title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_169


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_173

status: Public on Apr 01 2011

type: RNA

city: Seattle

first: Radu

last: Dobrin

state: WA

address: 401 Terry Ave N

country: USA

institute: Merck and Co. Inc.

description: Gene expression data from Human omental adipose tissue, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.

hyb_protocol: Microarrays are incubated at 40?C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver? system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

molecule: total RNA

organism: Homo sapiens

source_name: omental adipose

label_protocol: Samples were amplified and labeled using a custom automated two-cycle version of the MessageAmp II kit from Ambion. Hybridizations to custom Agilent microarrays were completed as described in by Hughes et al. Nat Biotech (2001), 19(4):342-7. Sample amplification, labeling, and microarray processing were performed by the Rosetta Inpharmatics Gene Expression Laboratory in Seattle, Wash.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: reference

tag: tissue

value: omental adipose

tag: ID


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_171


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_162


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_174


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_175


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_172


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_161


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_185


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_168


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_166


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_163


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_167


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_165


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_158


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_157


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_159


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_156


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_160


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_155


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_152


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_149


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_151


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_150


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_164


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_148


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_138


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_145


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_144


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_143


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_142


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_147


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_139


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_146


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_137


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_177


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_141


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_136


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_140


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_133


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_130


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_135


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_127


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_128


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_129


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_132


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_153


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_134


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_124


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_126


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_123


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_131


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_121


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_122


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_119


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_118


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_120


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_117


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_154


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_99


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_114


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_116


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_115


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_109


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_95


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_107


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_100


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_105


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_106


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_97


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_96


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_104


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_111


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_110


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_101


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_108


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_103


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_94


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_93


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_112


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_98


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_102


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_113


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_91


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_92


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_88


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_89


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_125


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_90


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_86


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_83


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_82


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_81


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_85


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_84


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_87


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_80


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_77


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_74


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_72


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_73


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_70


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_71


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_75


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_69


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_76


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_68


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_65


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_79


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_60


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_58


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_78


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_62


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_59


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_63


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_64


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_61


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_57


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_66


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_45


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_44


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_54


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_56


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_53


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_48


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_51


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_50


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_35


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_55


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_42


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_47


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_41


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_40


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_52


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_46


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_43


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_32


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_49


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_37


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_39


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_33


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_31


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_36


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_30


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_34


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_38


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_67


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_27


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_15


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_29


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_20


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_8


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_16


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_13


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_12


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_5


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_24


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_23


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_14


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_19


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_9


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_22


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_17


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_21


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_11


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_18


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_28


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_2


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_10


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_1


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_6


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_3


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_26


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_7


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_4


title: MGH_Omental_adipose_pool vs MGH_Omental_Adipose_25


title: MGH_Liver_pool vs MGH_Liver_651

description: Gene expression data from Human livers, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.

source_name: liver

value: liver


title: MGH_Liver_pool vs MGH_Liver_640


title: MGH_Liver_pool vs MGH_Liver_639


title: MGH_Liver_pool vs MGH_Liver_641


title: MGH_Liver_pool vs MGH_Liver_642


title: MGH_Liver_pool vs MGH_Liver_637


title: MGH_Liver_pool vs MGH_Liver_633


title: MGH_Liver_pool vs MGH_Liver_650


title: MGH_Liver_pool vs MGH_Liver_647


title: MGH_Liver_pool vs MGH_Liver_630


title: MGH_Liver_pool vs MGH_Liver_643


title: MGH_Liver_pool vs MGH_Liver_635


title: MGH_Liver_pool vs MGH_Liver_649


title: MGH_Liver_pool vs MGH_Liver_646


title: MGH_Liver_pool vs MGH_Liver_632


title: MGH_Liver_pool vs MGH_Liver_627


title: MGH_Liver_pool vs MGH_Liver_638


title: MGH_Liver_pool vs MGH_Liver_628


title: MGH_Liver_pool vs MGH_Liver_645


title: MGH_Liver_pool vs MGH_Liver_631


title: MGH_Liver_pool vs MGH_Liver_644


title: MGH_Liver_pool vs MGH_Liver_636


title: MGH_Liver_pool vs MGH_Liver_648


title: MGH_Liver_pool vs MGH_Liver_629


title: MGH_Liver_pool vs MGH_Liver_626


title: MGH_Liver_pool vs MGH_Liver_634


title: MGH_Liver_pool vs MGH_Liver_625


title: MGH_Liver_pool vs MGH_Liver_624


title: MGH_Liver_pool vs MGH_Liver_623


title: MGH_Liver_pool vs MGH_Liver_620


title: MGH_Liver_pool vs MGH_Liver_622


title: MGH_Liver_pool vs MGH_Liver_621


title: MGH_Liver_pool vs MGH_Liver_598


title: MGH_Liver_pool vs MGH_Liver_600


title: MGH_Liver_pool vs MGH_Liver_603


title: MGH_Liver_pool vs MGH_Liver_618


title: MGH_Liver_pool vs MGH_Liver_601


title: MGH_Liver_pool vs MGH_Liver_616


title: MGH_Liver_pool vs MGH_Liver_613


title: MGH_Liver_pool vs MGH_Liver_597


title: MGH_Liver_pool vs MGH_Liver_617


title: MGH_Liver_pool vs MGH_Liver_604


title: MGH_Liver_pool vs MGH_Liver_619


title: MGH_Liver_pool vs MGH_Liver_607


title: MGH_Liver_pool vs MGH_Liver_605


title: MGH_Liver_pool vs MGH_Liver_610


title: MGH_Liver_pool vs MGH_Liver_606


title: MGH_Liver_pool vs MGH_Liver_609


title: MGH_Liver_pool vs MGH_Liver_614


title: MGH_Liver_pool vs MGH_Liver_599


title: MGH_Liver_pool vs MGH_Liver_602


title: MGH_Liver_pool vs MGH_Liver_611


title: MGH_Liver_pool vs MGH_Liver_596


title: MGH_Liver_pool vs MGH_Liver_612


title: MGH_Liver_pool vs MGH_Liver_595


title: MGH_Liver_pool vs MGH_Liver_608


title: MGH_Liver_pool vs MGH_Liver_591


title: MGH_Liver_pool vs MGH_Liver_594


title: MGH_Liver_pool vs MGH_Liver_592


title: MGH_Liver_pool vs MGH_Liver_590


title: MGH_Liver_pool vs MGH_Liver_593


title: MGH_Liver_pool vs MGH_Liver_588


title: MGH_Liver_pool vs MGH_Liver_589


title: MGH_Liver_pool vs MGH_Liver_615


title: MGH_Liver_pool vs MGH_Liver_582


title: MGH_Liver_pool vs MGH_Liver_581


title: MGH_Liver_pool vs MGH_Liver_587


title: MGH_Liver_pool vs MGH_Liver_580


title: MGH_Liver_pool vs MGH_Liver_584


title: MGH_Liver_pool vs MGH_Liver_579


title: MGH_Liver_pool vs MGH_Liver_586


title: MGH_Liver_pool vs MGH_Liver_577


title: MGH_Liver_pool vs MGH_Liver_576


title: MGH_Liver_pool vs MGH_Liver_578


title: MGH_Liver_pool vs MGH_Liver_583


title: MGH_Liver_pool vs MGH_Liver_574


title: MGH_Liver_pool vs MGH_Liver_585


title: MGH_Liver_pool vs MGH_Liver_569


title: MGH_Liver_pool vs MGH_Liver_575


title: MGH_Liver_pool vs MGH_Liver_568


title: MGH_Liver_pool vs MGH_Liver_573


title: MGH_Liver_pool vs MGH_Liver_571


title: MGH_Liver_pool vs MGH_Liver_566


title: MGH_Liver_pool vs MGH_Liver_572


title: MGH_Liver_pool vs MGH_Liver_567


title: MGH_Liver_pool vs MGH_Liver_565


title: MGH_Liver_pool vs MGH_Liver_562


title: MGH_Liver_pool vs MGH_Liver_563


title: MGH_Liver_pool vs MGH_Liver_564


title: MGH_Liver_pool vs MGH_Liver_559


title: MGH_Liver_pool vs MGH_Liver_554


title: MGH_Liver_pool vs MGH_Liver_561


title: MGH_Liver_pool vs MGH_Liver_552


title: MGH_Liver_pool vs MGH_Liver_560


title: MGH_Liver_pool vs MGH_Liver_545


title: MGH_Liver_pool vs MGH_Liver_570


title: MGH_Liver_pool vs MGH_Liver_553


title: MGH_Liver_pool vs MGH_Liver_555


title: MGH_Liver_pool vs MGH_Liver_546


title: MGH_Liver_pool vs MGH_Liver_547


title: MGH_Liver_pool vs MGH_Liver_542


title: MGH_Liver_pool vs MGH_Liver_551


title: MGH_Liver_pool vs MGH_Liver_557


title: MGH_Liver_pool vs MGH_Liver_549


title: MGH_Liver_pool vs MGH_Liver_550


title: MGH_Liver_pool vs MGH_Liver_558


title: MGH_Liver_pool vs MGH_Liver_541


title: MGH_Liver_pool vs MGH_Liver_537


title: MGH_Liver_pool vs MGH_Liver_544


title: MGH_Liver_pool vs MGH_Liver_543


title: MGH_Liver_pool vs MGH_Liver_538


title: MGH_Liver_pool vs MGH_Liver_540


title: MGH_Liver_pool vs MGH_Liver_548


title: MGH_Liver_pool vs MGH_Liver_539


title: MGH_Liver_pool vs MGH_Liver_536


title: MGH_Liver_pool vs MGH_Liver_556


title: MGH_Liver_pool vs MGH_Liver_529


title: MGH_Liver_pool vs MGH_Liver_528


title: MGH_Liver_pool vs MGH_Liver_530


title: MGH_Liver_pool vs MGH_Liver_535


title: MGH_Liver_pool vs MGH_Liver_520


title: MGH_Liver_pool vs MGH_Liver_523


title: MGH_Liver_pool vs MGH_Liver_524


title: MGH_Liver_pool vs MGH_Liver_531


title: MGH_Liver_pool vs MGH_Liver_532


title: MGH_Liver_pool vs MGH_Liver_525


title: MGH_Liver_pool vs MGH_Liver_522


title: MGH_Liver_pool vs MGH_Liver_533


title: MGH_Liver_pool vs MGH_Liver_534


title: MGH_Liver_pool vs MGH_Liver_521


title: MGH_Liver_pool vs MGH_Liver_526


title: MGH_Liver_pool vs MGH_Liver_518


title: MGH_Liver_pool vs MGH_Liver_527


title: MGH_Liver_pool vs MGH_Liver_512


title: MGH_Liver_pool vs MGH_Liver_509


title: MGH_Liver_pool vs MGH_Liver_517


title: MGH_Liver_pool vs MGH_Liver_510


title: MGH_Liver_pool vs MGH_Liver_513


title: MGH_Liver_pool vs MGH_Liver_514


title: MGH_Liver_pool vs MGH_Liver_515


title: MGH_Liver_pool vs MGH_Liver_508


title: MGH_Liver_pool vs MGH_Liver_516


title: MGH_Liver_pool vs MGH_Liver_506


title: MGH_Liver_pool vs MGH_Liver_519


title: MGH_Liver_pool vs MGH_Liver_507


title: MGH_Liver_pool vs MGH_Liver_511


title: MGH_Liver_pool vs MGH_Liver_501


title: MGH_Liver_pool vs MGH_Liver_502


title: MGH_Liver_pool vs MGH_Liver_504


title: MGH_Liver_pool vs MGH_Liver_505


title: MGH_Liver_pool vs MGH_Liver_499


title: MGH_Liver_pool vs MGH_Liver_495


title: MGH_Liver_pool vs MGH_Liver_500


title: MGH_Liver_pool vs MGH_Liver_483


title: MGH_Liver_pool vs MGH_Liver_485


title: MGH_Liver_pool vs MGH_Liver_488


title: MGH_Liver_pool vs MGH_Liver_494


title: MGH_Liver_pool vs MGH_Liver_492


title: MGH_Liver_pool vs MGH_Liver_496


title: MGH_Liver_pool vs MGH_Liver_489


title: MGH_Liver_pool vs MGH_Liver_484


title: MGH_Liver_pool vs MGH_Liver_490


title: MGH_Liver_pool vs MGH_Liver_480


title: MGH_Liver_pool vs MGH_Liver_486


title: MGH_Liver_pool vs MGH_Liver_479


title: MGH_Liver_pool vs MGH_Liver_491


title: MGH_Liver_pool vs MGH_Liver_497


title: MGH_Liver_pool vs MGH_Liver_477


title: MGH_Liver_pool vs MGH_Liver_478


title: MGH_Liver_pool vs MGH_Liver_503


title: MGH_Liver_pool vs MGH_Liver_482


title: MGH_Liver_pool vs MGH_Liver_498


title: MGH_Liver_pool vs MGH_Liver_473


title: MGH_Liver_pool vs MGH_Liver_487


title: MGH_Liver_pool vs MGH_Liver_481


title: MGH_Liver_pool vs MGH_Liver_476


title: MGH_Liver_pool vs MGH_Liver_471


title: MGH_Liver_pool vs MGH_Liver_470


title: MGH_Liver_pool vs MGH_Liver_475


title: MGH_Liver_pool vs MGH_Liver_469


title: MGH_Liver_pool vs MGH_Liver_466


title: MGH_Liver_pool vs MGH_Liver_467


title: MGH_Liver_pool vs MGH_Liver_465


title: MGH_Liver_pool vs MGH_Liver_468


title: MGH_Liver_pool vs MGH_Liver_457


title: MGH_Liver_pool vs MGH_Liver_462


title: MGH_Liver_pool vs MGH_Liver_455


title: MGH_Liver_pool vs MGH_Liver_456


title: MGH_Liver_pool vs MGH_Liver_464


title: MGH_Liver_pool vs MGH_Liver_461


title: MGH_Liver_pool vs MGH_Liver_458


title: MGH_Liver_pool vs MGH_Liver_460


title: MGH_Liver_pool vs MGH_Liver_463


title: MGH_Liver_pool vs MGH_Liver_459


title: MGH_Liver_pool vs MGH_Liver_454


title: MGH_Liver_pool vs MGH_Liver_450


title: MGH_Liver_pool vs MGH_Liver_452


title: MGH_Liver_pool vs MGH_Liver_447


title: MGH_Liver_pool vs MGH_Liver_493


title: MGH_Liver_pool vs MGH_Liver_453


title: MGH_Liver_pool vs MGH_Liver_444


title: MGH_Liver_pool vs MGH_Liver_441


title: MGH_Liver_pool vs MGH_Liver_449


title: MGH_Liver_pool vs MGH_Liver_451


title: MGH_Liver_pool vs MGH_Liver_442


title: MGH_Liver_pool vs MGH_Liver_443


title: MGH_Liver_pool vs MGH_Liver_445


title: MGH_Liver_pool vs MGH_Liver_440


title: MGH_Liver_pool vs MGH_Liver_437


title: MGH_Liver_pool vs MGH_Liver_446


title: MGH_Liver_pool vs MGH_Liver_448


title: MGH_Liver_pool vs MGH_Liver_439


title: MGH_Liver_pool vs MGH_Liver_438


title: MGH_Liver_pool vs MGH_Liver_434


title: MGH_Liver_pool vs MGH_Liver_431


title: MGH_Liver_pool vs MGH_Liver_435


title: MGH_Liver_pool vs MGH_Liver_433


title: MGH_Liver_pool vs MGH_Liver_430


title: MGH_Liver_pool vs MGH_Liver_429


title: MGH_Liver_pool vs MGH_Liver_423


title: MGH_Liver_pool vs MGH_Liver_426


title: MGH_Liver_pool vs MGH_Liver_472


title: MGH_Liver_pool vs MGH_Liver_422


title: MGH_Liver_pool vs MGH_Liver_436


title: MGH_Liver_pool vs MGH_Liver_428


title: MGH_Liver_pool vs MGH_Liver_424


title: MGH_Liver_pool vs MGH_Liver_421


title: MGH_Liver_pool vs MGH_Liver_415


title: MGH_Liver_pool vs MGH_Liver_432


title: MGH_Liver_pool vs MGH_Liver_417


title: MGH_Liver_pool vs MGH_Liver_418


title: MGH_Liver_pool vs MGH_Liver_416


title: MGH_Liver_pool vs MGH_Liver_425


title: MGH_Liver_pool vs MGH_Liver_427


title: MGH_Liver_pool vs MGH_Liver_419


title: MGH_Liver_pool vs MGH_Liver_420


title: MGH_Liver_pool vs MGH_Liver_474


title: MGH_Liver_pool vs MGH_Liver_410


title: MGH_Liver_pool vs MGH_Liver_412


title: MGH_Liver_pool vs MGH_Liver_411


title: MGH_Liver_pool vs MGH_Liver_414


title: MGH_Liver_pool vs MGH_Liver_409


title: MGH_Liver_pool vs MGH_Liver_408


title: MGH_Liver_pool vs MGH_Liver_405


title: MGH_Liver_pool vs MGH_Liver_413


title: MGH_Liver_pool vs MGH_Liver_406


title: MGH_Liver_pool vs MGH_Liver_403


title: MGH_Liver_pool vs MGH_Liver_404


title: MGH_Liver_pool vs MGH_Liver_401


title: MGH_Liver_pool vs MGH_Liver_400


title: MGH_Liver_pool vs MGH_Liver_402


title: MGH_Liver_pool vs MGH_Liver_397


title: MGH_Liver_pool vs MGH_Liver_396


title: MGH_Liver_pool vs MGH_Liver_399


title: MGH_Liver_pool vs MGH_Liver_395


title: MGH_Liver_pool vs MGH_Liver_391


title: MGH_Liver_pool vs MGH_Liver_392


title: MGH_Liver_pool vs MGH_Liver_407


title: MGH_Liver_pool vs MGH_Liver_394


title: MGH_Liver_pool vs MGH_Liver_393


title: MGH_Liver_pool vs MGH_Liver_382


title: MGH_Liver_pool vs MGH_Liver_383


title: MGH_Liver_pool vs MGH_Liver_379


title: MGH_Liver_pool vs MGH_Liver_378


title: MGH_Liver_pool vs MGH_Liver_381


title: MGH_Liver_pool vs MGH_Liver_377


title: MGH_Liver_pool vs MGH_Liver_376


title: MGH_Liver_pool vs MGH_Liver_390


title: MGH_Liver_pool vs MGH_Liver_384


title: MGH_Liver_pool vs MGH_Liver_385


title: MGH_Liver_pool vs MGH_Liver_389


title: MGH_Liver_pool vs MGH_Liver_388


title: MGH_Liver_pool vs MGH_Liver_380


title: MGH_Liver_pool vs MGH_Liver_386


title: MGH_Liver_pool vs MGH_Liver_372


title: MGH_Liver_pool vs MGH_Liver_387


title: MGH_Liver_pool vs MGH_Liver_371


title: MGH_Liver_pool vs MGH_Liver_370


title: MGH_Liver_pool vs MGH_Liver_373


title: MGH_Liver_pool vs MGH_Liver_375


title: MGH_Liver_pool vs MGH_Liver_369


title: MGH_Liver_pool vs MGH_Liver_368


title: MGH_Liver_pool vs MGH_Liver_366


title: MGH_Liver_pool vs MGH_Liver_367


title: MGH_Liver_pool vs MGH_Liver_358


title: MGH_Liver_pool vs MGH_Liver_361


title: MGH_Liver_pool vs MGH_Liver_357


title: MGH_Liver_pool vs MGH_Liver_363


title: MGH_Liver_pool vs MGH_Liver_360


title: MGH_Liver_pool vs MGH_Liver_365


title: MGH_Liver_pool vs MGH_Liver_362


title: MGH_Liver_pool vs MGH_Liver_353


title: MGH_Liver_pool vs MGH_Liver_374


title: MGH_Liver_pool vs MGH_Liver_359


title: MGH_Liver_pool vs MGH_Liver_364


title: MGH_Liver_pool vs MGH_Liver_398


title: MGH_Liver_pool vs MGH_Liver_351


title: MGH_Liver_pool vs MGH_Liver_356


title: MGH_Liver_pool vs MGH_Liver_352


title: MGH_Liver_pool vs MGH_Liver_354


title: MGH_Liver_pool vs MGH_Liver_348


title: MGH_Liver_pool vs MGH_Liver_343


title: MGH_Liver_pool vs MGH_Liver_355


title: MGH_Liver_pool vs MGH_Liver_347


title: MGH_Liver_pool vs MGH_Liver_344


title: MGH_Liver_pool vs MGH_Liver_349


title: MGH_Liver_pool vs MGH_Liver_345


title: MGH_Liver_pool vs MGH_Liver_350


title: MGH_Liver_pool vs MGH_Liver_342


title: MGH_Liver_pool vs MGH_Liver_346


title: MGH_Liver_pool vs MGH_Liver_329


title: MGH_Liver_pool vs MGH_Liver_331


title: MGH_Liver_pool vs MGH_Liver_337


title: MGH_Liver_pool vs MGH_Liver_338


title: MGH_Liver_pool vs MGH_Liver_335


title: MGH_Liver_pool vs MGH_Liver_339


title: MGH_Liver_pool vs MGH_Liver_332


title: MGH_Liver_pool vs MGH_Liver_330


title: MGH_Liver_pool vs MGH_Liver_328


title: MGH_Liver_pool vs MGH_Liver_320


title: MGH_Liver_pool vs MGH_Liver_327


title: MGH_Liver_pool vs MGH_Liver_324


title: MGH_Liver_pool vs MGH_Liver_318


title: MGH_Liver_pool vs MGH_Liver_321


title: MGH_Liver_pool vs MGH_Liver_317


title: MGH_Liver_pool vs MGH_Liver_314


title: MGH_Liver_pool vs MGH_Liver_340


title: MGH_Liver_pool vs MGH_Liver_316


title: MGH_Liver_pool vs MGH_Liver_323


title: MGH_Liver_pool vs MGH_Liver_319


title: MGH_Liver_pool vs MGH_Liver_322


title: MGH_Liver_pool vs MGH_Liver_341


title: MGH_Liver_pool vs MGH_Liver_336


title: MGH_Liver_pool vs MGH_Liver_326


title: MGH_Liver_pool vs MGH_Liver_325


title: MGH_Liver_pool vs MGH_Liver_333


title: MGH_Liver_pool vs MGH_Liver_313


title: MGH_Liver_pool vs MGH_Liver_315


title: MGH_Liver_pool vs MGH_Liver_305


title: MGH_Liver_pool vs MGH_Liver_304


title: MGH_Liver_pool vs MGH_Liver_311


title: MGH_Liver_pool vs MGH_Liver_306


title: MGH_Liver_pool vs MGH_Liver_301


title: HPC5-HPC5M replicate 1

city: Leicestershire

first: Amy

last: John

address: Loughborough

country: United Kingdom

institute: University of Nottingham

description: Biological replicate 1 of 3. Control HPC5 to HPC5 grown in Mac

hyb_protocol: The slides used for the genome analysis were γ APS coated, A+ bar-coded Schott nexterion slides. The slides were printed according to campy dense array gal by Microgrid II 600 robot using TAS software version V2.4.03. They had 12 pins with a 26 x 26 pin grid configuration. The spacing between the spots was 0.165mm and the slides were prepared at 60% humidity. Each slide was printed with duplicate sets of oligos for NCTC 11168, RM1221 and RM2228. A sample of each labelled probe (one cy3, one cy5) for each slide was taken to be hybridized which contained 500ng of labelled DNA and placed them together in a 0.5 ml tube.  The volume was adjusted to 4.5µl total volume by adding nuclease free water. To each tube 0.5 µl of Fragmentation Buffer was added before being incubated at 70OC (in Thermo Cycler) for 2 min followed by 0.5 µl of Stop Solution (Ambion Kit #8740).  This was followed by the addition of 2µl Lithium Heperin (to reduce non specific hybridization). Add 100 µl of Schott 1x Hybridization Buffer which was pre-warmed to 50OC and added to the probe carefully to avoid introducing any air bubbles.  The total volume was 107.5 µl.  The DNA microarray slides were blocked before hybridisation by using blocking solution (5xSSC, 0.2%SDS, 1%BSA). After blocking, the slides were washed in ultra pure water and then in 100% ethanol. The prepared slides were kept in the slide holder and were inserted into the TECAN HS 4800 chamber. Approximately 5 min before the probes were inserted they were heated to 95o C for 2 min and then spun at 15.000rpm for 5 minutes in a microcentrifuge to pellet up any impurities. The probe was injected into the hybridisation chamber. The hybridisation was done at 45º C for 16h with gentle agitation. After hybridisation the slides were washed in 1 X SSC buffer with 0.6% SDS for 2 min, followed by two washes in 0.06 X SSC buffer, each for 2 min. The slides are then dried at 23º C with nitrogen.

scan_protocol: Slides were scanned using Axon Genepix 4200AL scanner (Molecular Devices Corporation, Sunnyvale, CA ) at 532 (Cy3) and 635 (Cy5) excitation wavelengths with 5 µm resolution. The slides were scanned using the Auto PMT function with the threshold for saturation set at 0.05%.  Fluorescent spot intensities were quantified using Genepix Pro 6.0 software. Spots were excluded from further analysis if they contain anomalous spot morphology or were within regions of non-specific fluorescence.

data_processing: The data was analysed by Genespring GX 7.3  and the oligos which have more than 2 fold change and p<0.05 were selected for further studies.

organism: Campylobacter jejuni

source_name: Campylobacter cells isolated from Chicken

label_protocol: 1. Add 5 μl of nuclease free water and heat it to 42°C for 5 min.  2. Add 3 μl labelling buffer to it (25 mg/ ml sodium bicarbonate).  3. Dissolve 1 vial of AF555/645 (Fisher, UK) in 2 μl DMSO and vortex it for 10 sec and add it to 8 μl cDNA labelling buffer mix.  4. Incubate at room temperature for 1 hr in the dark.  5. Add 80 μl water and 10 μl of sodium acetate (3M) and purify using QIA PCR purification kit but wash three times with 70% ethanol.  7. Precipitate DNA using 3M sodium acetate and 100% ethanol and resuspend it in nuclease free water.   8. Quantify and check label.

growth_protocol: C. jejuni HPC5 were grown in Nutrient broth (NB No. 2, Oxoid, UK) until it reaches 108 cfu /ml. For using it as a control C. jejuni HPC5 was grown in MAC which has an air composition of 5.6% oxygen, 3.6% hydrogen, 7.3% carbon dioxide and 83% nitrogen. As samples the same strain was grown in jar and in MAC. To set up a jar (3.5L, Oxoid) to the required microaerophilic conditions, a vacuum is created to -22 psi and then air mixture of 85% v/v nitrogen, 10% v/v carbon dioxide and 5% v/v hydrogen (Air Products, Crewe, UK) is introduced into the jar. This resulted in a microaerobic atmosphere containing approximately 5.6% oxygen, 3.6% hydrogen, 7.3% carbon dioxide and 83% nitrogen.

extract_protocol: The cells were collected by spinning it in pre chilled tubes @ 6000x g for 15 min in beckman centrifuge. Maximum Enhancement Reagent of 200 µl was preheated to 95ºC and was added to the tube. The cell mix was heated at 95 ºC for 4 min. To it 1ml of trizol was added and was mixed well. It was incubated at room temperature for 5 min. After incubation it was spun for 15 min at 12000 x g at 4 ºC. Approximately 400 µl of the top phase was transferred to a fresh eppendorf. To it 700 µl of 100% ethanol was added and mixed thoroughly. This was used in RNA clean up kit (Qiagen, UK) according to the manufacturer’s instructions. For the synthesis of cDNA, SuperscriptTM direct cDNA labelling system (Invitrogen, UK) was used according to manufacturer’s instructions.    QIA quick PCR Purification kit was used for purifying the product (Qiagen, UK).  The cDNA produced was ethanol precipitated by adding 0.1 v of sodium acetate (3M) and 2.5 v 100% ethanol.

treatment_protocol: Not applicable

tag: strain

tag: sample type

value: control (representing 7 independent preps of C. jejuni HPC5)

value: test

tag: growth protocol

value: anaerobic atmosphere


title: MGH_Liver_pool vs MGH_Liver_300


title: MGH_Liver_pool vs MGH_Liver_310


title: MGH_Liver_pool vs MGH_Liver_302


title: HPC5-HPC5M replicate 2

description: Biological replicate 2 of 3. Control HPC5 to HPC5 grown in Mac


title: HPC5-HPC5M replicate 3

description: Biological replicate 3 of 3. Control HPC5 to HPC5 grown in Mac


title: HPC5-HPC5J replicate 2

description: Biological replicate 2 of 3. Control HPC5 toHPC5 grown in Jar

value: microaerobic atmosphere


title: MGH_Liver_pool vs MGH_Liver_303


title: MGH_Liver_pool vs MGH_Liver_308


title: MGH_Liver_pool vs MGH_Liver_307


title: MGH_Liver_pool vs MGH_Liver_334


title: MGH_Liver_pool vs MGH_Liver_309


title: MGH_Liver_pool vs MGH_Liver_290


title: MGH_Liver_pool vs MGH_Liver_312


title: MGH_Liver_pool vs MGH_Liver_295


title: MGH_Liver_pool vs MGH_Liver_294


title: MGH_Liver_pool vs MGH_Liver_296


title: MGH_Liver_pool vs MGH_Liver_293


title: MGH_Liver_pool vs MGH_Liver_297


title: MGH_Liver_pool vs MGH_Liver_298


title: MGH_Liver_pool vs MGH_Liver_292


title: MGH_Liver_pool vs MGH_Liver_299


title: MGH_Liver_pool vs MGH_Liver_291


title: MGH_Liver_pool vs MGH_Liver_289


title: HPC5-HPC5J replicate 1

description: Biological replicate 1 of 3. Control HPC5 to HPC5 grown in Jar


title: MGH_Liver_pool vs MGH_Liver_288


title: MGH_Liver_pool vs MGH_Liver_283


title: MGH_Liver_pool vs MGH_Liver_285


title: CD11b+ F4/80+ FOXP3+ rep2

city: Scottsdale

first: Cheryl

middle: E

last: Myers

state: AZ

address: 13400 E Shea Blvd

department: Immunology

institute: Mayo Clinic College of Medicine

description: MacReg

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used according to manufacturers instructions, and labeled samples were hybridized to the Mouse whole genome 4X44k chip.

scan_protocol: GE2-v5_95_Feb07 (Read Only), using Agilent Technologies Scanner G2505B US45102967

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1). Using Genespring GX11, the data was normalized   to the 75th percentile and a   baseline transformation to median of all samples was performed. Probes were filtered by percentile, removing those that fall beneath the 20th %. Probes were then filtered by flags removing those that did not have passing or marginal in 3 of the 6 samples. The two treatment populations (Mac Foxp3 neg and Mac Foxp3 pos were averaged and a t-test was performed to select genes that were significantly differentialy expressed between both populations. This list was further screened for a minimum of 2 fold change between the populations.

organism: Mus musculus

source_name: spleen of C57 FOXP3 GFP mice

label_protocol: Agilent Low RNA Input Linear Amplification Kit PLUS  was used incorporating cy3, according to manufacturers instructions

growth_protocol: Freshly isolated Macrophages and MacRegs were derived from 4-6  month old  C57 FOXP3/GFP mice through two consecutive rounds of fluorescent cell sorting using CD11b and F4/80 and GFP FOXP3. Freshly isolated CD4+Foxp3- and CD4+Foxp3+ cells were obtained from C57 FOXP3/GFP mice of the same age, through two consecutive rounds of fluorescent cell sorting.  Three independent isolations were executed on separate days to obtain biological replicates.

extract_protocol: RNA was extracted according to manufacturers instructionsusing the  Rneasy MiniKit (Qiagen)  , RNA was measured with the NanoDrop 1000 (Thermo Scientific) and  integrity verified through  Agilent Bioanalyzer 2100  using the nano chip.

tag: cell type

value: C57 FOXP3/GFP


title: lateral nasal gland_2g1-3

city: Albany

first: Xin

last: Zhou

state: NY

address: Empire State Plaza P.O. Box 509

department: NY State Dept. of Health

institute: Wadsworth Center

description: Gene expression data from lateral nasal gland of male Cyp2g1-null mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Expression Set 430A 2.0 Chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Cyp2g1-null male mouse 2-3-month-old lateral nasal gland

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: lateral nasal gland

value: 129/Sv x C57BL/6 mixed

tag: genotype

tag: gender

value: male

tag: age


title: MGH_Liver_pool vs MGH_Liver_284


title: MGH_Liver_pool vs MGH_Liver_287


title: CD4+Foxp3-_rep3

description: Tconvetional

value: CD4+ Foxp3-


title: MGH_Liver_pool vs MGH_Liver_286


title: MGH_Liver_pool vs MGH_Liver_278


title: lateral nasal gland_2g1-2


title: CD4+Foxp3+_rep1

description: Treg

value: CD4+ Foxp3+


title: CD11b+ F4/80+ FOXP3+ rep1

description: MacReg


title: MGH_Liver_pool vs MGH_Liver_280


title: CD11b+ F4/80+ FOXP3- rep2

description: Macrophage


title: CD11b+ F4/80+ FOXP3+ rep3

description: MacReg


title: CD11b+ F4/80+ FOXP3- rep1

description: Macrophage


title: CD11b+ F4/80+ FOXP3- rep3

description: Macrophage


title: MGH_Liver_pool vs MGH_Liver_282


title: CD4+Foxp3-_rep1

description: Tconvetional


title: MGH_Liver_pool vs MGH_Liver_276


title: MGH_Liver_pool vs MGH_Liver_279


title: CD4+Foxp3+_rep2

description: Treg


title: MGH_Liver_pool vs MGH_Liver_275


title: MGH_Liver_pool vs MGH_Liver_277


title: MGH_Liver_pool vs MGH_Liver_281


title: MGH_Liver_pool vs MGH_Liver_274


title: CD4+Foxp3-_rep2

description: Tconvetional


title: CD4+Foxp3+_rep3

description: Treg


title: HPC5-HPC5J replicate 3

description: Biological replicate 3 of 3. Control HPC5 to HPC5 grown in Jar


title: lateral nasal gland_B6-4

description: Gene expression data from lateral nasal gland of male B6 mice

source_name: B6 male mouse 2-3-month-old lateral nasal gland

value: wild type


title: lateral nasal gland_B6-2


title: lateral nasal gland_B6-1


title: lateral nasal gland_129-2

description: Gene expression data from lateral nasal gland of male 129/Sv mice

source_name: 129/Sv male mouse 2-3-month-old lateral nasal gland


title: lateral nasal gland_2g1-1


title: lateral nasal gland_129-1


title: MGH_Liver_pool vs MGH_Liver_273


title: MGH_Liver_pool vs MGH_Liver_272


title: MGH_Liver_pool vs MGH_Liver_268


title: lateral nasal gland_B6-3


title: Mouse PDA cell line (P53 17.1)

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

institute: Institute of Cancer Research (ICR), London

description: Mouse pancreatic ductal adenocarcinoma cell line derived from p48-cre, kras, p53 fl/wt mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430a  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed using Bioconductor and normalized using RMA using R package.

source_name: p48-cre, Kras, p53 fl/wt mouse

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

extract_protocol: Extracted RNA using RNAeasy kit

tag: cell line


title: Mouse PDA cell line (P53 10.1)

value: pancreatic ductal adenocarcinoma cell line derived from p48-cre, kras, p53 fl/wt mice


title: Mouse PDA cell line (P53 12.4)


title: MGH_Liver_pool vs MGH_Liver_269


title: MGH_Liver_pool vs MGH_Liver_270


title: MGH_Liver_pool vs MGH_Liver_266


title: Mouse PDA cell line (P53 11.5)


title: Mouse PDA cell line (p53 2.1.1)


title: Mouse PDA cell line (P53 13.1)


title: MGH_Liver_pool vs MGH_Liver_267


title: MGH_Liver_pool vs MGH_Liver_261


title: MGH_Liver_pool vs MGH_Liver_264


title: Mouse PDA cell line (P53 11.1)


title: MGH_Liver_pool vs MGH_Liver_265


title: MGH_Liver_pool vs MGH_Liver_262


title: MGH_Liver_pool vs MGH_Liver_263


title: MGH_Liver_pool vs MGH_Liver_271


title: Mouse PDA cell line (Ink5.1)

description: Mouse pancreatic ductal adenocarcinoma cell line derived from p48-cre, kras, Ink4a/Arf mice

source_name: p48-cre, Kras, Ink4a/Arf fl/wt mouse


title: Mouse PDA cell line (P53 1.1D3)


title: MGH_Liver_pool vs MGH_Liver_256


title: Mouse PDA cell line (Ink2.7)

value: pancreatic ductal adenocarcinoma cell line derived from p48-cre, kras, Ink4a/Arf mice


title: Mouse PDA cell line (Ink3.1)


title: MGH_Liver_pool vs MGH_Liver_259


title: Mouse PDA cell line (Ink4.1)


title: Mouse PDA cell line (Ink10.1)


title: MGH_Liver_pool vs MGH_Liver_260


title: MGH_Liver_pool vs MGH_Liver_258


title: Mouse PDA cell line (Ink2.2)


title: Mouse PDA cell line (Ink12.1)


title: MGH_Liver_pool vs MGH_Liver_255


title: MGH_Liver_pool vs MGH_Liver_251


title: MGH_Liver_pool vs MGH_Liver_257


title: REST shRNA KD 2

city: Singapore

first: hongbing

last: yu

address: 60 biopolis street, #02-01, genome

department: stem cell and development

country: Singapore

institute: genome institute of singapore

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: REST shRNA KD 2

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: treatment

value: REST knockdown


title: REST shRNA KD 3

description: replicate 3

source_name: REST shRNA KD 3


title: MGH_Liver_pool vs MGH_Liver_249


title: pSuper vector control 3

description: replicate 3

source_name: pSuper vector control 3

value: control


title: MGH_Liver_pool vs MGH_Liver_247


title: Activated medium Experiment 3

city: New York

first: Sally

last: Amundson

department: Center for Radiological Research

institute: Columbia University

description: biological repeat 3

hyb_protocol: Hybridization was carried out with active mixing using the MAUI Hybridization System (BioMicro Systems, Salt Lake City, UT) for 16 hours in Deposition Hybridization Buffer (Agilent) at 65oC in the presence of the blockers human CoT1, yeast tRNA and poly dA.  Hybridized slides were washed at room temperature once in 0.5X SSC, 0.01% SDS for 5 minutes and again in 0.06X SSC for 5 minutes.

scan_protocol: Slides were scanned on an Agilent Microarray Scanner, 100% PMT voltage, 10 uM resolution scans.

data_processing: Images were processed using ArraySuite 2.1 extensions in the IPLab program (Scanalytics Inc., Fairfax, VA) as described in Chen et al., 2002 (PMID: 12217912).

source_name: TK6 exposed to activated medium 3 hours

label_protocol: Fluorescently labeled cDNA was prepared from mock-irradiated control and activated medium control whole-cell RNA by a single round of reverse transcription (BRL Superscript II) in the presence of aminoallyl dUTP (Sigma-Aldrich), followed by coupling to monofunctional NHS-ester Cy3 or Cy5 dye (Amersham) (Amundson and Fornace, 2004. PMID:14970650)

growth_protocol: TK6 cells were maintained in exponential growth at densities of 1-10 x 10E5 cells/ml in RPMI 1640 medium supplemented with 10% heat-inactivated (56oC for 45 minutes) fetal calf serum and 100 U/ml penicillin and 100 μg/ml streptomycin in a humidified, 5% CO2 atmosphere in a 37oC incubator.

extract_protocol: RNA was extracted using a modified guanidine thiocyanate method, (Chomczynski and Sacchi, 1987, PMID: 2440339) followed by purification with RNeasy columns (Qiagen, Valencia, CA).  RNA samples were quantified using a Nanodrop spectrophotometer and monitored for quality using an Agilent Bioanalyzer prior to labeling for microarray analysis.

treatment_protocol: HZE particle irradiation was performed at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory.  Exponentially growing cells were concentrated by centrifugation and exposed to graded doses of 1 GeV/amu 56Fe ions (150 keV/μm) in a volume of 10 ml per culture point to limit the amount of medium activated during the irradiation.  Dosimetry was performed by the NSRL Physics Group.  Tubes containing the cells were placed perpendicular to the beam in the center of the field, where the variation in fluence was <5%. Control cultures were prepared in the same way and mock irradiated.  An activated-medium control was prepared by irradiating 10 ml of medium without cells to the highest dose used (2.5 Gy).  Immediately after irradiation, medium was added to bring the cells to normal culture densities (4-5 x 105cells/ml).  The cells for the activated control were resuspended in the activated medium prior to addition of the remaining medium.

value: lymphoblastoid


title: MGH_Liver_pool vs MGH_Liver_252

value: liver


title: MGH_Liver_pool vs MGH_Liver_246


title: MGH_Liver_pool vs MGH_Liver_253


title: MGH_Liver_pool vs MGH_Liver_248


title: MGH_Liver_pool vs MGH_Liver_254


title: REST shRNA KD 1

description: replicate 1

source_name: REST shRNA KD 1


title: pSuper vector control 2

description: replicate 2

source_name: pSuper vector control 2


title: Mock-irradiated control Experiment 2

description: biological repeat 2

source_name: TK6 mock irradiated


title: MGH_Liver_pool vs MGH_Liver_250


title: Activated medium Experiment 2

description: biological repeat 2


title: Mock-irradiated control Experiment 1

description: biological repeat 1


title: Gamma 3

description: biological replicate 3

source_name: TK6 24 hours after irradiation with 2.5 Gy gamma-rays

label_protocol: 24 hours after treatment, fluorescently labeled cDNA was prepared from mock-irradiated control and irradiated whole-cell RNA by a single round of reverse transcription (BRL Superscript II) in the presence of aminoallyl dUTP (Sigma-Aldrich), followed by coupling to monofunctional NHS-ester Cy3 or Cy5 dye (Amersham) (Amundson and Fornace, 2004. PMID:14970650)

treatment_protocol: HZE particle irradiation was performed at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory.  Exponentially growing cells were concentrated by centrifugation and exposed to graded doses of 1 GeV/amu 56Fe ions (150 keV/μm) in a volume of 10 ml per culture point to limit the amount of medium activated during the irradiation.  Dosimetry was performed by the NSRL Physics Group.  Tubes containing the cells were placed perpendicular to the beam in the center of the field, where the variation in fluence was <5%. Control cultures were prepared in the same way and mock irradiated.  An activated-medium control was prepared by irradiating 10 ml of medium without cells to the highest dose used (2.5 Gy).  Immediately after irradiation, medium was added to bring the cells to normal culture densities (4-5 x 105cells/ml).  Gamma-ray irradiation was performed at Columbia University using an AECL Gammacell-40 137Cs irradiator with a dose rate of 1.1 Gy/min.


title: Mock-irradiated control Experiment 3

description: biological repeat 3


title: Gamma 2

description: biological replicate 2


title: Control for gamma 3

description: biological replicate 3

source_name: TK6 24 hours after mock gamma irradiation


title: Activated medium Experiment 1

description: biological repeat 1


title: MGH_Liver_pool vs MGH_Liver_245

source_name: liver


title: Control for gamma 2

description: biological replicate 2


title: MGH_Liver_pool vs MGH_Liver_243


title: Control for gamma 1

description: biological replicate 1


title: pSuper vector control 1

description: replicate 1

source_name: pSuper vector control 1


title: MGH_Liver_pool vs MGH_Liver_241


title: Gamma 1

description: biological replicate 1


title: MGH_Liver_pool vs MGH_Liver_242


title: MGH_Liver_pool vs MGH_Liver_238


title: Iron 3

description: biological replicate 3

source_name: TK6 24 hours after irradiation with 1.67 Gy iron ions


title: Control for iron 3

description: biological replicate 3

source_name: TK6 24 hours after mock HZE irradiation


title: MGH_Liver_pool vs MGH_Liver_240


title: Iron 2

description: biological replicate 2


title: MGH_Liver_pool vs MGH_Liver_244


title: MGH_Liver_pool vs MGH_Liver_236


title: MGH_Liver_pool vs MGH_Liver_234


title: MGH_Liver_pool vs MGH_Liver_237


title: MGH_Liver_pool vs MGH_Liver_235


title: MGH_Liver_pool vs MGH_Liver_233


title: MGH_Liver_pool vs MGH_Liver_232


title: Control for iron 1

description: biological replicate 1


title: MGH_Liver_pool vs MGH_Liver_231


title: Control for iron 2

description: biological replicate 2


title: MGH_Liver_pool vs MGH_Liver_230


title: MGH_Liver_pool vs MGH_Liver_228


title: MGH_Liver_pool vs MGH_Liver_229


title: blood_GlobinReduced_IVT_C00027

city: Grand Rapids

first: Mary

last: Winn

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

description: C00027 (GC RNA)

hyb_protocol: Illumina IVT or DASL hybridization protocol.

scan_protocol: Illumina protocol for the HumanRefv3 BeadChip.

data_processing: No data processing was performed.

source_name: whole blood, GLOBINclear, IVT

label_protocol: Illumina IVT or DASL labeling protocol.

extract_protocol: RNA isolation was performed using the PAXGene Blood RNA Isolation System (Qiagen, Valencia, CA, USA). Alpha and beta globin mRNA were reduced from a portion of the total RNA samples using the GLOBINclear™ Human kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions with the recommended start quantity of 2 μg of total RNA.

treatment_protocol: 2.5 ml whole blood was collected in a PAXgene Blood RNA collection tube (Qiagen, Valencia, CA, USA) and stored frozen at -80C prior to RNA isolation.

value: peripheral whole blood

tag: globin treatment

value: GLOBINclear

tag: target preparation

value: in vitro transcription-based direct hybridization (IVT)

tag: donor identifier


title: MGH_Liver_pool vs MGH_Liver_227


title: blood_GlobinReduced_IVT_C00342

description: C00342 (GC RNA)


title: MGH_Liver_pool vs MGH_Liver_226


title: blood_GlobinReduced_IVT_C00304

description: C00304 (GC RNA)


title: blood_GlobinReduced_IVT_C00175

description: C00275 (GC RNA)


title: blood_GlobinReduced_IVT_C00179

description: C00179 (GC RNA)


title: Iron 1

description: biological replicate 1


title: blood_GlobinReduced_IVT_C00169

description: C00169 (GC RNA)


title: MGH_Liver_pool vs MGH_Liver_224


title: MGH_Liver_pool vs MGH_Liver_223


title: blood_whole_IVT_C00342

description: C00342 (tRNA)

source_name: whole blood, untreated, IVT

value: untreated


title: MGH_Liver_pool vs MGH_Liver_222


title: blood_GlobinReduced_IVT_C00311

description: C00311 (GC RNA)


title: MGH_Liver_pool vs MGH_Liver_221


title: blood_whole_IVT_C00311

description: C00311 (tRNA)


title: blood_GlobinReduced_IVT_C00023

description: C00023 (GC RNA)


title: MGH_Liver_pool vs MGH_Liver_225


title: MGH_Liver_pool vs MGH_Liver_220


title: MGH_Liver_pool vs MGH_Liver_239


title: blood_whole_IVT_C00304

description: C00304 (tRNA)


title: blood_whole_IVT_C00027

description: C00027 (tRNA)


title: blood_whole_IVT_C00169

description: C00169 (tRNA)


title: blood_whole_IVT_C00179

description: C00179 (tRNA)


title: blood_whole_IVT_C00023

description: C00023 (tRNA)


title: blood_whole_IVT_C00175

description: C00275 (tRNA)


title: MGH_Liver_pool vs MGH_Liver_213


title: MGH_Liver_pool vs MGH_Liver_219


title: MGH_Liver_pool vs MGH_Liver_216


title: MGH_Liver_pool vs MGH_Liver_217


title: MGH_Liver_pool vs MGH_Liver_218


title: MGH_Liver_pool vs MGH_Liver_210


title: MGH_Liver_pool vs MGH_Liver_211


title: non-smoker 411D

city: Prague 2

first: Hana

last: Bruchova

address: U nemocnice 1

department: Molecular Genetics

country: Czech Republic

institute: Institute of Hematology and Transfusion

hyb_protocol: 750 ng of biotinylated cRNA was hybridized to the array for 17 hours according to the manufacturer manual. Final staining was performed with streptavidin conjugated to Cy-3 fluorescent dye.

scan_protocol: Arrays were scanned using BeadArray Reader (Illumina), and bead level data were extracted by BeadStudio Software (Illumina).

data_processing: Bead summary data were imported into the R statistical environment (www.r-project.org) and normalized by the quantile method in the Lumi package. Only probes that reached detection P-value < 0.01 in all samples were used for further analyses. Differentially expressed genes were analysed in the Limma package. A linear model was fitted for each gene given a series of arrays using the lmFit function. Using the Benjamini and Hochberg method, P-values were corrected for multiple testing. The M, PL, and D groups were normalized separately.

source_name: cord blood, non-smoker

label_protocol: Biotinylated cRNA was prepared from 200 ng of total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion). In vitro transcription (IVT) was performed at 37°C for 14 hours.

extract_protocol: Umbilical cord blood was sampled and processed using the LeukoLOCK™ Total RNA Isolation System (Ambion, Austin, TX, USA) according to the manufacturer manual. The system employs filter-based leukocyte-depletion technology to isolate leukocytes from whole blood and RNAlater™ (Ambion) to stabilize the cells on the filter. By removal of red blood cells, the RNA purified from captured leukocytes is inherently depleted of globin mRNA, which improves sample quality for expression profiling and other applications. Integrity of the total RNAs was assayed by the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), and only samples with RNA integrity number (RIN) above 7.0 were used for gene expression profiling.

value: cord blood

tag: smoking status

value: non-smoker

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

value: vaginal

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: MGH_Liver_pool vs MGH_Liver_207

tag: reference

tag: tissue

tag: ID


title: MGH_Liver_pool vs MGH_Liver_209


title: MGH_Liver_pool vs MGH_Liver_212


title: non-smoker 409D


title: non-smoker 410D


title: non-smoker 402D


title: MGH_Liver_pool vs MGH_Liver_205


title: non-smoker 407D


title: MGH_Liver_pool vs MGH_Liver_206


title: MGH_Liver_pool vs MGH_Liver_215


title: MGH_Liver_pool vs MGH_Liver_214


title: smoker 408D

source_name: cord blood, smoker

value: smoker


title: MGH_Liver_pool vs MGH_Liver_204


title: MGH_Liver_pool vs MGH_Liver_203


title: non-smoker 383D


title: non-smoker 399D


title: smoker 395D


title: MGH_Liver_pool vs MGH_Liver_208


title: non-smoker 403D


title: non-smoker 398D


title: non-smoker 401D


title: smoker 400D


title: non-smoker 388D


title: non-smoker 389D


title: smoker 384D


title: non-smoker 392D


title: non-smoker 381D


title: non-smoker 379D


title: MGH_Liver_pool vs MGH_Liver_197


title: smoker 377D


title: MGH_Liver_pool vs MGH_Liver_200


title: non-smoker 378D


title: MGH_Liver_pool vs MGH_Liver_198


title: MGH_Liver_pool vs MGH_Liver_199


title: MGH_Liver_pool vs MGH_Liver_194


title: MGH_Liver_pool vs MGH_Liver_195


title: MGH_Liver_pool vs MGH_Liver_201


title: MGH_Liver_pool vs MGH_Liver_192


title: MGH_Liver_pool vs MGH_Liver_196


title: MGH_Liver_pool vs MGH_Liver_193


title: non-smoker 371D


title: 14162690 - ddm1-2,rdr2-1 repet2 vs. ddm1-2 repet2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Impact of loss of DNA methylation and small interference RNAs (siRNAs) on gene expression.

hyb_protocol: ddm1-2 repet2 Cy5 / ddm1-2,rdr2-1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0. Cy3: pmt voltage 532nm, 480V, laser power 35%. Cy5: 635nm, pmt voltage 480V, laser power 30%.

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: Seedling. Media=soil. Hygrometry=65%/75%. Temperature=22.5°C/18°C. Light=16h light/8h dark (8000 lux).

extract_protocol: ddm1-2 repet2:10ug. Qiagen RNeasy kit.

treatment_protocol: no treatment

tag: ecotype

value: Columbia

tag: genotype

value: mutant (ddm1-2)

value: seedling

tag: developmental stage

value: Boyes 1.02 (Boyes et al. Plant Cell 2001)

extract_protocol: ddm1-2,rdr2-1 repet2:10ug. Qiagen RNeasy kit.

value: mutant (ddm1-2,rdr2-1)


title: MGH_Liver_pool vs MGH_Liver_189


title: 14162689 - ddm1-2,rdr2-1 repet1 vs. ddm1-2 repet1

hyb_protocol: ddm1-2 repet1 Cy5 / ddm1-2,rdr2-1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: ddm1-2 repet1:10ug. Qiagen RNeasy kit.

extract_protocol: ddm1-2,rdr2-1 repet1:10ug. Qiagen RNeasy kit.


title: 14162688 - ddm1-2 repet2 vs. ddm1-2,rdr2-1 repet2

hyb_protocol: ddm1-2,rdr2-1 repet2 Cy5 / ddm1-2 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969176 - 35S:SDC repet1 vs. wt repet1

hyb_protocol: wt repet1 Cy5 / 35S:SDC repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wt

extract_protocol: wt repet1:10ug. Qiagen RNeasy kit.

value: wt

extract_protocol: 35S:SDC repet1:10ug. Qiagen RNeasy kit.

value: mutant (35s:SDC)


title: smoker 374D

tag: smoking status

tag: age (years)


title: 14162687 - ddm1-2 repet1 vs. ddm1-2,rdr2-1 repet1

hyb_protocol: ddm1-2,rdr2-1 repet1 Cy5 / ddm1-2 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969174 - ddm1-2,rdr2-1 repet2 vs. rdr2-1 repet2

hyb_protocol: rdr2-1 repet2 Cy5 / ddm1-2,rdr2-1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: rdr2-1 repet2:10ug. Qiagen RNeasy kit.

value: mutant (rdr2-1)


title: 13969171 - rdr2-1 repet1 vs. ddm1-2,rdr2-1 repet1

hyb_protocol: ddm1-2,rdr2-1 repet1 Cy5 / rdr2-1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: rdr2-1 repet1:10ug. Qiagen RNeasy kit.


title: smoker 356D

tag: maternal bmi

tag: parity


title: 13969180 - wt repet2 vs. 35S:SDC repet2

hyb_protocol: 35S:SDC repet2 Cy5 / wt repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 35S:SDC repet2:10ug. Qiagen RNeasy kit.

extract_protocol: wt repet2:10ug. Qiagen RNeasy kit.


title: 13969181 - 35S:SDC repet2 vs. wt repet2

hyb_protocol: wt repet2 Cy5 / 35S:SDC repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: non-smoker 354D

tag: gestational age (weeks)

tag: mode of delivery


title: non-smoker 355D

tag: placental weight (g)

tag: newborn weight (g)


title: 13969173 - rdr2-1 repet2 vs. ddm1-2,rdr2-1 repet2

hyb_protocol: ddm1-2,rdr2-1 repet2 Cy5 / rdr2-1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MGH_Liver_pool vs MGH_Liver_191

hyb_protocol: Microarrays are incubated at 40?C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

value: liver


title: MGH_Liver_pool vs MGH_Liver_190


title: MGH_Liver_pool vs MGH_Liver_186


title: 13969175 - wt repet1 vs. 35S:SDC repet1

hyb_protocol: 35S:SDC repet1 Cy5 / wt repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969172 - ddm1-2,rdr2-1 repet1 vs. rdr2-1 repet1

hyb_protocol: rdr2-1 repet1 Cy5 / ddm1-2,rdr2-1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: non-smoker 353D

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)


title: MGH_Liver_pool vs MGH_Liver_188


title: MGH_Liver_pool vs MGH_Liver_187


title: 13969374 - wt repet1 vs. fwa-d repet1

hyb_protocol: fwa-d repet1 Cy5 / wt repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: fwa-d

extract_protocol: fwa-d repet1:10ug. Qiagen RNeasy kit.

value: mutant (fwa-d)


title: 13969377 - fwa-d repet1 vs. wt repet1

hyb_protocol: wt repet1 Cy5 / fwa-d repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MGH_Liver_pool vs MGH_Liver_185


title: 13969373 - ddm1-2,rdr2-1 repet1 vs. wt repet1

hyb_protocol: wt repet1 Cy5 / ddm1-2,rdr2-1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: non-smoker 352D

hyb_protocol: 750 ng of biotinylated cRNA was hybridized to the array for 17 hours according to the manufacturer manual. Final staining was performed with streptavidin conjugated to Cy-3 fluorescent dye.

tag: cord blood cotinine (ng/ml)

tag: individual


title: MGH_Liver_pool vs MGH_Liver_184

tag: reference

tag: tissue


title: 13969369 - ddm1-2 repet1 vs. wt repet1

hyb_protocol: wt repet1 Cy5 / ddm1-2 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype


title: 13969371 - rdr2-1 repet1 vs. wt repet1

hyb_protocol: wt repet1 Cy5 / rdr2-1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype


title: 13969372 - wt repet1 vs. ddm1-2,rdr2-1 repet1

hyb_protocol: ddm1-2,rdr2-1 repet1 Cy5 / wt repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: developmental stage


title: 13969367 - wt repet1 vs. ddm1-2 repet1

hyb_protocol: ddm1-2 repet1 Cy5 / wt repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969370 - wt repet1 vs. rdr2-1 repet1

hyb_protocol: rdr2-1 repet1 Cy5 / wt repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: smoker 350D

tag: smoking status


title: 13969167 - wt repet2 vs. ddm1-2,rdr2-1 repet2

hyb_protocol: ddm1-2,rdr2-1 repet2 Cy5 / wt repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969364 - fwa-d repet2 vs. wt repet2

hyb_protocol: wt repet2 Cy5 / fwa-d repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: fwa-d repet2:10ug. Qiagen RNeasy kit.


title: smoker 351D

tag: age (years)


title: 13969168 - ddm1-2,rdr2-1 repet2 vs. wt repet2

hyb_protocol: wt repet2 Cy5 / ddm1-2,rdr2-1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: non-smoker 347D

tag: maternal bmi


title: MGH_Liver_pool vs MGH_Liver_183

tag: ID


title: smoker 344D

tag: parity

tag: gestational age (weeks)


title: MGH_Liver_pool vs MGH_Liver_181


title: 13969166 - rdr2-1 repet2 vs. wt repet2

hyb_protocol: wt repet2 Cy5 / rdr2-1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969165 - wt repet2 vs. rdr2-1 repet2

hyb_protocol: rdr2-1 repet2 Cy5 / wt repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969164 - ddm1-2 repet2 vs. wt repet2

hyb_protocol: wt repet2 Cy5 / ddm1-2 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: smoker 349D

tag: mode of delivery

tag: placental weight (g)


title: 13969169 - wt repet2 vs. fwa-d repet2

hyb_protocol: fwa-d repet2 Cy5 / wt repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: non-smoker 343D

tag: newborn weight (g)

tag: apgar score (5s)


title: MGH_Liver_pool vs MGH_Liver_202

hyb_protocol: Microarrays are incubated at 40?C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.


title: MGH_Liver_pool vs MGH_Liver_179


title: MGH_Liver_pool vs MGH_Liver_178


title: MGH_Liver_pool vs MGH_Liver_180


title: 13969163 - wt repet2 vs. ddm1-2 repet2

hyb_protocol: ddm1-2 repet2 Cy5 / wt repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MGH_Liver_pool vs MGH_Liver_177


title: non-smoker 368D

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)


title: 13912823 - fwa vs. wt

hyb_protocol: wt Cy5 / fwa Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: Rosette. Media=soil. Hygrometry=65%/75%. Temperature=22.5°C/18°C. Light=16h light/8h dark (8000 lux).

extract_protocol: wt:10ug. Qiagen RNeasy kit.

value: rosette

value: Boyes 1.10 (Boyes et al. Plant Cell 2001)

source_name: fwa

extract_protocol: fwa:10ug. Qiagen RNeasy kit.

value: mutant (fwa)


title: non-smoker 340D

value: cord blood

tag: individual


title: non-smoker 338D

tag: tissue

value: non-smoker