld status

value: no NAFLD


title: Liver, medium fat diet (25% energy), age 24 months, replicate 6

value: medium fat (25energy%) (MF)

value: NAFLD (IHTG >5%)


title: FAP_012b


title: FAP_007b


title: FAP_009b


title: FAP_008b


title: Liver, calorie restriction (30%), age 24 months, replicate 4

value: caloric restriction, 30% (CR)


title: Liver, calorie restriction (30%), age 12 months, replicate 3

value: 12 months


title: FAP_043b

value: Peripheral Whole Blood


title: FAP_016b


title: FAP_010b


title: FAP_004b


title: Liver, medium fat diet (25% energy), age 24 months, replicate 5


title: FAP_006b


title: FAP_003b


title: Liver, medium fat diet (25% energy), age 12 months, replicate 3


title: Liver, AIN 93W (control) diet, age 24 months, replicate 1


title: FAP_002b


title: Liver, calorie restriction (30%), age 24 months, replicate 2


title: Liver, calorie restriction (30%), age 6 months, replicate 3

value: 6 months


title: FAP_001b


title: Control_079


title: Liver, medium fat diet (25% energy), age 24 months, replicate 8


title: Liver, AIN 93W (control) diet, age 24 months, replicate 7


title: FAP_005b


title: Control_080

source_name: Female Control


title: Control_077


title: Liver, medium fat diet (25% energy), age 12 months, replicate 5


title: Liver, medium fat diet (25% energy), age 12 months, replicate 4


title: Control_076


title: Control_075


title: Liver, AIN 93W (control) diet, age 12 months, replicate 5


title: Control_074


title: Liver, calorie restriction (30%), age 12 months, replicate 1


title: Control_073


title: Control_078


title: Liver, AIN 93W (control) diet, age 12 months, replicate 1


title: Liver, medium fat diet (25% energy), age 6 months, replicate 3


title: Liver, calorie restriction (30%), age 6 months, replicate 2


title: Control_068