title: Kidney Cortex F2 pool vs. 491038_F2_4


title: Kidney Cortex F2 pool vs. 496909_F2_34

status: Public on Jan 13 2011

type: RNA

city: Seattle

first: Jonathan

middle: M

last: Derry

state: WA

address: 1100 Fairview Ave N

country: USA

institute: Sage Bionetworks

description: Derry J, Zhong H, Molony C et al ABSTRACT:  To identify the genes and pathways that underlie cardiovascular and metabolic phenotypes we performed an integrated analysis of a mouse C57BL/6J x A/J F2 (B6AF2) cross by relating genome-wide gene expression data from adipose, kidney, and liver tissues to physiological endpoints measured in the population. We have identified a large number of trait QTLs including loci driving variation in cardiac function on chromosomes 2 and 6 and a hotspot for adiposity, energy metabolism, and glucose traits on chromosome 8. Integration of adipose gene expression data identified a core set of genes that drive the chromosome 8 adiposity QTL. This chromosome 8 trans eQTL signature contains genes associated with mitochondrial function and oxidative phosphorylation and maps to a subnetwork with conserved function in humans that was previously implicated in human obesity. In addition, human eSNPs corresponding to orthologous genes from the signature show enrichment for association to type II diabetes in the DIAGRAM cohort, supporting the idea that the chromosome 8 locus perturbs a molecular network that in humans senses variations in DNA and in turn affects metabolic disease risk. We functionally validate predictions from this approach by demonstrating metabolic phenotypes in knockout mice for three genes from the trans eQTL signature, Akr1b8, Emr1, and Rgs2. In addition we show that the transcriptional signatures for knockout of two of these genes, Akr1b8 and Rgs2, map to the F2 network modules associated with the chromosome 8 trans eQTL signature and that these modules are in turn very significantly correlated with adiposity in the F2 population. Overall this study demonstrates how integrating gene expression data with QTL analysis in a network-based framework can aid in the elucidation of the molecular drivers of disease that can be translated from mice to humans.

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: Mus musculus

source_name: Kidney Cortex

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: sample type

value: Kidney Cortex F2 pool

tag: animal id

tag: strain

tag: gender

value: F

tag: generation

tag: tissue

value: kidney cortex


title: Kidney Cortex F2 pool vs. 491037_F2_20


title: Kidney Cortex F2 pool vs. 491040_F2_6

value: M


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title: Kidney Cortex F2 pool vs. 490055_AJ_8

value: A/J

value: Parental


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title: Kidney Medulla F2 pool vs. 530418_F2_233_F

source_name: Kidney Medulla

value: Kidney Medulla F2 pool

value: kidney medulla


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title: Kidney Medulla F2 pool vs. 505344_F2_85_M


title: Kidney Medulla F2 pool vs. 516135_F2_153_M


title: Kidney Medulla F2 pool vs. 510622_F2_115_M


title: Kidney Medulla F2 pool vs. 510611_F2_110_F


title: Kidney Medulla F2 pool vs. 510613_F2_112_F


title: Kidney Medulla F2 pool vs. 493702_F1_45_F


title: Kidney Medulla F2 pool vs. 510612_F2_111_F


title: Kidney Medulla F2 pool vs. 500878_F2_51_M


title: Kidney Medulla F2 pool vs. 500865_F2_53_F


title: Kidney Medulla F2 pool vs. 510615_F2_114_F


title: Kidney Medulla F2 pool vs. 500864_F2_52_F


title: Kidney Medulla F2 pool vs. 500880_F2_56_M


title: Kidney Medulla F2 pool vs. 510623_F2_116_M


title: Kidney Medulla F2 pool vs. 500872_F2_71_M


title: Kidney Medulla F2 pool vs. 500887_F2_59_F


title: Kidney Medulla F2 pool vs. 538350_F2_266_M


title: Kidney Medulla F2 pool vs. 500871_F2_72_M


title: Kidney Medulla F2 pool vs. 512415_F2_132_F


title: Kidney Medulla F2 pool vs. 500867_F2_58_F


title: Kidney Medulla F2 pool vs. 538349_F2_265_M


title: Kidney Medulla F2 pool vs. 512433_F2_144_M


title: Kidney Medulla F2 pool vs. 516125_F2_148_M


title: Kidney Medulla F2 pool vs. 538360_F2_267_M


title: Kidney Medulla F2 pool vs. 512413_F2_130_F


title: Kidney Medulla F2 pool vs. 512432_F2_143_M


title: Kidney Medulla F2 pool vs. 500866_F2_54_F


title: Kidney Medulla F2 pool vs. 516115_F2_147_F


title: Kidney Medulla F2 pool vs. 516113_F2_145_F


title: Kidney Medulla F2 pool vs. 516114_F2_146_F


title: Kidney Medulla F2 pool vs. 512431_F2_142_M


title: Kidney Medulla F2 pool vs. 496916_F2_47_F


title: Kidney Medulla F2 pool vs. 500879_F2_55_M


title: Kidney Medulla F2 pool vs. 538348_F2_269_F


title: Kidney Medulla F2 pool vs. 538338_F2_270_F


title: Kidney Medulla F2 pool vs. 538357_F2_273_M


title: Kidney Medulla F2 pool vs. 500885_F2_62_F


title: Kidney Medulla F2 pool vs. 538337_F2_268_F


title: Kidney Medulla F2 pool vs. 538340_F2_275_F


title: Kidney Medulla F2 pool vs. 500870_F2_68_F


title: Kidney Medulla F2 pool vs. 500883_F2_64_M


title: Kidney Medulla F2 pool vs. 512425_F2_127_M


title: Kidney Medulla F2 pool vs. 500882_F2_65_M


title: Kidney Medulla F2 pool vs. 493705_F1_48_F


title: Kidney Medulla F2 pool vs. 493704_F1_47_F


title: Kidney Medulla F2 pool vs. 512424_F2_123_M


title: Kidney Medulla F2 pool vs. 538359_F2_271_M


title: Kidney Medulla F2 pool vs. 500877_F2_50_M


title: Kidney Medulla F2 pool vs. 512422_F2_121_M


title: Kidney Medulla F2 pool vs. 500886_F2_61_F


title: Kidney Medulla F2 pool vs. 496909_F2_34_F


title: Kidney Medulla F2 pool vs. 500884_F2_63_F


title: Kidney Medulla F2 pool vs. 512412_F2_126_F


title: Kidney Medulla F2 pool vs. 525912_F2_195_F


title: Kidney Medulla F2 pool vs. 512423_F2_122_M


title: Kidney Medulla F2 pool vs. 525911_F2_194_F


title: Kidney Medulla F2 pool vs. 512410_F2_124_F


title: Kidney Medulla F2 pool vs. 512427_F2_129_M


title: Kidney Medulla F2 pool vs. 512411_F2_125_F


title: Kidney Medulla F2 pool vs. 500869_F2_69_F


title: Kidney Medulla F2 pool vs. 525914_F2_200_F


title: Kidney Medulla F2 pool vs. 525924_F2_198_M


title: Kidney Medulla F2 pool vs. 525922_F2_196_M


title: Kidney Medulla F2 pool vs. 525910_F2_193_F


title: Kidney Medulla F2 pool vs. 525915_F2_201_F


title: Kidney Medulla F2 pool vs. 510620_F2_107_M


title: Kidney Medulla F2 pool vs. 510616_F2_103_M


title: Kidney Medulla F2 pool vs. 510605_F2_98_F


title: Kidney Medulla F2 pool vs. 510609_F2_102_F


title: Kidney Medulla F2 pool vs. 510608_F2_101_F


title: Kidney Medulla F2 pool vs. 510625_F2_118_M


title: Kidney Medulla F2 pool vs. 491043_F2_12_M


title: Kidney Medulla F2 pool vs. 510618_F2_105_M


title: Kidney Medulla F2 pool vs. 510627_F2_120_M


title: Kidney Medulla F2 pool vs. 491039_F2_5_M


title: Kidney Medulla F2 pool vs. 490047_B6_4_M


title: Kidney Medulla F2 pool vs. 491041_F2_10_M


title: Kidney Medulla F2 pool vs. 491044_F2_16_M


title: Kidney Medulla F2 pool vs. 491042_F2_11_M


title: Kidney Medulla F2 pool vs. 490055_AJ_8_M


title: Kidney Medulla F2 pool vs. 510626_F2_119_M


title: Kidney Medulla F2 pool vs. 490046_B6_3_M


title: Kidney Medulla F2 pool vs. 490052_AJ_5_M


title: Kidney Medulla F2 pool vs. 490062_F1_11_M


title: Kidney Medulla F2 pool vs. 490044_B6_1_M


title: Kidney Medulla F2 pool vs. 490058_F1_23_F


title: Kidney Medulla F2 pool vs. 490057_F1_22_F


title: Kidney Medulla F2 pool vs. 491049_F2_18_M


title: Kidney Medulla F2 pool vs. 500873_F2_70_M


title: Kidney Medulla F2 pool vs. 490054_AJ_7_M


title: Kidney Medulla F2 pool vs. 491046_F2_22_M


title: Kidney Medulla F2 pool vs. 490061_F1_10_M


title: Kidney Medulla F2 pool vs. 491048_F2_23_M


title: Kidney Medulla F2 pool vs. 490056_F1_21_F


title: Kidney Medulla F2 pool vs. 491045_F2_17_M


title: Kidney Medulla F2 pool vs. 491040_F2_6_M


title: Kidney Medulla F2 pool vs. 490045_B6_2_M


title: Kidney Medulla F2 pool vs. 491047_F2_24_M


title: Kidney Medulla F2 pool vs. 491038_F2_4_M


title: Kidney Medulla F2 pool vs. 490043_B6_16_F


title: Kidney Medulla F2 pool vs. 490051_AJ_20_F


title: Kidney Medulla F2 pool vs. 490050_AJ_19_F


title: Kidney Medulla F2 pool vs. 490041_B6_14_F


title: Kidney Medulla F2 pool vs. 490060_F1_9_M


title: Kidney Medulla F2 pool vs. 491029_F2_7_F


title: Kidney Medulla F2 pool vs. 491032_F2_13_F


title: Kidney Medulla F2 pool vs. 490059_F1_24_F


title: Kidney Medulla F2 pool vs. 490048_AJ_17_F


title: Kidney Medulla F2 pool vs. 491030_F2_8_F


title: Kidney Medulla F2 pool vs. 490040_B6_13_F


title: Kidney Medulla F2 pool vs. 493681_B6_28_M


title: Kidney Medulla F2 pool vs. 493699_AJ_30_M


title: Kidney Medulla F2 pool vs. 491033_F2_14_F


title: Kidney Medulla F2 pool vs. 491028_F2_3_F


title: Kidney Medulla F2 pool vs. 505333_F2_80_F


title: Kidney Medulla F2 pool vs. 493708_F1_35_M


title: Kidney Medulla F2 pool vs. 491027_F2_2_F


title: Kidney Medulla F2 pool vs. 490042_B6_15_F


title: Kidney Medulla F2 pool vs. 491034_F2_15_F


title: Kidney Medulla F2 pool vs. 505341_F2_76_M


title: Kidney Medulla F2 pool vs. 493700_AJ_31_M


title: Kidney Medulla F2 pool vs. 493698_AJ_29_M


title: Kidney Medulla F2 pool vs. 491026_F2_1_F


title: Kidney Medulla F2 pool vs. 490063_F1_12_M


title: Kidney Medulla F2 pool vs. 493707_F1_34_M


title: Kidney Medulla F2 pool vs. 505331_F2_75_F


title: Kidney Medulla F2 pool vs. 505343_F2_78_M


title: Kidney Medulla F2 pool vs. 505334_F2_81_F


title: Kidney Medulla F2 pool vs. 505329_F2_73_F


title: Kidney Medulla F2 pool vs. 491037_F2_20_F


title: Kidney Medulla F2 pool vs. 505336_F2_83_F


title: Kidney Medulla F2 pool vs. 493679_B6_26_M


title: Kidney Medulla F2 pool vs. 491035_F2_19_F


title: Kidney Medulla F2 pool vs. 493706_F1_33_M


title: Kidney Medulla F2 pool vs. 505330_F2_74_F


title: Kidney Medulla F2 pool vs. 493678_B6_25_M


title: Kidney Medulla F2 pool vs. 493680_B6_27_M


title: Kidney Medulla F2 pool vs. 496907_F2_32_F


title: Kidney Medulla F2 pool vs. 496923_F2_30_M


title: Kidney Medulla F2 pool vs. 493709_F1_36_M


title: Kidney Medulla F2 pool vs. 505342_F2_77_M


title: Kidney Medulla F2 pool vs. 496918_F2_25_M


title: Kidney Medulla F2 pool vs. 530431_F2_231_M


title: Liver F2 Control Pool (n=294) vs. 530431_F2_231

source_name: Liver

value: Liver F2 Control Pool (n=294)

value: liver


title: Liver F2 Control Pool (n=294) vs. 530421_F2_239


title: Liver F2 Control Pool (n=294) vs. 530416_F2_228


title: Liver F2 Control Pool (n=294) vs. 530417_F2_232


title: Liver F2 Control Pool (n=294) vs. 530414_F2_226


title: Liver F2 Control Pool (n=294) vs. 540137_F2_311


title: Liver F2 Control Pool (n=294) vs. 530415_F2_227


title: Liver F2 Control Pool (n=294) vs. 530419_F2_234


title: Liver F2 Control Pool (n=294) vs. 539018_B6_52


title: Liver F2 Control Pool (n=294) vs. 530433_F2_236


title: Liver F2 Control Pool (n=294) vs. 530418_F2_233


title: Kidney Medulla F2 pool vs. 530417_F2_232_F


title: Liver F2 Control Pool (n=294) vs. 530429_F2_229


title: Liver F2 Control Pool (n=294) vs. 549348_F2_313


title: Liver F2 Control Pool (n=294) vs. 540138_F2_312


title: Liver F2 Control Pool (n=294) vs. 552556_F2_359


title: Liver F2 Control Pool (n=294) vs. 552557_F2_360


title: Liver F2 Control Pool (n=294) vs. 539016_B6_50


title: Liver F2 Control Pool (n=294) vs. 539017_B6_51


title: Liver F2 Control Pool (n=294) vs. 549349_F2_314


title: Liver F2 Control Pool (n=294) vs. 539015_B6_49


title: Liver F2 Control Pool (n=294) vs. 538668_AJ_65


title: Liver F2 Control Pool (n=294) vs. 530434_F2_237


title: Liver F2 Control Pool (n=294) vs. 533809_F2_263


title: Liver F2 Control Pool (n=294) vs. 525932_F2_214


title: Liver F2 Control Pool (n=294) vs. 525930_F2_216


title: Liver F2 Control Pool (n=294) vs. 539011_B6_61


title: Liver F2 Control Pool (n=294) vs. 533796_F2_259


title: Liver F2 Control Pool (n=294) vs. 533798_F2_260


title: Liver F2 Control Pool (n=294) vs. 538671_AJ_68


title: Liver F2 Control Pool (n=294) vs. 525931_F2_215


title: Liver F2 Control Pool (n=294) vs. 538675_AJ_56


title: Liver F2 Control Pool (n=294) vs. 539014_B6_64


title: Liver F2 Control Pool (n=294) vs. 533810_F2_258


title: Liver F2 Control Pool (n=294) vs. 522506_F2_183


title: Kidney Medulla F2 pool vs. 496920_F2_27_M


title: Kidney Medulla F2 pool vs. 496921_F2_28_M


title: Liver F2 Control Pool (n=294) vs. 530430_F2_230


title: Liver F2 Control Pool (n=294) vs. 552564_F2_348


title: Liver F2 Control Pool (n=294) vs. 522508_F2_180


title: Liver F2 Control Pool (n=294) vs. 552565_F2_347


title: Liver F2 Control Pool (n=294) vs. 533807_F2_262


title: Liver F2 Control Pool (n=294) vs. 522507_F2_182


title: Liver F2 Control Pool (n=294) vs. 533811_F2_257


title: Liver F2 Control Pool (n=294) vs. 522505_F2_181


title: Liver F2 Control Pool (n=294) vs. 533797_F2_261


title: Liver F2 Control Pool (n=294) vs. 540134_F2_309


title: Liver F2 Control Pool (n=294) vs. 540133_F2_308


title: Liver F2 Control Pool (n=294) vs. 540132_F2_307


title: Liver F2 Control Pool (n=294) vs. 538341_F2_276


title: Liver F2 Control Pool (n=294) vs. 540136_F2_310


title: Liver F2 Control Pool (n=294) vs. 540140_F2_305


title: Liver F2 Control Pool (n=294) vs. 540130_F2_302


title: Liver F2 Control Pool (n=294) vs. 540131_F2_303


title: Liver F2 Control Pool (n=294) vs. 540126_F2_291


title: Liver F2 Control Pool (n=294) vs. 540125_F2_290


title: Liver F2 Control Pool (n=294) vs. 540129_F2_301


title: Liver F2 Control Pool (n=294) vs. 540146_F2_293


title: Liver F2 Control Pool (n=294) vs. 540141_F2_304


title: Liver F2 Control Pool (n=294) vs. 530422_F2_240


title: Liver F2 Control Pool (n=294) vs. 540145_F2_294


title: Liver F2 Control Pool (n=294) vs. 530425_F2_222


title: Liver F2 Control Pool (n=294) vs. 530426_F2_223


title: Liver F2 Control Pool (n=294) vs. 533808_F2_264


title: Liver F2 Control Pool (n=294) vs. 530423_F2_220


title: Liver F2 Control Pool (n=294) vs. 530424_F2_221


title: Liver F2 Control Pool (n=294) vs. 533790_F2_243


title: Liver F2 Control Pool (n=294) vs. 530413_F2_219


title: Liver F2 Control Pool (n=294) vs. 533800_F2_244


title: Liver F2 Control Pool (n=294) vs. 533803_F2_247


title: Liver F2 Control Pool (n=294) vs. 530428_F2_225


title: Liver F2 Control Pool (n=294) vs. 533801_F2_245


title: Liver F2 Control Pool (n=294) vs. 552560_F2_343


title: Liver F2 Control Pool (n=294) vs. 552559_F2_342


title: Liver F2 Control Pool (n=294) vs. 552562_F2_345


title: Liver F2 Control Pool (n=294) vs. 552563_F2_346


title: Liver F2 Control Pool (n=294) vs. 552561_F2_344


title: Liver F2 Control Pool (n=294) vs. 530427_F2_224


title: Liver F2 Control Pool (n=294) vs. 552547_F2_338


title: Liver F2 Control Pool (n=294) vs. 552549_F2_340


title: Liver F2 Control Pool (n=294) vs. 533802_F2_246


title: Liver F2 Control Pool (n=294) vs. 552558_F2_341


title: Liver F2 Control Pool (n=294) vs. 540144_F2_295


title: Liver F2 Control Pool (n=294) vs. 533791_F2_250


title: Liver F2 Control Pool (n=294) vs. 530420_F2_238


title: Liver F2 Control Pool (n=294) vs. 533789_F2_242


title: Liver F2 Control Pool (n=294) vs. 530411_F2_217


title: Liver F2 Control Pool (n=294) vs. 533805_F2_249


title: Liver F2 Control Pool (n=294) vs. 538345_F2_283


title: Liver F2 Control Pool (n=294) vs. 530412_F2_218


title: Liver F2 Control Pool (n=294) vs. 549366_F2_331


title: Liver F2 Control Pool (n=294) vs. 538344_F2_279


title: Liver F2 Control Pool (n=294) vs. 533804_F2_248


title: Liver F2 Control Pool (n=294) vs. 549371_F2_336


title: Liver F2 Control Pool (n=294) vs. 549350_F2_315


title: Liver F2 Control Pool (n=294) vs. 549370_F2_335


title: Liver F2 Control Pool (n=294) vs. 549367_F2_332


title: Liver F2 Control Pool (n=294) vs. 549364_F2_329


title: Liver F2 Control Pool (n=294) vs. 549359_F2_327


title: Liver F2 Control Pool (n=294) vs. 538351_F2_280


title: Liver F2 Control Pool (n=294) vs. 552546_F2_337


title: Liver F2 Control Pool (n=294) vs. 538356_F2_281


title: Liver F2 Control Pool (n=294) vs. 538342_F2_277


title: Liver F2 Control Pool (n=294) vs. 538355_F2_282


title: Liver F2 Control Pool (n=294) vs. 549363_F2_328


title: Liver F2 Control Pool (n=294) vs. 549354_F2_319


title: Liver F2 Control Pool (n=294) vs. 549351_F2_316


title: Liver F2 Control Pool (n=294) vs. 549369_F2_334


title: Liver F2 Control Pool (n=294) vs. 549352_F2_317


title: Liver F2 Control Pool (n=294) vs. 549355_F2_320


title: Liver F2 Control Pool (n=294) vs. 522494_F2_190


title: Liver F2 Control Pool (n=294) vs. 522490_F2_185


title: Liver F2 Control Pool (n=294) vs. 522497_F2_187


title: Liver F2 Control Pool (n=294) vs. 522495_F2_189


title: Liver F2 Control Pool (n=294) vs. 522491_F2_186


title: Liver F2 Control Pool (n=294) vs. 549360_F2_322


title: Liver F2 Control Pool (n=294) vs. 525916_F2_202


title: Liver F2 Control Pool (n=294) vs. 522492_F2_192


title: Liver F2 Control Pool (n=294) vs. 522493_F2_191


title: Liver F2 Control Pool (n=294) vs. 549361_F2_323


title: Liver F2 Control Pool (n=294) vs. 525918_F2_204


title: Liver F2 Control Pool (n=294) vs. 552554_F2_357


title: Liver F2 Control Pool (n=294) vs. 538347_F2_285


title: Liver F2 Control Pool (n=294) vs. 538352_F2_286


title: Liver F2 Control Pool (n=294) vs. 552553_F2_356


title: Liver F2 Control Pool (n=294) vs. 522500_F2_171


title: Liver F2 Control Pool (n=294) vs. 522498_F2_169


title: Liver F2 Control Pool (n=294) vs. 549353_F2_318


title: Liver F2 Control Pool (n=294) vs. 522509_F2_179


title: Liver F2 Control Pool (n=294) vs. 522501_F2_172


title: Liver F2 Control Pool (n=294) vs. 522486_F2_175


title: Liver F2 Control Pool (n=294) vs. 522502_F2_173


title: Liver F2 Control Pool (n=294) vs. 522487_F2_176


title: Liver F2 Control Pool (n=294) vs. 522499_F2_170


title: Liver F2 Control Pool (n=294) vs. 552551_F2_354


title: Liver F2 Control Pool (n=294) vs. 552552_F2_355


title: Liver F2 Control Pool (n=294) vs. 522488_F2_177


title: Liver F2 Control Pool (n=294) vs. 538343_F2_278


title: Liver F2 Control Pool (n=294) vs. 552566_F2_349


title: Liver F2 Control Pool (n=294) vs. 552568_F2_351


title: Liver F2 Control Pool (n=294) vs. 549365_F2_330


title: Liver F2 Control Pool (n=294) vs. 552569_F2_352


title: Liver F2 Control Pool (n=294) vs. 549362_F2_324


title: Liver F2 Control Pool (n=294) vs. 549357_F2_325


title: Liver F2 Control Pool (n=294) vs. 552550_F2_353


title: Liver F2 Control Pool (n=294) vs. 522489_F2_184


title: Liver F2 Control Pool (n=294) vs. 533795_F2_254


title: Liver F2 Control Pool (n=294) vs. 533794_F2_253


title: Liver F2 Control Pool (n=294) vs. 540142_F2_297


title: Liver F2 Control Pool (n=294) vs. 538354_F2_287


title: Liver F2 Control Pool (n=294) vs. 533793_F2_252


title: Liver F2 Control Pool (n=294) vs. 540143_F2_296


title: Liver F2 Control Pool (n=294) vs. 533806_F2_256


title: Liver F2 Control Pool (n=294) vs. 533799_F2_255


title: Liver F2 Control Pool (n=294) vs. 540127_F2_298


title: Liver F2 Control Pool (n=294) vs. 525933_F2_207


title: Liver F2 Control Pool (n=294) vs. 540128_F2_299


title: Liver F2 Control Pool (n=294) vs. 552567_F2_350


title: Liver F2 Control Pool (n=294) vs. 533792_F2_251


title: Liver F2 Control Pool (n=294) vs. 549358_F2_326


title: Liver F2 Control Pool (n=294) vs. 540124_F2_289


title: Liver F2 Control Pool (n=294) vs. 525929_F2_213


title: Liver F2 Control Pool (n=294) vs. 525926_F2_206


title: Liver F2 Control Pool (n=294) vs. 525925_F2_205


title: Liver F2 Control Pool (n=294) vs. 525928_F2_212


title: Liver F2 Control Pool (n=294) vs. 525919_F2_208


title: Liver F2 Control Pool (n=294) vs. 516116_F2_157


title: Liver F2 Control Pool (n=294) vs. 525920_F2_209


title: Liver F2 Control Pool (n=294) vs. 525927_F2_211


title: Liver F2 Control Pool (n=294) vs. 516124_F2_166


title: Liver F2 Control Pool (n=294) vs. 516121_F2_162


title: Liver F2 Control Pool (n=294) vs. 516119_F2_160


title: Liver F2 Control Pool (n=294) vs. 516129_F2_163


title: Liver F2 Control Pool (n=294) vs. 516118_F2_159


title: Liver F2 Control Pool (n=294) vs. 516130_F2_165


title: Liver F2 Control Pool (n=294) vs. 538693_F1_59


title: Liver F2 Control Pool (n=294) vs. 516120_F2_161


title: Liver F2 Control Pool (n=294) vs. 516122_F2_168


title: Liver F2 Control Pool (n=294) vs. 538691_F1_57


title: Liver F2 Control Pool (n=294) vs. 538690_F1_70


title: Liver F2 Control Pool (n=294) vs. 525921_F2_210


title: Liver F2 Control Pool (n=294) vs. 516123_F2_167


title: Liver F2 Control Pool (n=294) vs. 538694_F1_60


title: Liver F2 Control Pool (n=294) vs. 505346_F2_87


title: Liver F2 Control Pool (n=294) vs. 505339_F2_89


title: Liver F2 Control Pool (n=294) vs. 505347_F2_91


title: Liver F2 Control Pool (n=294) vs. 539007_F1_71


title: Liver F2 Control Pool (n=294) vs. 505338_F2_88


title: Liver F2 Control Pool (n=294) vs. 505350_F2_94


title: Liver F2 Control Pool (n=294) vs. 539008_F1_72


title: Liver F2 Control Pool (n=294) vs. 505351_F2_96


title: Liver F2 Control Pool (n=294) vs. 505340_F2_90


title: Liver F2 Control Pool (n=294) vs. 505349_F2_93


title: Liver F2 Control Pool (n=294) vs. 505348_F2_92


title: Liver F2 Control Pool (n=294) vs. 493677_B6_37


title: Liver F2 Control Pool (n=294) vs. 505352_F2_95


title: Liver F2 Control Pool (n=294) vs. 493675_B6_39


title: Liver F2 Control Pool (n=294) vs. 516117_F2_158


title: Liver F2 Control Pool (n=294) vs. 512420_F2_140


title: Liver F2 Control Pool (n=294) vs. 493674_B6_40


title: Liver F2 Control Pool (n=294) vs. 512417_F2_137


title: Liver F2 Control Pool (n=294) vs. 512419_F2_139


title: Liver F2 Control Pool (n=294) vs. 512421_F2_141


title: Liver F2 Control Pool (n=294) vs. 512416_F2_136


title: Liver F2 Control Pool (n=294) vs. 493697_AJ_44


title: Liver F2 Control Pool (n=294) vs. 493702_F1_45


title: Liver F2 Control Pool (n=294) vs. 493694_AJ_41


title: Liver F2 Control Pool (n=294) vs. 516133_F2_155


title: Liver F2 Control Pool (n=294) vs. 516126_F2_149


title: Liver F2 Control Pool (n=294) vs. 496912_F2_37


title: Liver F2 Control Pool (n=294) vs. 516132_F2_156


title: Liver F2 Control Pool (n=294) vs. 493703_F1_46


title: Liver F2 Control Pool (n=294) vs. 512430_F2_135


title: Liver F2 Control Pool (n=294) vs. 516135_F2_153


title: Liver F2 Control Pool (n=294) vs. 512428_F2_133


title: Liver F2 Control Pool (n=294) vs. 516128_F2_151


title: Liver F2 Control Pool (n=294) vs. 516136_F2_152


title: Liver F2 Control Pool (n=294) vs. 516127_F2_150


title: Liver F2 Control Pool (n=294) vs. 496928_F2_44


title: Liver F2 Control Pool (n=294) vs. 512429_F2_134


title: Liver F2 Control Pool (n=294) vs. 493696_AJ_43


title: Liver F2 Control Pool (n=294) vs. 512418_F2_138


title: Liver F2 Control Pool (n=294) vs. 516134_F2_154


title: Liver F2 Control Pool (n=294) vs. 496927_F2_43


title: Liver F2 Control Pool (n=294) vs. 496929_F2_45


title: Liver F2 Control Pool (n=294) vs. 505345_F2_86


title: Liver F2 Control Pool (n=294) vs. 510611_F2_110


title: Liver F2 Control Pool (n=294) vs. 510614_F2_113


title: Liver F2 Control Pool (n=294) vs. 510610_F2_109


title: Liver F2 Control Pool (n=294) vs. 496924_F2_40


title: Liver F2 Control Pool (n=294) vs. 510613_F2_112


title: Liver F2 Control Pool (n=294) vs. 510622_F2_115


title: Liver F2 Control Pool (n=294) vs. 496926_F2_42


title: Liver F2 Control Pool (n=294) vs. 496913_F2_38


title: Liver F2 Control Pool (n=294) vs. 496925_F2_41


title: Liver F2 Control Pool (n=294) vs. 496914_F2_39


title: Liver F2 Control Pool (n=294) vs. 512413_F2_130


title: Liver F2 Control Pool (n=294) vs. 510612_F2_111


title: Liver F2 Control Pool (n=294) vs. 500865_F2_53


title: Liver F2 Control Pool (n=294) vs. 500880_F2_56


title: Liver F2 Control Pool (n=294) vs. 496915_F2_46


title: Liver F2 Control Pool (n=294) vs. 500866_F2_54


title: Liver F2 Control Pool (n=294) vs. 500879_F2_55


title: Liver F2 Control Pool (n=294) vs. 500878_F2_51


title: Liver F2 Control Pool (n=294) vs. 510624_F2_117


title: Liver F2 Control Pool (n=294) vs. 500864_F2_52


title: Liver F2 Control Pool (n=294) vs. 512415_F2_132


title: Liver F2 Control Pool (n=294) vs. 500881_F2_57


title: Liver F2 Control Pool (n=294) vs. 500887_F2_59


title: Liver F2 Control Pool (n=294) vs. 516113_F2_145


title: Liver F2 Control Pool (n=294) vs. 500867_F2_58


title: Liver F2 Control Pool (n=294) vs. 505344_F2_85


title: Liver F2 Control Pool (n=294) vs. 516125_F2_148


title: Liver F2 Control Pool (n=294) vs. 512432_F2_143


title: Liver F2 Control Pool (n=294) vs. 496916_F2_47


title: Liver F2 Control Pool (n=294) vs. 500872_F2_71


title: Liver F2 Control Pool (n=294) vs. 510623_F2_116


title: Liver F2 Control Pool (n=294) vs. 510615_F2_114


title: Liver F2 Control Pool (n=294) vs. 496917_F2_48


title: Liver F2 Control Pool (n=294) vs. 500871_F2_72


title: Liver F2 Control Pool (n=294) vs. 516114_F2_146


title: Liver F2 Control Pool (n=294) vs. 512433_F2_144


title: Liver F2 Control Pool (n=294) vs. 512431_F2_142


title: Liver F2 Control Pool (n=294) vs. 516115_F2_147


title: Liver F2 Control Pool (n=294) vs. 538350_F2_266


title: Liver F2 Control Pool (n=294) vs. 538360_F2_267


title: Liver F2 Control Pool (n=294) vs. 538337_F2_268


title: Liver F2 Control Pool (n=294) vs. 538340_F2_275


title: Liver F2 Control Pool (n=294) vs. 538349_F2_265


title: Liver F2 Control Pool (n=294) vs. 500884_F2_63


title: Liver F2 Control Pool (n=294) vs. 538357_F2_273


title: Liver F2 Control Pool (n=294) vs. 538348_F2_269


title: Liver F2 Control Pool (n=294) vs. 500882_F2_65


title: Liver F2 Control Pool (n=294) vs. 500869_F2_69


title: Liver F2 Control Pool (n=294) vs. 500886_F2_61


title: Liver F2 Control Pool (n=294) vs. 500883_F2_64


title: Liver F2 Control Pool (n=294) vs. 538338_F2_270


title: Liver F2 Control Pool (n=294) vs. 500874_F2_66


title: Liver F2 Control Pool (n=294) vs. 500868_F2_67


title: Liver F2 Control Pool (n=294) vs. 538359_F2_271


title: Liver F2 Control Pool (n=294) vs. 512426_F2_128


title: Liver F2 Control Pool (n=294) vs. 512427_F2_129


title: Liver F2 Control Pool (n=294) vs. 493704_F1_47


title: Liver F2 Control Pool (n=294) vs. 500870_F2_68


title: Liver F2 Control Pool (n=294) vs. 512423_F2_122


title: Liver F2 Control Pool (n=294) vs. 500876_F2_49


title: Liver F2 Control Pool (n=294) vs. 500877_F2_50


title: Liver F2 Control Pool (n=294) vs. 512422_F2_121


title: Liver F2 Control Pool (n=294) vs. 512425_F2_127


title: Liver F2 Control Pool (n=294) vs. 512412_F2_126


title: Liver F2 Control Pool (n=294) vs. 512411_F2_125


title: Liver F2 Control Pool (n=294) vs. 512424_F2_123


title: Liver F2 Control Pool (n=294) vs. 496910_F2_35


title: Liver F2 Control Pool (n=294) vs. 496909_F2_34


title: Liver F2 Control Pool (n=294) vs. 525910_F2_193


title: Liver F2 Control Pool (n=294) vs. 493705_F1_48


title: Liver F2 Control Pool (n=294) vs. 525911_F2_194


title: Liver F2 Control Pool (n=294) vs. 525924_F2_198


title: Liver F2 Control Pool (n=294) vs. 525912_F2_195


title: Liver F2 Control Pool (n=294) vs. 525913_F2_199


title: Liver F2 Control Pool (n=294) vs. 525914_F2_200


title: Liver F2 Control Pool (n=294) vs. 525922_F2_196


title: Liver F2 Control Pool (n=294) vs. 510620_F2_107


title: Liver F2 Control Pool (n=294) vs. 525915_F2_201


title: Liver F2 Control Pool (n=294) vs. 510604_F2_97


title: Liver F2 Control Pool (n=294) vs. 510616_F2_103


title: Liver F2 Control Pool (n=294) vs. 510618_F2_105


title: Liver F2 Control Pool (n=294) vs. 510605_F2_98


title: Liver F2 Control Pool (n=294) vs. 500873_F2_70


title: Liver F2 Control Pool (n=294) vs. 510609_F2_102


title: Liver F2 Control Pool (n=294) vs. 510606_F2_99


title: Liver F2 Control Pool (n=294) vs. 510621_F2_108


title: Liver F2 Control Pool (n=294) vs. 510617_F2_104


title: Liver F2 Control Pool (n=294) vs. 510607_F2_100


title: Liver F2 Control Pool (n=294) vs. 510626_F2_119


title: Liver F2 Control Pool (n=294) vs. 510625_F2_118


title: Liver F2 Control Pool (n=294) vs. 510608_F2_101


title: Liver F2 Control Pool (n=294) vs. 510627_F2_120


title: Liver F2 Control Pool (n=294) vs. 491044_F2_16


title: Liver F2 Control Pool (n=294) vs. 491042_F2_11


title: Liver F2 Control Pool (n=294) vs. 491043_F2_12


title: Liver F2 Control Pool (n=294) vs. 491040_F2_6


title: Liver F2 Control Pool (n=294) vs. 491039_F2_5


title: Liver F2 Control Pool (n=294) vs. 491041_F2_10


title: Liver F2 Control Pool (n=294) vs. 490061_F1_10


title: Liver F2 Control Pool (n=294) vs. 491038_F2_4


title: Liver F2 Control Pool (n=294) vs. 490052_AJ_5


title: Liver F2 Control Pool (n=294) vs. 490055_AJ_8


title: Liver F2 Control Pool (n=294) vs. 491045_F2_17


title: Liver F2 Control Pool (n=294) vs. 491049_F2_18


title: Liver F2 Control Pool (n=294) vs. 490047_B6_4


title: Liver F2 Control Pool (n=294) vs. 491047_F2_24


title: Liver F2 Control Pool (n=294) vs. 491046_F2_22


title: Liver F2 Control Pool (n=294) vs. 490057_F1_22


title: Liver F2 Control Pool (n=294) vs. 490045_B6_2


title: Liver F2 Control Pool (n=294) vs. 490059_F1_24


title: Liver F2 Control Pool (n=294) vs. 490051_AJ_20


title: Liver F2 Control Pool (n=294) vs. 491048_F2_23


title: Liver F2 Control Pool (n=294) vs. 491028_F2_3


title: Liver F2 Control Pool (n=294) vs. 491026_F2_1


title: Liver F2 Control Pool (n=294) vs. 490050_AJ_19


title: Liver F2 Control Pool (n=294) vs. 491029_F2_7


title: Liver F2 Control Pool (n=294) vs. 491027_F2_2


title: Liver F2 Control Pool (n=294) vs. 491031_F2_9


title: Liver F2 Control Pool (n=294) vs. 490054_AJ_7


title: Liver F2 Control Pool (n=294) vs. 490058_F1_23


title: Liver F2 Control Pool (n=294) vs. 491030_F2_8


title: Liver F2 Control Pool (n=294) vs. 491032_F2_13


title: Liver F2 Control Pool (n=294) vs. 491034_F2_15


title: Liver F2 Control Pool (n=294) vs. 491033_F2_14


title: Liver F2 Control Pool (n=294) vs. 490063_F1_12


title: Liver F2 Control Pool (n=294) vs. 490040_B6_13


title: Liver F2 Control Pool (n=294) vs. 490060_F1_9


title: Liver F2 Control Pool (n=294) vs. 490042_B6_15


title: Liver F2 Control Pool (n=294) vs. 493708_F1_35


title: Liver F2 Control Pool (n=294) vs. 505332_F2_79


title: Liver F2 Control Pool (n=294) vs. 493698_AJ_29


title: Liver F2 Control Pool (n=294) vs. 505333_F2_80


title: Liver F2 Control Pool (n=294) vs. 505330_F2_74


title: Liver F2 Control Pool (n=294) vs. 505329_F2_73


title: Liver F2 Control Pool (n=294) vs. 505331_F2_75


title: Liver F2 Control Pool (n=294) vs. 505336_F2_83


title: Liver F2 Control Pool (n=294) vs. 491037_F2_20


title: Liver F2 Control Pool (n=294) vs. 496911_F2_36


title: Liver F2 Control Pool (n=294) vs. 493707_F1_34


title: Liver F2 Control Pool (n=294) vs. 493700_AJ_31


title: Liver F2 Control Pool (n=294) vs. 505341_F2_76


title: Liver F2 Control Pool (n=294) vs. 505335_F2_82


title: Liver F2 Control Pool (n=294) vs. 505337_F2_84


title: Liver F2 Control Pool (n=294) vs. 491036_F2_21


title: Liver F2 Control Pool (n=294) vs. 505334_F2_81


title: Liver F2 Control Pool (n=294) vs. 493699_AJ_30


title: Liver F2 Control Pool (n=294) vs. 505343_F2_78


title: Liver F2 Control Pool (n=294) vs. 505342_F2_77


title: Liver F2 Control Pool (n=294) vs. 490046_B6_3


title: Liver F2 Control Pool (n=294) vs. 493678_B6_25


title: Liver F2 Control Pool (n=294) vs. 493679_B6_26


title: Liver F2 Control Pool (n=294) vs. 491035_F2_19


title: wild-type 5 hours hypoxia, replicate 1

city: Princeton

first: Mark

last: Hickman

state: NJ

address: Washington Road

department: Lewis-Sigler Institute of Integrative Genomics

institute: Princeton University

description:
WT hypoxic rep 1
Comparing WT aerobic to WT hypoxic.
Biological replicate 1 of 2.

hyb_protocol: 2.5 pmol of Cy3-RNA and 2.5 pmol Cy5-RNA were added to arrays and incubated 65°C for 17 hours. Arrays were washed with Agilent buffers.

scan_protocol: Scanned on an Agilent G2505B scanner using Agilent scanning software (v. A.7.0.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.

organism: Saccharomyces cerevisiae S288C

source_name: wild-type, aerobic

label_protocol: Agilent Quick-Amp Labeling Kit (cDNA using T7 promoter primer and MMLV reverse-transcriptase, then transcription with T7 RNA polymerase and Cy3/Cy5-CTP).

growth_protocol: Cells were grown to saturation overnight in YPD, then diluted 1:50 in YPD and grown for 4 hours to mid-log (aerobically).

extract_protocol: Hot phenol, chloroform extraction, ethanol precipitation.

treatment_protocol: Mid-log cells were diluted appropriately and grown for 5 hours in high-purity 100% nitrogen to mid-log.

tag: strain/background

tag: genotype

value: ura3D0 his3D200 leu2D0 lys2-128d HAP1

tag: condition

value: aerobic

source_name: wild-type, hypoxia, 5 hours

value: hypoxia

tag: time

value: 5 hours


title: wild-type 5 hours hypoxia, replicate 2

description:
WT hypoxic rep 2
Comparing WT aerobic to WT hypoxic.
Biological replicate 2 of 2.


title: hog1 deletion 5 hours hypoxia, replicate 1

description:
hog1 hypoxic rep 1
Comparing WT aerobic to hog1 hypoxic.
Biological replicate 1 of 2.

source_name: hog1 deletion, hypoxia, 5 hours

value: ura3D0 his3D200 leu2D0 lys2-128d HAP1 hog1D0:LEU2


title: Liver F2 Control Pool (n=294) vs. 496920_F2_27


title: Liver F2 Control Pool (n=294) vs. 496922_F2_29


title: Liver F2 Control Pool (n=294) vs. 496921_F2_28


title: hog1 deletion aerobic, replicate 2

description:
hog1 aerobic rep 2
Comparing WT aerobic to hog1 aerobic.
Biological replicate 2 of 2.

source_name: hog1 deletion, aerobic


title: hog1 deletion 5 hours hypoxia, replicate 2

description:
hog1 hypoxic rep 2
Comparing WT aerobic to hog1 hypoxic.
Biological replicate 2 of 2.


title: Liver F2 Control Pool (n=294) vs. 493680_B6_27


title: Liver F2 Control Pool (n=294) vs. 496918_F2_25


title: Liver F2 Control Pool (n=294) vs. 496923_F2_30


title: Liver F2 Control Pool (n=294) vs. 493706_F1_33


title: hog1 deletion aerobic, replicate 1

description:
hog1 aerobic rep 1
Comparing WT aerobic to hog1 aerobic.
Biological replicate 1 of 2.


title: Liver F2 Control Pool (n=294) vs. 493709_F1_36


title: Liver F2 Control Pool (n=294) vs. 496919_F2_26


title: CTCF_293T_rep3

type: genomic

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: CTCF ChIP-chip 293T cells, rep3.

hyb_protocol: See manufacturer's web site (www.nimblegen.com).

scan_protocol: Scanning was perfomed by NimbleGen using NimbleScan.

data_processing: Tukey biweight-scaled log2 ratio GFF files were created by NimbleGen.  Replicates were combined into single GFF files by computing average value for each probe across replicates (e.g., log2(mean((value1^2, value2^2, value3^2))) ) then re-scaling all new values by Tukey bi-weight.  Resulting GFF files were used with the ACME package for R as described in the paper.

molecule: genomic DNA

organism: Homo sapiens

source_name: CTCF ChIP DNA, 293T cells

extract_protocol: ChIP assays were carried out as described by Song et al. 2007 (PMID 18082606). Briefly, ~50 million cells were cross-linked with 1% formaldehyde, and nuclei were sonicated and digested with 200 U/mL of MNase to an average chromatin fragment size of 200-500 bp. Precleared chromatin was incubated with antibodies overnight at 4 °C and immunoprecipitated with protein A/G agarose beads. Immunoprecipitated material was extensively purified after reversal of the cross-links and was dissolved in Tris-EDTA for ChIP-chip or real-time PCR. The ratio of input DNA to immunoprecipitated DNA isolated from the same number of cells was maintained at 1/25.

tag: cell line

tag: cell type

value: fibroblast

tag: chip antibody

value: anti-CTCF

tag: antibody vendor

value: Millipore

tag: antibody catalog number

source_name: Input DNA, 293T cells


title: Liver F2 Control Pool (n=294) vs. 496907_F2_32

value: F


title: CTCF_K562_rep3

description: CTCF ChIP-chip K562 cells, rep3.

source_name: CTCF ChIP DNA, K562 cells

label_protocol: See manufacturer's web site (www.nimblegen.com).

value: erythroid

source_name: Input DNA, K562 cells


title: Cell line SKBR3_DR_4

city: São Paulo

first: Adriana

middle: Priscila

last: Trapé

state: São Paulo

address: Av. Dr Arnaldo

department: Radiologia e Oncologia

country: Brazil

institute: Faculdade de Medicina Universidade de São Paulo

hyb_protocol: Following fragmentation, 12,48 ug of cRNA were hybridized for 17 hr at 45C on GeneChip Human Genome U133 plus v.2.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 G7.

data_processing: Data were processed using RMA express 1.0 Release to yield normalized expression values. These values were calculated based on signal intensity generated by perfect match (PM)  probe

label: biotin

source_name: SKBR3 cell line - RAPAMYCIN (20nM) + DOXORUBICIN (30nM) treatment

label_protocol: Biotinylated cRNA were prepared using the kit GeneChip® 3’IVT Expression Kit Assay from Affymetrix according to manufacturer's protocol from 250ng total RNA (3’IVT Expression Kit Manual, 2008/2009, Affymetrix).

growth_protocol: All cells lines were maintained in RPMI supplemented with 10% heat-inactivated fetal bovine serum and 2mM glutamine. For HB4A and C5.2, 5 mg/mL insulin, 5mg/mL hydrocortisone, 100mg/mL ampicillin and 50 µg/mL  de gentamycin were added to the medium whereas SKBR3 was cultured in the presence of 50 mg/mL ampicillin and 50 mg/mL streptomycin. The cells were incubated at 37oC in a humidified atmosphere containing 5% CO2.

extract_protocol: Trizol extraction of total RNA followed with clean up (using Qiagen kit) was performed according to the manufacturers' instructions.

treatment_protocol: The cells were seeded in 25 cm2 flasks or 96-well culture plates at a density ranging from 5x103 cells/cm2 (HB4a and C5.2)  to 15x103 cells/cm2 (SKBR3). After 24 hours, the medium was replaced by another containing only vehicle (C), 20 hM of RAPAMYCIN alone (R) and 30  hM of DOXORUBICIN alone (D). The combined treatment consisted of 20hM of RAPAMYCIN associated with DOXORUBICIN of 30 hM  (DRC).

tag: cell line origin

value: SKBR3 was originated from mammary adenocarcinomas and constitutively over expresses HER-2

value: Mammary adenocarcinoma - over express HER2 receptor


title: Liver F2 Control Pool (n=294) vs. 496906_F2_31


title: CTCF_293T_rep2

description: CTCF ChIP-chip 293T cells, rep2.


title: Cell line SKBR3_DR_3


title: CTCF_293T_rep1

description: CTCF ChIP-chip 293T cells, rep1.


title: Cell line SKBR3_DR_2


title: Cell line SKBR3_DR_6


title: CTCF_K562_rep2

description: CTCF ChIP-chip K562 cells, rep2.


title: CTCF_K562_rep1

description: CTCF ChIP-chip K562 cells, rep1.


title: FlagLeaf_Sterile_3WAH_rep_1

city: Tsukuba

first: Baltazar

last: Antonio

state: Ibaraki

address: Kannondai 2-1-2

department: Genome and Biodiversity Research

country: Japan

institute: National Institute of Agrobiological Sciences

description: Gene expression of flag leaf at 3 weeks after heading in the sterile plant, pair1 mutant

hyb_protocol: For hybridization, 1650 ng of cyanine 3-labeled cRNA was fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um,  Dye channel is set to Green PMT: XDR Hi 100%; XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75 percentile normalization and log2 transformation with GenespringGX11(Agilent).

organism: Oryza sativa Japonica Group

source_name: Flag Leaf, Sterile plant, 3 weeks after heading, replicate 1

label_protocol: 400 ng of total RNA was added with one-color spike-mix and labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent) in the presence of cyanine-3-CTP accoring to the manufacturer's protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN), and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during normal rice growing season in 2009.

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer's protocol, quantitied using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: synonym

value: Oryza sativa L. ssp. japonica

tag: organ/tissue

value: Flag leaf

tag: phenotype

value: Sterile

tag: stage

value: 3 weeks after heading

tag: accession

value: ND0016 (Tos17 mutant line)


title: Cell line SKBR3_DR_1


title: Cell line SKBR3_R_6

source_name: SKBR3 cell line - RAPAMYCIN (20nM) treatment


title: Cell line SKBR3_R_2


title: FlagLeaf_Sterile_3WAH_rep_3

description: Gene expression of flag leaf at 3 weeks after heading in the sterile plant, mel1-1 mutant

source_name: Flag Leaf, Sterile plant, 3 weeks after heading, replicate 3

value: NC0005 (Tos17 mutant line)


title: Cell line SKBR3_R_4


title: FlagLeaf_Sterile_2WAH_rep_2

description: Gene expression of flag leaf at 2 weeks after heading in the sterile plant, pair2 mutant

source_name: Flag Leaf, Sterile plant, 2 weeks after heading, replicate 2

value: 2 weeks after heading

value: NC0122 (Tos17 mutant line)


title: Cell line SKBR3_R_1


title: FlagLeaf_Sterile_1WAH_rep_2

description: Gene expression of flag leaf at 1 week after heading in the sterile plant, pair2 mutant

source_name: Flag Leaf, Sterile plant, 1 week after heading, replicate 2

value: 1 week after heading


title: Cell line SKBR3_D_3

source_name: SKBR3 cell line - DOXORUBICIN (30nM) treatment


title: FlagLeaf_Sterile_3WAH_rep_2

description: Gene expression of flag leaf at 3 weeks after heading in the sterile plant, pair2 mutant

source_name: Flag Leaf, Sterile plant, 3 weeks after heading, replicate 2


title: FlagLeaf_Sterile_2WAH_rep_1

description: Gene expression of flag leaf at 2 weeks after heading in the sterile plant, pair1 mutant

source_name: Flag Leaf, Sterile plant, 2 weeks after heading, replicate 1


title: Cell line SKBR3_R_3


title: Liver F2 Control Pool (n=294) vs. 496908_F2_33

source_name: Liver

tag: sample type

value: Liver F2 Control Pool (n=294)

tag: animal id

tag: strain

tag: gender

tag: generation

value: liver


title: FlagLeaf_Sterile_1WAH_rep_1

description: Gene expression of flag leaf at 1 week after heading in the sterile plant, pair1 mutant

source_name: Flag Leaf, Sterile plant, 1 week after heading, replicate 1

tag: genotype


title: FlagLeaf_Sterile_0WAH_rep_2

description: Gene expression of flag leaf at initiation of heading in the sterile plant, pair2 mutant

source_name: Flag Leaf, Sterile plant, initiation of heading, replicate 2

value: initiation of heading


title: FlagLeaf_Sterile_0WAH_rep_1

description: Gene expression of flag leaf at initiation of heading in the sterile plant, pair1 mutant

source_name: Flag Leaf, Sterile plant, initiation of heading, replicate 1


title: FlagLeaf_Sterile_0WAH_rep_3

description: Gene expression of flag leaf at initiation of heading in the sterile plant, mel1-1 mutant

source_name: Flag Leaf, Sterile plant, initiation of heading, replicate 3


title: FlagLeaf_Sterile_1WAH_rep_3

description: Gene expression of flag leaf at 1 week after heading in the sterile plant, mel1-1 mutant

source_name: Flag Leaf, Sterile plant, 1 week after heading, replicate 3


title: FlagLeaf_Sterile_2WAH_rep_3

description: Gene expression of flag leaf at 2 weeks after heading in the sterile plant, mel1-1 mutant

source_name: Flag Leaf, Sterile plant, 2 weeks after heading, replicate 3


title: Cell line SKBR3_D_4

tag: cell line


title: Cell line SKBR3_D_6

tag: cell type


title: Cell line SKBR3_D_2


title: Cell line SKBR3_DRC_3

source_name: SKBR3 cell line - vehicle (DMSO)


title: Cell line SKBR3_D_1


title: FlagLeaf_Fertile_3WAH_rep_1

description: Gene expression of flag leaf at 3 weeks after heading in the fertile plant

source_name: Flag Leaf, Fertile plant, 3 weeks after heading, replicate 1

value: Fertile


title: FlagLeaf_Fertile_2WAH_rep_3

description: Gene expression of flag leaf at 2 weeks after heading in the fertile plant

source_name: Flag Leaf, Fertile plant, 2 weeks after heading, replicate 3


title: Cell line SKBR3_DRC_6


title: FlagLeaf_Fertile_3WAH_rep_2

source_name: Flag Leaf, Fertile plant, 3 weeks after heading, replicate 2


title: FlagLeaf_Fertile_3WAH_rep_3

source_name: Flag Leaf, Fertile plant, 3 weeks after heading, replicate 3


title: Cell line C5.2_DR_4

source_name: C5.2a cell line - RAPAMYCIN (20nM) + DOXORUBICIN (30nM) treatment

value: C5.2 cell was derived by the transfection of HB4a with the cDNA full-lenght corresponding to the HER-2

value: Human Breast Epithelial cell line -tranfected with HER2 cDNA


title: FlagLeaf_Fertile_2WAH_rep_2

source_name: Flag Leaf, Fertile plant, 2 weeks after heading, replicate 2


title: FlagLeaf_Fertile_2WAH_rep_1

source_name: Flag Leaf, Fertile plant, 2 weeks after heading, replicate 1


title: Cell line C5.2_DR_6


title: Cell line SKBR3_DRC_4

value: SKBR3 was originated from mammary adenocarcinomas and constitutively over expresses HER-2


title: FlagLeaf_Fertile_1WAH_rep_1

description: Gene expression of flag leaf at 1 week after heading in the fertile plant

source_name: Flag Leaf, Fertile plant, 1 week after heading, replicate 1


title: Cell line C5.2_DR_1


title: Cell line C5.2_DR_3


title: FlagLeaf_Fertile_1WAH_rep_2

source_name: Flag Leaf, Fertile plant, 1 week after heading, replicate 2


title: LeafBlade_118DAT_12:00_rep2

description: Gene expression of leaf blade at daytime 118 days after transplanting

hyb_protocol: For hybridization, 1650 ng of cyanine 3-labeled cRNA is fragmented and hybridized on the slide of rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

source_name: Leaf blade, 118 days after transplanting, 12:00, replicate 2

growth_protocol: All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during a normal rice growing season in 2008.

tag: cultivar

value: Nipponbare

value: Leaf Blade

tag: growth/development stage

value: 118 days after transplanting

tag: sampling time

value: Daytime 12:00


title: Cell line SKBR3_DRC_1

tag: cell line origin

value: Mammary adenocarcinoma - over express HER2 receptor


title: FlagLeaf_Fertile_1WAH_rep_3

source_name: Flag Leaf, Fertile plant, 1 week after heading, replicate 3

tag: synonym

value: Oryza sativa L. ssp. japonica

value: Flag leaf


title: Cell line C5.2_DR_2


title: FlagLeaf_Fertile_0WAH_rep_3

description: Gene expression of flag leaf at initiation of heading in the fertile plant

source_name: Flag Leaf, Fertile plant, initiation of heading, replicate 3

tag: organ/tissue

value: NC0005 (Tos17 mutant line)


title: FlagLeaf_Fertile_0WAH_rep_2

source_name: Flag Leaf, Fertile plant, initiation of heading, replicate 2

tag: phenotype

value: NC0122 (Tos17 mutant line)


title: Cell line C5.2_R_4

source_name: C5.2a cell line - RAPAMYCIN (20nM) treatment


title: Cell line C5.2_R_3


title: LeafBlade_118DAT_12:00_rep3

source_name: Leaf blade, 118 days after transplanting, 12:00, replicate 3


title: Cell line C5.2_R_6


title: FlagLeaf_Fertile_0WAH_rep_1

source_name: Flag Leaf, Fertile plant, initiation of heading, replicate 1

tag: stage

value: ND0016 (Tos17 mutant line)


title: LeafBlade_111DAT_12:00_rep2

description: Gene expression of leaf blade at daytime 111 days after transplanting

source_name: Leaf blade, 111 days after transplanting, 12:00, replicate 2

value: 111 days after transplanting


title: LeafBlade_118DAT_12:00_rep1

source_name: Leaf blade, 118 days after transplanting, 12:00, replicate 1


title: Cell line C5.2_D_4

source_name: C5.2a cell line - DOXORUBICIN (30nM) treatment


title: Cell line C5.2_R_2


title: Cell line C5.2_D_6


title: Cell line C5.2_D_1


title: LeafBlade_104DAT_12:00_rep2

description: Gene expression of leaf blade at daytime 104 days after transplanting

source_name: Leaf blade, 104 days after transplanting, 12:00, replicate 2

value: 104 days after transplanting


title: LeafBlade_104DAT_12:00_rep1

source_name: Leaf blade, 104 days after transplanting, 12:00, replicate 1


title: LeafBlade_104DAT_12:00_rep3

source_name: Leaf blade, 104 days after transplanting, 12:00, replicate 3


title: Cell line C5.2_R_1


title: Cell line C5.2_D_3


title: Cell line C5.2_DRC_4

source_name: C5.2a cell line - vehicle (DMSO)


title: LeafBlade_97DAT_12:00_rep3

description: Gene expression of leaf blade at daytime 97 days after transplanting

source_name: Leaf blade, 97 days after transplanting, 12:00, replicate 3

value: 97 days after transplanting


title: LeafBlade_111DAT_12:00_rep3

source_name: Leaf blade, 111 days after transplanting, 12:00, replicate 3


title: Cell line C5.2_DRC_6


title: Cell line C5.2_DRC_1


title: Cell line C5.2_DRC_3


title: Cell line C5.2_D_2


title: LeafBlade_90DAT_12:00_rep1

description: Gene expression of leaf blade at daytime 90 days after transplanting

source_name: Leaf blade, 90 days after transplanting, 12:00, replicate 1

value: 90 days after transplanting


title: Cell line C5.2_DRC_2

value: C5.2 cell was derived by the transfection of HB4a with the cDNA full-lenght corresponding to the HER-2


title: LeafBlade_90DAT_12:00_rep2

source_name: Leaf blade, 90 days after transplanting, 12:00, replicate 2


title: LeafBlade_90DAT_12:00_rep3

source_name: Leaf blade, 90 days after transplanting, 12:00, replicate 3


title: LeafBlade_97DAT_12:00_rep1

source_name: Leaf blade, 97 days after transplanting, 12:00, replicate 1


title: LeafBlade_97DAT_12:00_rep2

source_name: Leaf blade, 97 days after transplanting, 12:00, replicate 2


title: Cell line HB4a_DR6

source_name: HB4a cell line - RAPAMYCIN (20nM) + DOXORUBICIN (30nM) treatment

value: Normal Breast Epithelial

value: Human Normal Breast Epithelial cell line


title: Cell line HB4a_DR4


title: LeafBlade_111DAT_12:00_rep1

source_name: Leaf blade, 111 days after transplanting, 12:00, replicate 1

value: Nipponbare


title: Cell line HB4a_DR2


title: LeafBlade_83DAT_12:00_rep3

description: Gene expression of leaf blade at daytime 83 days after transplanting

source_name: Leaf blade, 83 days after transplanting, 12:00, replicate 3

value: Leaf Blade

value: 83 days after transplanting


title: LeafBlade_83DAT_12:00_rep1

source_name: Leaf blade, 83 days after transplanting, 12:00, replicate 1

value: Daytime 12:00


title: Cell line HB4a_DR3


title: Cell line HB4a_R6

source_name: HB4a cell line - RAPAMYCIN (20nM) treatment


title: LeafBlade_62DAT_12:00_rep3

description: Gene expression of leaf blade at daytime 62 days after transplanting

source_name: Leaf blade, 62 days after transplanting, 12:00, replicate 3

value: 62 days after transplanting


title: Cell line HB4a_DR1


title: Cell line HB4a_R4


title: LeafBlade_69DAT_12:00_rep2

description: Gene expression of leaf blade at daytime 69 days after transplanting

source_name: Leaf blade, 69 days after transplanting, 12:00, replicate 2

value: Oryza sativa L. ssp. japonica

value: 69 days after transplanting


title: Cell line HB4a_R3


title: LeafBlade_83DAT_12:00_rep2

source_name: Leaf blade, 83 days after transplanting, 12:00, replicate 2


title: Cell line HB4a_D_6

source_name: HB4a cell line -DOXORUBICIN (30nM) treatment


title: LeafBlade_62DAT_12:00_rep1

source_name: Leaf blade, 62 days after transplanting, 12:00, replicate 1


title: LeafBlade_55DAT_12:00_rep3

description: Gene expression of leaf blade at daytime 55 days after transplanting

source_name: Leaf blade, 55 days after transplanting, 12:00, replicate 3

value: 55 days after transplanting


title: LeafBlade_69DAT_12:00_rep1

source_name: Leaf blade, 69 days after transplanting, 12:00, replicate 1


title: LeafBlade_48DAT_12:00_rep3

description: Gene expression of leaf blade at daytime 48 days after transplanting

source_name: Leaf blade, 48 days after transplanting, 12:00, replicate 3

value: 48 days after transplanting


title: Cell line HB4a_R2


title: Cell line HB4a_R1


title: Cell line HB4a_DRC_6

source_name: HB4a cell line - vehicle (DMSO)


title: LeafBlade_55DAT_12:00_rep1

source_name: Leaf blade, 55 days after transplanting, 12:00, replicate 1


title: Cell line HB4a_D_3


title: Cell line HB4a_D_1


title: LeafBlade_48DAT_12:00_rep2

source_name: Leaf blade, 48 days after transplanting, 12:00, replicate 2


title: Cell line HB4a_D_4


title: Cell line HB4a_D_2


title: LeafBlade_62DAT_12:00_rep2

source_name: Leaf blade, 62 days after transplanting, 12:00, replicate 2


title: LeafBlade_55DAT_12:00_rep2

source_name: Leaf blade, 55 days after transplanting, 12:00, replicate 2


title: Cell line SKBR3_DRC_2

source_name: SKBR3 cell line - vehicle (DMSO)

value: SKBR3 was originated from mammary adenocarcinomas and constitutively over expresses HER-2

value: Mammary adenocarcinoma - over express HER2 receptor


title: LeafBlade_48DAT_12:00_rep1

source_name: Leaf blade, 48 days after transplanting, 12:00, replicate 1


title: LeafBlade_41DAT_12:00_rep2

description: Gene expression of leaf blade at daytime 41 days after transplanting

source_name: Leaf blade, 41 days after transplanting, 12:00, replicate 2

value: 41 days after transplanting


title: LeafBlade_69DAT_12:00_rep3

source_name: Leaf blade, 69 days after transplanting, 12:00, replicate 3


title: Cell line HB4a_DRC_3


title: LeafBlade_41DAT_12:00_rep1

source_name: Leaf blade, 41 days after transplanting, 12:00, replicate 1


title: Cell line HB4a_DRC_4


title: Cell line HB4a_DRC_2


title: LeafBlade_34DAT_12:00_rep3

description: Gene expression of leaf blade at daytime 34 days after transplanting

source_name: Leaf blade, 34 days after transplanting, 12:00, replicate 3

value: 34 days after transplanting


title: MRC5 cell line, stimulated, biological rep2

city: Aurora

first: Michael

last: Edwards

state: CO

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures, using the Affy GCS3000

data_processing: GCRMA normalization with Partek Genomics Suite 6.5.

source_name: Human fetal lung fibroblast cell line treated for 36 hr with TNF-α (10 ng/ml) and IFN-γ (50 U/ml).

label_protocol: Approximately 5 micrograms of total RNA was processed to produce biotinylated cRNA targets using the older (ENZO) Affymetrix protocol

growth_protocol: All cell lines used in the study were maintained in modified Eagle’s Minimum Essential Medium, supplemented 100 U/ml penicillin, 100 µg/ml streptomycin and 10% (v/v) heat inactivated fetal bovine serum, under a 5% CO2

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

treatment_protocol: Each cell line was divided into two groups and half of each was treated with TNF-α (10 ng/ml) and IFN-γ (50 U/ml) added directly to the growing media and both groups allowed to incubate for 36 hr at standard conditions.

tag: treatment group

value: TNF-α and IFN-γ stimulated

value: Human fetal lung fibroblast cell line


title: LeafBlade_20DAT_12:00_rep3

description: Gene expression of leaf blade at daytime 20 days after transplanting

source_name: Leaf blade, 20 days after transplanting, 12:00, replicate 3

value: 20 days after transplanting


title: LeafBlade_34DAT_12:00_rep1

source_name: Leaf blade, 34 days after transplanting, 12:00, replicate 1


title: N78 cell line, stimulated, biological rep3

source_name: Human primary lung fibroblast from a control subject treated for 36 hr with TNF-α (10 ng/ml) and IFN-γ (50 U/ml).

value: Human primary lung fibroblast


title: LeafBlade_20DAT_12:00_rep2

source_name: Leaf blade, 20 days after transplanting, 12:00, replicate 2

value: Nipponbare


title: LeafBlade_41DAT_12:00_rep3

source_name: Leaf blade, 41 days after transplanting, 12:00, replicate 3

value: Leaf Blade


title: Cell line HB4a_DRC_1

source_name: HB4a cell line - vehicle (DMSO)

value: Normal Breast Epithelial

value: Human Normal Breast Epithelial cell line


title: LeafBlade_13DAT_12:00_rep3

description: Gene expression of leaf blade at daytime 13 days after transplanting

source_name: Leaf blade, 13 days after transplanting, 12:00, replicate 3

value: 13 days after transplanting

value: Daytime 12:00


title: LeafBlade_34DAT_12:00_rep2

source_name: Leaf blade, 34 days after transplanting, 12:00, replicate 2

value: Oryza sativa L. ssp. japonica


title: LeafBlade_20DAT_12:00_rep1

source_name: Leaf blade, 20 days after transplanting, 12:00, replicate 1


title: LeafBlade_13DAT_12:00_rep1

source_name: Leaf blade, 13 days after transplanting, 12:00, replicate 1


title: MRC5 cell line, control, biological rep2

source_name: Human fetal lung fibroblast cell line maintained in standard culture

value: Unstimulated


title: N78 cell line, control, biological rep3

source_name: Human primary lung fibroblast from a control subject maintained in standard culture


title: FS087 cell line, stimulated, biological rep1

source_name: Human primary lung fibroblast from an IPF patient treated for 36 hr with TNF-α (10 ng/ml) and IFN-γ (50 U/ml).


title: LeafBlade_13DAT_12:00_rep2

source_name: Leaf blade, 13 days after transplanting, 12:00, replicate 2


title: Patient 2 ABCB5 positive cells

city: Boston

first: Natasha

middle: Y

last: Frank

state: MA

address: 320 Longwood Avenue

department: Medicine

institute: Children's Hospital Boston

hyb_protocol: Incubation of arrays was done for 16 hr at 45°C in an Affymetrix Model 640 Oven. Washing of the hybridized arrays was done on Model 450 Fluidics stations using methods described in the GeneChipR Expression Wash, Stain and Scan User Manual For Cartridge Arrays (P/N 702731 Rev. 3).

scan_protocol: Genechips were scanned using Affymetrix Model 3000 scanner.

data_processing: Data were analyzed using Affymetrix GCOS software and subsequent anaysis was completed using GenePattern software.

source_name: clinical melanoma specimen

label_protocol: Biotinylated cRNA were prepared using NuGEN Ovation reagents (Ovation AMP V2, cat.# 3100-12) according to the NuGEN Biotin Protocol (Encore Biotin Module Part No. 4200).

extract_protocol: Total RNA was isolated using RNAeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: ABCB5-positive cells were isolated by positive selection and ABCB5-negative cell populations were generated by removing ABCB5-positive cells using anti-ABCB5 mAb magnetic bead cell sorting as described (Schatton et al., Nature, 2008). Microarray analyses were performed on purified ABCB5+ (n=5) and ABCB5- (n=5) cell subsets derived from the established human melanoma cell lines G3361 and A375 and from three distinct clinical melanoma specimen.

value: ABCB5 positive melanoma cells


title: Endosperm_42 DAF_rep1

description: Gene expression of endosperm at 42 days after flowering

hyb_protocol: For microarray hybridization, 1650 ng of cyanine 3-labeled cRNA (or entire labeled cRNA for samples with low yield) were fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

source_name: Endosperm at 42 days after flowering, replicate 1

label_protocol: One-color spike-mix was added to the RNA prior to labeling reaction. Labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3-CTP according to the manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN) and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during normal rice growing season in 2008.

extract_protocol: For leaf blade, leaf sheath, root, stem, inflorescence, pistil, anther, lemma, palea, ovary and embryo samples, total RNA was extracted using RNeasy plant minikit (QIAGEN). For endosperm samples, total RNA was extracted with phenol and purified using the RNeasy mini spin column of the RNeasy plant mini kit. The extracted RNA was quantified using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

value: Endosperm

value: 42 days after flowering


title: Patient 3 ABCB5 positive cells


title: Patient 3 ABCB5 negative cells

value: ABCB5 negative melanoma cells


title: FS087 cell line, control, biological rep1

source_name: Human primary lung fibroblast from an IPF patient maintained in standard culture


title: Endosperm_14 DAF_rep3

description: Gene expression of endosperm at 14 days after flowering

source_name: Endosperm at 14 days after flowering, replicate 3

value: 14 days after flowering


title: G3361 ABCB5 negative cells

source_name: melanoma cell line

value: G3361 ABCB5 negative melanoma cells


title: Endosperm_28 DAF_rep3

description: Gene expression of endosperm at 28 days after flowering

source_name: Endosperm at 28 days after flowering, replicate 3

value: 28 days after flowering


title: Endosperm_42 DAF_rep2

source_name: Endosperm at 42 days after flowering, replicate 2


title: A375 ABCB5 negative cells

value: A375 ABCB5 negative melanoma cells


title: Patient 2 ABCB5 negative cells


title: Patient 1 ABCB5 negative cells


title: A375 ABCB5 positive cells

value: A375 ABCB5 positive melanoma cells


title: Endosperm_28 DAF_rep2

source_name: Endosperm at 28 days after flowering, replicate 2

value: Nipponbare


title: Patient 1 ABCB5 positive cells


title: G3361 ABCB5 positive cells

value: G3361 ABCB5 positive melanoma cells


title: Endosperm_14 DAF_rep2

source_name: Endosperm at 14 days after flowering, replicate 2


title: Endosperm_42 DAF_rep3

source_name: Endosperm at 42 days after flowering, replicate 3


title: PBS-exposed mouse lung MSC in vitro mix (human array)

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 h at 45°C on MG-430 2.0 arrays in the Affymetrix Hybridization Oven 640. Arrays were washed and stained (GeneChip Hybridization, Wash and Stain Kit; Affymterix) using Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with GeneChip 7G Scanner (Affymetrix)

data_processing: Array CEL-files were transferred onto Partek Genomics Suite and normalized with RMA.

source_name: PBS-exposed mouse lung_MSC in vitro mix

label_protocol: Biotinylated cRNA was prepared according to the One-Cycle cDNA Synthesis Protocol (Affymetrix)l from 3 ug of total RNA.

extract_protocol: Total RNA was obtained from lung tissue homogenized in TriPure Isolation Reagent (Roche) and was purified with RNeasy Mini Kit (Qiagen).

tag: tissue

value: lung and MSC

tag: exposure

value: PBS


title: Endosperm_28 DAF_rep1

source_name: Endosperm at 28 days after flowering, replicate 1


title: Endosperm_10 DAF_rep2

description: Gene expression of endosperm at 10 days after flowering

source_name: Endosperm at 10 days after flowering, replicate 2

value: 10 days after flowering


title: LPS-exposed mouse lung MSC in vitro mix (human array)

source_name: LPS-exposed mouse lung_MSC in vitro mix

value: LPS


title: Endosperm_10 DAF_rep3

source_name: Endosperm at 10 days after flowering, replicate 3

value: Oryza sativa L. ssp. japonica


title: Endosperm_14 DAF_rep1

source_name: Endosperm at 14 days after flowering, replicate 1


title: Endosperm_10 DAF_rep1

source_name: Endosperm at 10 days after flowering, replicate 1


title: LPS-exposed mouse lung MSC treated (human array)

source_name: LPS-exposed mouse lung_MSC treated

tag: treatment

value: MSC


title: Endosperm_07 DAF_rep3

description: Gene expression of endosperm at 7 days after flowering

source_name: Endosperm at 7 days after flowering, replicate 3

value: 7 days after flowering


title: Endosperm_07 DAF_rep2

source_name: Endosperm at 7 days after flowering, replicate 2

value: Endosperm


title: LPS-exposed mouse lung PBS treated (human array)

source_name: LPS-exposed mouse lung_PBS treated

value: lung


title: PBS-exposed mouse lung MSC treated (human array)

source_name: PBS-exposed mouse lung_MSC treated


title: Embryo_42 DAF_rep3

description: Gene expression of embryo at 42 days after flowering

source_name: Embryo at 42 days after flowering, replicate 3

value: Embryo

value: 42 days after flowering


title: Embryo_42 DAF_rep1

source_name: Embryo at 42 days after flowering, replicate 1


title: Endosperm_07 DAF_rep1

source_name: Endosperm at 7 days after flowering, replicate 1


title: Embryo_28 DAF_rep3

description: Gene expression of embryo at 28 days after flowering

source_name: Embryo at 28 days after flowering, replicate 3


title: Embryo_28 DAF_rep2

source_name: Embryo at 28 days after flowering, replicate 2


title: Septic Shock_biological rep92 20-0002

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Avenue

department: Pediatrics

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from septic shock patient

hyb_protocol: Standard Affymetrix

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Gene expression was measured using one patient sample per chip. Image files were captured using an Affymetrix GeneChip Scanner 3000. CEL files were subsequently preprocessed using Robust Multiple-Array Average (RMA) normalization and GeneSpring GX 7.3 software (Agilent Technologies, Palo Alto, CA). All signal intensity-based data were used after RMA normalization, which specifically suppresses all but significant variation among lower intensity probe sets. All chips representing patient samples were then normalized to the respective median values of controls.

source_name: Children ≤ 10 years old

label_protocol: WT-Ovation Pico (NuGen)

extract_protocol: Qiagen extraction from PaxGene whole blood RNA collection tubes

treatment_protocol: standard ICU care for septic shock

value: whole blood

tag: disease state

value: septic shock patient

tag: age (years)

tag: outcome

value: Survivor

tag: group

value: C


title: Embryo_14 DAF_rep1

description: Gene expression of embryo at 14 days after flowering

source_name: Embryo at 14 days after flowering, replicate 1

value: Nipponbare

value: 14 days after flowering


title: Septic Shock_biological rep97 26-260611

value: Nonsurvivor

value: A


title: Septic Shock_biological rep98 25-070603

value: B


title: Septic Shock_biological rep88 17-0001A


title: Embryo_10 DAF_rep3

description: Gene expression of embryo at 10 days after flowering

source_name: Embryo at 10 days after flowering, replicate 3

value: 10 days after flowering


title: Septic Shock_biological rep94 04-0004


title: Embryo_07 DAF_rep2

description: Gene expression of embryo at 7 days after flowering

source_name: Embryo at 7 days after flowering, replicate 2

value: Oryza sativa L. ssp. japonica


title: Septic Shock_biological rep86 15-0011A


title: Embryo_28 DAF_rep1

source_name: Embryo at 28 days after flowering, replicate 1

value: 28 days after flowering


title: Embryo_14 DAF_rep2

source_name: Embryo at 14 days after flowering, replicate 2


title: Septic Shock_biological rep87 15-0012A


title: Embryo_14 DAF_rep3

source_name: Embryo at 14 days after flowering, replicate 3


title: Septic Shock_biological rep84 15-0008


title: Embryo_10 DAF_rep2

source_name: Embryo at 10 days after flowering, replicate 2


title: Embryo_10 DAF_rep1

source_name: Embryo at 10 days after flowering, replicate 1


title: Embryo_42 DAF_rep2

source_name: Embryo at 42 days after flowering, replicate 2


title: Embryo_07 DAF_rep3

source_name: Embryo at 7 days after flowering, replicate 3

value: 7 days after flowering


title: Septic Shock_biological rep83 15-0007


title: Control_biological rep32 15-0005

description: Gene expression data from normal control

value: normal control


title: Ovary_07 DAF_rep3

description: Gene expression of ovary at 7 days after flowering

source_name: Ovary at 7 days after flowering, replicate 3

value: Ovary

value: Daytime 10:00


title: Septic Shock_biological rep82 15-0004


title: Control_biological rep31 15-0003


title: Septic Shock_biological rep81 14-0004A


title: Embryo_07 DAF_rep1

source_name: Embryo at 7 days after flowering, replicate 1

value: Embryo


title: Control_biological rep30 15-0002

value: whole blood


title: Control_biological rep29 15-0001


title: Ovary_07 DAF_rep2

source_name: Ovary at 7 days after flowering, replicate 2


title: Ovary_07 DAF_rep1

source_name: Ovary at 7 days after flowering, replicate 1


title: Ovary_03 DAF_rep3

description: Gene expression of ovary at 3 days after flowering

source_name: Ovary at 3 days after flowering, replicate 3

value: 3 days after flowering


title: Ovary_01 DAF_rep3

description: Gene expression of ovary at 1 day after flowering

source_name: Ovary at 1 day after flowering, replicate 3

value: 1 day after flowering


title: Ovary_05 DAF_rep3

description: Gene expression of ovary at 5 days after flowering

source_name: Ovary at 5 days after flowering, replicate 3

value: 5 days after flowering


title: Septic Shock_biological rep79 13-0002A

source_name: Children ≤ 10 years old

value: septic shock patient

value: Survivor


title: Control_biological rep22 11-0052


title: Ovary_05 DAF_rep1

source_name: Ovary at 5 days after flowering, replicate 1

value: Nipponbare


title: Ovary_05 DAF_rep2

source_name: Ovary at 5 days after flowering, replicate 2


title: Septic Shock_biological rep78 12-0002A

value: A


title: Ovary_03 DAF_rep2

source_name: Ovary at 3 days after flowering, replicate 2


title: Control_biological rep20 11-0036


title: Palea_7.0 mm floret_rep2

description: Gene expression of palea from 7.0 mm floret

source_name: Palea from 7.0 mm floret, replicate 1

value: Palea

value: 7.0 mm floret

value: Daytime


title: Ovary_01 DAF_rep2

source_name: Ovary at 1 day after flowering, replicate 2

value: Oryza sativa L. ssp. japonica


title: Septic Shock_biological rep80 14-0002A

value: B


title: Palea_7.0 mm floret_rep1


title: Control_biological rep21 11-0052C

value: normal control


title: Lemma_7.0 mm floret_rep1

description: Gene expression of lemma from 7.0 mm floret

source_name: Lemma from 7.0 mm floret, replicate 1

value: Lemma


title: Lemma_4.0-5.0 mm floret_rep3

description: Gene expression of lemma from 4.0-5.0 mm floret

source_name: Lemma from 4.0-5.0 mm floret, replicate 3

value: 4.0-5.0 mm floret


title: Ovary_01 DAF_rep1

source_name: Ovary at 1 day after flowering, replicate 1

value: Ovary

value: Daytime 10:00


title: Septic Shock_biological rep73 11-0029

value: whole blood


title: Palea_4.0-5.0 mm floret_rep2

description: Gene expression of palea from 4.0-5.0 mm floret

source_name: Palea from 4.0-5.0 mm floret, replicate 2


title: Lemma_7.0 mm floret_rep3

source_name: Lemma from 7.0 mm floret, replicate 3


title: Ovary_03 DAF_rep1

source_name: Ovary at 3 days after flowering, replicate 1

value: 3 days after flowering


title: Palea_4.0-5.0 mm floret_rep3

source_name: Palea from 4.0-5.0 mm floret, replicate 3


title: Lemma_4.0-5.0 mm floret_rep2

source_name: Lemma from 4.0-5.0 mm floret, replicate 2


title: Lemma_4.0-5.0 mm floret_rep1

source_name: Lemma from 4.0-5.0 mm floret, replicate 1


title: Palea_1.5-2.0 mm floret_rep2

description: Gene expression of palea from 1.5-2.0 mm floret

source_name: Palea from 1.5-2.0 mm floret, replicate 2

value: 1.5-2.0 mm floret


title: Palea_4.0-5.0 mm floret_rep1

source_name: Palea from 4.0-5.0 mm floret, replicate 1


title: Lemma_7.0 mm floret_rep2

source_name: Lemma from 7.0 mm floret, replicate 2


title: Palea_7.0 mm floret_rep3


title: Control_biological rep19 11-0037

source_name: Children ≤ 10 years old


title: Control_biological rep16 11-0019


title: Control_biological rep15 11-0018


title: Palea_1.5-2.0 mm floret_rep3

source_name: Palea from 1.5-2.0 mm floret, replicate 3


title: Septic Shock_biological rep74 11-0054A

value: septic shock patient


title: Control_biological rep17 11-0020

value: Survivor


title: Control_biological rep18 11-0027


title: Septic Shock_biological rep72 11-0017

value: Nonsurvivor


title: Lemma_1.5-2.0 mm floret_rep2

description: Gene expression of lemma from 1.5-2.0 mm floret

source_name: Lemma from 1.5-2.0 mm floret, replicate 2

value: Nipponbare


title: Palea_1.5-2.0 mm floret_rep1

source_name: Palea from 1.5-2.0 mm floret, replicate 1

value: Palea


title: Control_biological rep14 11-0014


title: Control_biological rep10 11-0009


title: Control_biological rep12 11-0012


title: Lemma_1.5-2.0 mm floret_rep3

source_name: Lemma from 1.5-2.0 mm floret, replicate 3


title: Pistil_10-14 cm inflorescence_rep2

description: Gene expression of pistil from 10-14 cm inflorescence

source_name: Pistil from 10-14 cm inflorescence, replicate 2

value: Pistil

value: 10-14 cm inflorescence


title: Pistil_14-18 cm inflorescence_rep2

description: Gene expression of pistil from 14-18 cm inflorescence

source_name: Pistil from 14-18 cm inflorescence, replicate 2

value: Oryza sativa L. ssp. japonica

value: 14-18 cm inflorescence

value: Daytime


title: Pistil_10-14 cm inflorescence_rep1

source_name: Pistil from 10-14 cm inflorescence, replicate 1


title: Septic Shock_biological rep69 10-0021A

description: Gene expression data from septic shock patient

value: B


title: Control_biological rep13 11-0013

value: normal control


title: Anther_1.6-2.0 mm_rep1

description: Gene expression of 1.6-2.0 mm anther

source_name: 1.6-2.0 mm anther, replicate 1

value: Anther


title: Pistil_14-18 cm inflorescence_rep1

source_name: Pistil from 14-18 cm inflorescence, replicate 1


title: Control_biological rep11 11-0011


title: Pistil_05-10 cm inflorescence_rep2

description: Gene expression of pistil from 5-10 cm inflorescence

source_name: Pistil from 05-10 cm inflorescence, replicate 2

value: 05-10 cm inflorescence


title: Pistil_14-18 cm inflorescence_rep3

source_name: Pistil from 14-18 cm inflorescence, replicate 3


title: Septic Shock_biological rep71 11-0010

value: whole blood

value: C


title: Pistil_10-14 cm inflorescence_rep3

source_name: Pistil from 10-14 cm inflorescence, replicate 3


title: Lemma_1.5-2.0 mm floret_rep1

source_name: Lemma from 1.5-2.0 mm floret, replicate 1

value: Lemma

value: 1.5-2.0 mm floret


title: Septic Shock_biological rep63 10-0020

value: septic shock patient


title: Septic Shock_biological rep70 11-0001

value: Survivor

value: A


title: Anther_1.6-2.0 mm_rep2

description: Gene expression of 1.6-2.0 mm anther

source_name: 1.6-2.0 mm anther, replicate 2

value: Nipponbare


title: Control_biological rep9 11-0008


title: Pistil_05-10 cm inflorescence_rep3

source_name: Pistil from 05-10 cm inflorescence, replicate 3

value: Pistil


title: Pistil_05-10 cm inflorescence_rep1

source_name: Pistil from 05-10 cm inflorescence, replicate 1


title: Septic Shock_biological rep65 10-0005

source_name: Children ≤ 10 years old


title: Anther_1.6-2.0 mm_rep3

description: Gene expression of 1.6-2.0 mm anther

source_name: 1.6-2.0 mm anther, replicate 3


title: Anther_1.2-1.5 mm_rep3

description: Gene expression of 1.2-1.5 mm anther

source_name: 1.2-1.5 mm anther, replicate 3


title: Anther_0.7-1.0 mm_rep2

description: Gene expression of 0.7-1.0 mm anther

source_name: 0.7-1.0 mm anther, replicate 2


title: Anther_1.2-1.5 mm_rep2

description: Gene expression of 1.2-1.5 mm anther

source_name: 1.2-1.5 mm anther, replicate 2


title: Inflorescence_5.0-10 mm_rep2

description: Gene expression of 5.0-10 mm inflorescence

source_name: 5.0-10 mm inflorescence, replicate 2

value: Inflorescence


title: Septic Shock_biological rep56 07-0006A

value: Nonsurvivor


title: Septic Shock_biological rep54 06-0009A


title: Inflorescence_5.0-10 mm_rep3

source_name: 5.0-10 mm inflorescence, replicate 3

value: Oryza sativa L. ssp. japonica


title: Anther_0.7-1.0 mm_rep1

description: Gene expression of 0.7-1.0 mm anther

source_name: 0.7-1.0 mm anther, replicate 1

value: Daytime


title: Septic Shock_biological rep59 09-0002


title: Septic Shock_biological rep51 06-0003

value: B


title: Anther_0.7-1.0 mm_rep3

description: Gene expression of 0.7-1.0 mm anther

source_name: 0.7-1.0 mm anther, replicate 3


title: Septic Shock_biological rep62 10-0017


title: Anther_0.3-0.6 mm_rep1

description: Gene expression of 0.3-0.6 mm anther

source_name: 0.3-0.6 mm anther, replicate 1


title: Septic Shock_biological rep55 07-0002


title: Septic Shock_biological rep47 05-0008


title: Septic Shock_biological rep61 10-0012


title: Septic Shock_biological rep52 06-0004


title: Inflorescence_3.0-4.0 mm_rep2

description: Gene expression of 3.0-4.0 mm inflorescence

source_name: 3.0-4.0 mm inflorescence, replicate 2


title: Septic Shock_biological rep48 05-0010


title: Inflorescence_5.0-10 mm_rep1

source_name: 5.0-10 mm inflorescence, replicate 1


title: Anther_1.2-1.5 mm_rep1

description: Gene expression of 1.2-1.5 mm anther

source_name: 1.2-1.5 mm anther, replicate 1


title: Anther_0.3-0.6 mm_rep2

description: Gene expression of 0.3-0.6 mm anther

source_name: 0.3-0.6 mm anther, replicate 2


title: Septic Shock_biological rep49 05-0011


title: Septic Shock_biological rep53 06-0006


title: Inflorescence_3.0-4.0 mm_rep3

source_name: 3.0-4.0 mm inflorescence, replicate 3


title: Septic Shock_biological rep60 10-0001


title: Inflorescence_3.0-4.0 mm_rep1

source_name: 3.0-4.0 mm inflorescence, replicate 1


title: Septic Shock_biological rep50 06-0001


title: Septic Shock_biological rep58 09-0001


title: Inflorescence_0.6-1.0 mm_rep3

description: Gene expression of 0.6-1.0 mm inflorescence

source_name: 0.6-1.0 mm inflorescence, replicate 3


title: Control_biological rep7 04-0011

description: Gene expression data from normal control

source_name: Children ≤ 10 years old

value: normal control


title: Septic Shock_biological rep46 05-0006


title: Stem_83DAT_12:00_rep1

description: Gene expression of stem at daytime 83 days after transplanting

source_name: Stem, 83 days after transplanting, 12:00, replicate 1

value: Stem

value: 83 days after transplanting

value: Daytime 12:00


title: Control_biological rep4 04-0010C

value: whole blood


title: Stem_90DAT_24:00_rep3

description: Gene expression of stem at nighttime 90 days after transplanting

source_name: Stem, 90 days after transplanting, 24:00, replicate 3

value: 90 days after transplanting

value: Nighttime 24:00


title: Control_biological rep6 04-0011C


title: Stem_83DAT_24:00_rep2

description: Gene expression of stem at nighttime 83 days after transplanting

source_name: Stem, 83 days after transplanting, 24:00, replicate 2


title: Control_biological rep5 04-0010


title: Inflorescence_0.6-1.0 mm_rep2

source_name: 0.6-1.0 mm inflorescence, replicate 2


title: Stem_83DAT_12:00_rep2

source_name: Stem, 83 days after transplanting, 12:00, replicate 2


title: Septic Shock_biological rep41 02-0001

value: septic shock patient


title: Stem_90DAT_12:00_rep1

description: Gene expression of stem at daytime 90 days after transplanting

source_name: Stem, 90 days after transplanting, 12:00, replicate 1


title: Stem_83DAT_12:00_rep3

source_name: Stem, 83 days after transplanting, 12:00, replicate 3


title: Root_76DAT_24:00_rep1

description: Gene expression of root at nighttime 76 days after transplanting

source_name: Root, 76 days after transplanting, 24:00, replicate 1

value: Root

value: 76 days after transplanting


title: Stem_90DAT_12:00_rep2

source_name: Stem, 90 days after transplanting, 12:00, replicate 2

value: Nipponbare


title: Septic Shock_biological rep45 05-0003

value: Survivor

value: A


title: Septic Shock_biological rep42 02-0002A


title: Stem_90DAT_24:00_rep1

source_name: Stem, 90 days after transplanting, 24:00, replicate 1


title: Stem_90DAT_24:00_rep2

source_name: Stem, 90 days after transplanting, 24:00, replicate 2


title: Septic Shock_biological rep43 04-0003

value: Nonsurvivor


title: Septic Shock_biological rep37 01-0066A

value: C


title: Septic Shock_biological rep44 04-0005


title: Inflorescence_0.6-1.0 mm_rep1

source_name: 0.6-1.0 mm inflorescence, replicate 1

value: Oryza sativa L. ssp. japonica

value: Inflorescence

value: Daytime


title: Root_76DAT_12:00_rep2

description: Gene expression of root at daytime 76 days after transplanting

source_name: Root, 76 days after transplanting, 12:00, replicate 2