title: Patient genomic DNA from sample 536


title: Patient genomic DNA from sample 520

status: Public on Jan 21 2013

type: genomic

city: Shanghai

first: Yun

last: Liu

address: 130 Dong An Road

country: China

institute: Fudan University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: minfi, R

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: PBL

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions

tag: cell type

value: PBL

tag: disease state

value: rheumatoid arthritis

tag: subject

value: Patient

tag: age

tag: gender

value: f

tag: smoking status

value: ex


title: Patient genomic DNA from sample 521

value: current


title: Patient genomic DNA from sample 518


title: Normal genomic DNA from sample 512

value: Normal

value: m


title: Normal genomic DNA from sample 524

value: never


title: Patient genomic DNA from sample 532

value: occasional


title: Normal genomic DNA from sample 513


title: Normal genomic DNA from sample 515


title: Patient genomic DNA from sample 519


title: Normal genomic DNA from sample 517


title: Patient genomic DNA from sample 530


title: Normal genomic DNA from sample 516


title: Patient genomic DNA from sample 522


title: Patient genomic DNA from sample 505


title: Normal genomic DNA from sample 510


title: Patient genomic DNA from sample 508


title: Normal genomic DNA from sample 511


title: Patient genomic DNA from sample 509


title: Patient genomic DNA from sample 507


title: Normal genomic DNA from sample 514


title: Patient genomic DNA from sample 504


title: Normal genomic DNA from sample 497


title: Patient genomic DNA from sample 503


title: Patient genomic DNA from sample 490


title: Patient genomic DNA from sample 502


title: Patient genomic DNA from sample 500


title: Patient genomic DNA from sample 501


title: Normal genomic DNA from sample 493


title: Normal genomic DNA from sample 498


title: Normal genomic DNA from sample 491


title: Patient genomic DNA from sample 489


title: Normal genomic DNA from sample 494


title: Patient genomic DNA from sample 487


title: Patient genomic DNA from sample 499


title: Patient genomic DNA from sample 483


title: Patient genomic DNA from sample 482


title: Normal genomic DNA from sample 492


title: Patient genomic DNA from sample 506


title: Patient genomic DNA from sample 481


title: Patient genomic DNA from sample 485


title: Patient genomic DNA from sample 480


title: Normal genomic DNA from sample 495


title: Patient genomic DNA from sample 486


title: Normal genomic DNA from sample 496


title: Patient genomic DNA from sample 484


title: Patient genomic DNA from sample 475


title: Patient genomic DNA from sample 476


title: Patient genomic DNA from sample 467


title: Patient genomic DNA from sample 473


title: Patient genomic DNA from sample 472


title: Patient genomic DNA from sample 466


title: Patient genomic DNA from sample 471


title: Patient genomic DNA from sample 478


title: Patient genomic DNA from sample 474


title: Patient genomic DNA from sample 468


title: Patient genomic DNA from sample 463


title: Patient genomic DNA from sample 479


title: Patient genomic DNA from sample 464


title: Patient genomic DNA from sample 465


title: Patient genomic DNA from sample 457


title: Patient genomic DNA from sample 459


title: Patient genomic DNA from sample 460


title: Patient genomic DNA from sample 488


title: Patient genomic DNA from sample 456


title: Patient genomic DNA from sample 461


title: Patient genomic DNA from sample 470


title: Patient genomic DNA from sample 458


title: Patient genomic DNA from sample 455


title: Patient genomic DNA from sample 452


title: Patient genomic DNA from sample 451


title: Patient genomic DNA from sample 454


title: Patient genomic DNA from sample 477


title: Patient genomic DNA from sample 453


title: Patient genomic DNA from sample 469


title: Patient genomic DNA from sample 450


title: Patient genomic DNA from sample 449


title: Patient genomic DNA from sample 462


title: Patient genomic DNA from sample 448


title: Normal genomic DNA from sample 441


title: Normal genomic DNA from sample 442


title: Normal genomic DNA from sample 444


title: Patient genomic DNA from sample 447


title: Normal genomic DNA from sample 443


title: Patient genomic DNA from sample 436


title: Normal genomic DNA from sample 439


title: Normal genomic DNA from sample 438


title: Patient genomic DNA from sample 445


title: Patient genomic DNA from sample 446


title: Patient genomic DNA from sample 437


title: Normal genomic DNA from sample 440


title: Normal genomic DNA from sample 431


title: Patient genomic DNA from sample 433


title: Patient genomic DNA from sample 435


title: Normal genomic DNA from sample 430


title: Patient genomic DNA from sample 434


title: Patient genomic DNA from sample 432


title: Patient genomic DNA from sample 424


title: Normal genomic DNA from sample 429


title: Normal genomic DNA from sample 427


title: Normal genomic DNA from sample 428


title: Patient genomic DNA from sample 418


title: Normal genomic DNA from sample 426


title: Normal genomic DNA from sample 425


title: Patient genomic DNA from sample 423


title: Patient genomic DNA from sample 422


title: Patient genomic DNA from sample 420


title: Patient genomic DNA from sample 421


title: Patient genomic DNA from sample 414


title: Patient genomic DNA from sample 416


title: Patient genomic DNA from sample 415


title: Patient genomic DNA from sample 411


title: Patient genomic DNA from sample 412


title: Patient genomic DNA from sample 408


title: Patient genomic DNA from sample 406


title: Normal genomic DNA from sample 405


title: Normal genomic DNA from sample 402


title: Patient genomic DNA from sample 419


title: Patient genomic DNA from sample 409


title: Patient genomic DNA from sample 417


title: Normal genomic DNA from sample 399


title: Patient genomic DNA from sample 413


title: Patient genomic DNA from sample 410


title: Normal genomic DNA from sample 403


title: Normal genomic DNA from sample 401


title: Patient genomic DNA from sample 397


title: Patient genomic DNA from sample 392


title: Normal genomic DNA from sample 400


title: Patient genomic DNA from sample 396


title: Patient genomic DNA from sample 391


title: Patient genomic DNA from sample 393


title: Patient genomic DNA from sample 398


title: Patient genomic DNA from sample 387


title: Patient genomic DNA from sample 390


title: Patient genomic DNA from sample 394


title: Patient genomic DNA from sample 389


title: Patient genomic DNA from sample 395


title: Normal genomic DNA from sample 382


title: Patient genomic DNA from sample 386


title: Patient genomic DNA from sample 384


title: Patient genomic DNA from sample 407


title: Normal genomic DNA from sample 404


title: Patient genomic DNA from sample 385


title: Normal genomic DNA from sample 383


title: Patient genomic DNA from sample 388


title: Patient genomic DNA from sample 376


title: Normal genomic DNA from sample 377


title: Normal genomic DNA from sample 380


title: Normal genomic DNA from sample 381


title: Normal genomic DNA from sample 378


title: Patient genomic DNA from sample 375


title: Normal genomic DNA from sample 379


title: Patient genomic DNA from sample 371


title: Patient genomic DNA from sample 369


title: Patient genomic DNA from sample 372


title: Patient genomic DNA from sample 368


title: Patient genomic DNA from sample 367


title: Patient genomic DNA from sample 374


title: Patient genomic DNA from sample 373


title: Patient genomic DNA from sample 365


title: Normal genomic DNA from sample 360


title: Patient genomic DNA from sample 363


title: Patient genomic DNA from sample 366


title: Patient genomic DNA from sample 355


title: Patient genomic DNA from sample 364


title: Patient genomic DNA from sample 361


title: Patient genomic DNA from sample 362


title: Normal genomic DNA from sample 359


title: Patient genomic DNA from sample 357


title: Patient genomic DNA from sample 370


title: Patient genomic DNA from sample 356


title: Patient genomic DNA from sample 353


title: Patient genomic DNA from sample 354


title: Normal genomic DNA from sample 350


title: Patient genomic DNA from sample 344


title: Normal genomic DNA from sample 341


title: Patient genomic DNA from sample 351


title: Patient genomic DNA from sample 348


title: Normal genomic DNA from sample 349


title: Patient genomic DNA from sample 347


title: Normal genomic DNA from sample 352


title: Patient genomic DNA from sample 345


title: Patient genomic DNA from sample 342


title: Patient genomic DNA from sample 346


title: Patient genomic DNA from sample 343


title: Patient genomic DNA from sample 337


title: Normal genomic DNA from sample 340


title: Normal genomic DNA from sample 336


title: Patient genomic DNA from sample 334


title: Normal genomic DNA from sample 338


title: Normal genomic DNA from sample 331


title: Normal genomic DNA from sample 322


title: Normal genomic DNA from sample 323


title: Normal genomic DNA from sample 329


title: Normal genomic DNA from sample 327


title: Normal genomic DNA from sample 328


title: Normal genomic DNA from sample 324


title: Normal genomic DNA from sample 321


title: Patient genomic DNA from sample 332


title: Patient genomic DNA from sample 325


title: Normal genomic DNA from sample 310


title: Normal genomic DNA from sample 314


title: Normal genomic DNA from sample 320


title: Normal genomic DNA from sample 317


title: Normal genomic DNA from sample 316


title: Normal genomic DNA from sample 309


title: Normal genomic DNA from sample 326


title: Patient genomic DNA from sample 358


title: Normal genomic DNA from sample 333


title: Normal genomic DNA from sample 335


title: Normal genomic DNA from sample 312


title: Normal genomic DNA from sample 311


title: Normal genomic DNA from sample 315


title: Patient genomic DNA from sample 305


title: Normal genomic DNA from sample 308


title: Normal genomic DNA from sample 307


title: Normal genomic DNA from sample 313


title: Normal genomic DNA from sample 300


title: Normal genomic DNA from sample 302


title: Normal genomic DNA from sample 299


title: Normal genomic DNA from sample 304


title: Normal genomic DNA from sample 319


title: Normal genomic DNA from sample 298


title: Normal genomic DNA from sample 303


title: Normal genomic DNA from sample 297


title: Normal genomic DNA from sample 330


title: Normal genomic DNA from sample 339


title: Normal genomic DNA from sample 318


title: Patient genomic DNA from sample 295


title: Normal genomic DNA from sample 293


title: Normal genomic DNA from sample 292


title: Normal genomic DNA from sample 282


title: Normal genomic DNA from sample 284


title: Normal genomic DNA from sample 281


title: Normal genomic DNA from sample 286


title: Normal genomic DNA from sample 289


title: Normal genomic DNA from sample 285


title: Normal genomic DNA from sample 290


title: Normal genomic DNA from sample 291


title: Normal genomic DNA from sample 296


title: Normal genomic DNA from sample 288


title: Patient genomic DNA from sample 294


title: Normal genomic DNA from sample 280


title: Normal genomic DNA from sample 278


title: Normal genomic DNA from sample 283


title: Normal genomic DNA from sample 279


title: Normal genomic DNA from sample 287


title: Patient genomic DNA from sample 306


title: Patient genomic DNA from sample 272


title: Patient genomic DNA from sample 274


title: Patient genomic DNA from sample 276


title: Patient genomic DNA from sample 275


title: Normal genomic DNA from sample 267


title: Patient genomic DNA from sample 271


title: Normal genomic DNA from sample 268


title: Normal genomic DNA from sample 266


title: Normal genomic DNA from sample 258


title: Patient genomic DNA from sample 259


title: Patient genomic DNA from sample 273


title: Patient genomic DNA from sample 255


title: Patient genomic DNA from sample 261


title: Normal genomic DNA from sample 262


title: Patient genomic DNA from sample 270


title: Normal genomic DNA from sample 260


title: Normal genomic DNA from sample 265


title: Normal genomic DNA from sample 264


title: Normal genomic DNA from sample 269


title: Patient genomic DNA from sample 254


title: Patient genomic DNA from sample 252


title: Normal genomic DNA from sample 257


title: Normal genomic DNA from sample 263


title: Patient genomic DNA from sample 256


title: Normal genomic DNA from sample 301


title: Normal genomic DNA from sample 253


title: Normal genomic DNA from sample 247


title: Normal genomic DNA from sample 246


title: Normal genomic DNA from sample 245


title: Normal genomic DNA from sample 251


title: Normal genomic DNA from sample 241


title: Normal genomic DNA from sample 249


title: Normal genomic DNA from sample 236


title: Normal genomic DNA from sample 244


title: Normal genomic DNA from sample 242


title: Normal genomic DNA from sample 234


title: Patient genomic DNA from sample 226


title: Normal genomic DNA from sample 238


title: Normal genomic DNA from sample 248


title: Normal genomic DNA from sample 250


title: Patient genomic DNA from sample 229


title: Normal genomic DNA from sample 232


title: Normal genomic DNA from sample 240


title: Normal genomic DNA from sample 225


title: Normal genomic DNA from sample 233


title: Normal genomic DNA from sample 239


title: Normal genomic DNA from sample 227


title: Normal genomic DNA from sample 221


title: Normal genomic DNA from sample 220


title: Normal genomic DNA from sample 231


title: Normal genomic DNA from sample 237


title: Patient genomic DNA from sample 223


title: Patient genomic DNA from sample 219


title: Normal genomic DNA from sample 243


title: Patient genomic DNA from sample 217


title: Patient genomic DNA from sample 216


title: Patient genomic DNA from sample 211


title: Normal genomic DNA from sample 218


title: Patient genomic DNA from sample 224


title: Patient genomic DNA from sample 215


title: Patient genomic DNA from sample 213


title: Patient genomic DNA from sample 212


title: Patient genomic DNA from sample 205


title: Normal genomic DNA from sample 228


title: Normal genomic DNA from sample 207


title: Normal genomic DNA from sample 209


title: Patient genomic DNA from sample 204


title: Normal genomic DNA from sample 206


title: Patient genomic DNA from sample 198


title: Patient genomic DNA from sample 210


title: Patient genomic DNA from sample 201


title: Patient genomic DNA from sample 214


title: Patient genomic DNA from sample 197


title: Normal genomic DNA from sample 235


title: Patient genomic DNA from sample 196


title: Normal genomic DNA from sample 191


title: Normal genomic DNA from sample 203


title: Patient genomic DNA from sample 200


title: Patient genomic DNA from sample 195


title: Patient genomic DNA from sample 199


title: Normal genomic DNA from sample 230


title: Normal genomic DNA from sample 202


title: Normal genomic DNA from sample 208


title: Normal genomic DNA from sample 189


title: Normal genomic DNA from sample 188


title: Patient genomic DNA from sample 277


title: Patient genomic DNA from sample 194


title: Patient genomic DNA from sample 187


title: Normal genomic DNA from sample 222


title: Normal genomic DNA from sample 186


title: Patient genomic DNA from sample 185


title: Patient genomic DNA from sample 179


title: Patient genomic DNA from sample 181


title: Patient genomic DNA from sample 177


title: Patient genomic DNA from sample 172


title: Normal genomic DNA from sample 190


title: Patient genomic DNA from sample 182


title: Patient genomic DNA from sample 184


title: Patient genomic DNA from sample 180


title: Normal genomic DNA from sample 193


title: Patient genomic DNA from sample 183


title: Patient genomic DNA from sample 178


title: Patient genomic DNA from sample 176


title: Patient genomic DNA from sample 175


title: Normal genomic DNA from sample 165


title: Patient genomic DNA from sample 170


title: Patient genomic DNA from sample 173


title: Normal genomic DNA from sample 169


title: Normal genomic DNA from sample 192


title: Patient genomic DNA from sample 160


title: Normal genomic DNA from sample 168


title: Patient genomic DNA from sample 171


title: Normal genomic DNA from sample 166


title: Normal genomic DNA from sample 167


title: Patient genomic DNA from sample 161


title: Normal genomic DNA from sample 164


title: Patient genomic DNA from sample 162


title: Patient genomic DNA from sample 155


title: Patient genomic DNA from sample 156


title: Patient genomic DNA from sample 158


title: Patient genomic DNA from sample 157


title: Normal genomic DNA from sample 148


title: Normal genomic DNA from sample 147


title: Patient genomic DNA from sample 146


title: Normal genomic DNA from sample 151


title: Patient genomic DNA from sample 154


title: Patient genomic DNA from sample 159


title: Normal genomic DNA from sample 150


title: Normal genomic DNA from sample 142


title: Normal genomic DNA from sample 143


title: Normal genomic DNA from sample 163


title: Patient genomic DNA from sample 174


title: Normal genomic DNA from sample 141


title: Normal genomic DNA from sample 138


title: Normal genomic DNA from sample 149


title: Normal genomic DNA from sample 139


title: Normal genomic DNA from sample 140


title: Normal genomic DNA from sample 134


title: Normal genomic DNA from sample 131


title: Normal genomic DNA from sample 145


title: Normal genomic DNA from sample 137


title: Patient genomic DNA from sample 152


title: Normal genomic DNA from sample 136


title: Normal genomic DNA from sample 144


title: Patient genomic DNA from sample 153


title: Normal genomic DNA from sample 124


title: Normal genomic DNA from sample 132


title: Normal genomic DNA from sample 129


title: Normal genomic DNA from sample 126


title: Normal genomic DNA from sample 125


title: Normal genomic DNA from sample 135


title: Normal genomic DNA from sample 130


title: Normal genomic DNA from sample 122


title: Normal genomic DNA from sample 127


title: Normal genomic DNA from sample 133


title: Normal genomic DNA from sample 120


title: Normal genomic DNA from sample 115


title: Normal genomic DNA from sample 121


title: Normal genomic DNA from sample 123


title: Normal genomic DNA from sample 117


title: Normal genomic DNA from sample 110


title: Normal genomic DNA from sample 128


title: Patient genomic DNA from sample 112


title: Normal genomic DNA from sample 119


title: Patient genomic DNA from sample 113


title: Patient genomic DNA from sample 116


title: Normal genomic DNA from sample 104


title: Normal genomic DNA from sample 107


title: Normal genomic DNA from sample 109


title: Normal genomic DNA from sample 108


title: Normal genomic DNA from sample 111


title: Normal genomic DNA from sample 114


title: Normal genomic DNA from sample 106


title: Normal genomic DNA from sample 118


title: Normal genomic DNA from sample 100


title: Normal genomic DNA from sample 96


title: Normal genomic DNA from sample 95


title: Normal genomic DNA from sample 103


title: Normal genomic DNA from sample 101


title: Normal genomic DNA from sample 102


title: Normal genomic DNA from sample 99


title: Patient genomic DNA from sample 92


title: Normal genomic DNA from sample 94


title: Patient genomic DNA from sample 91


title: Normal genomic DNA from sample 97


title: Patient genomic DNA from sample 90


title: Patient genomic DNA from sample 93


title: Normal genomic DNA from sample 105


title: Normal genomic DNA from sample 86


title: Normal genomic DNA from sample 98


title: Normal genomic DNA from sample 83


title: Patient genomic DNA from sample 89


title: Patient genomic DNA from sample 76


title: Normal genomic DNA from sample 82


title: Normal genomic DNA from sample 75


title: Normal genomic DNA from sample 78


title: Patient genomic DNA from sample 88


title: Normal genomic DNA from sample 70


title: Patient genomic DNA from sample 87


title: Normal genomic DNA from sample 85


title: Normal genomic DNA from sample 81


title: Normal genomic DNA from sample 69


title: Normal genomic DNA from sample 79


title: Normal genomic DNA from sample 73


title: Normal genomic DNA from sample 71


title: Normal genomic DNA from sample 80


title: Normal genomic DNA from sample 72


title: Patient genomic DNA from sample 74


title: Normal genomic DNA from sample 77


title: Normal genomic DNA from sample 68


title: Normal genomic DNA from sample 67


title: Normal genomic DNA from sample 84


title: Normal genomic DNA from sample 64


title: Normal genomic DNA from sample 66


title: Normal genomic DNA from sample 63


title: Normal genomic DNA from sample 65


title: Normal genomic DNA from sample 57


title: Normal genomic DNA from sample 62


title: Normal genomic DNA from sample 59


title: Normal genomic DNA from sample 56


title: Normal genomic DNA from sample 52


title: Normal genomic DNA from sample 60


title: Normal genomic DNA from sample 61


title: Normal genomic DNA from sample 51


title: Normal genomic DNA from sample 48


title: Normal genomic DNA from sample 54


title: Normal genomic DNA from sample 47


title: Normal genomic DNA from sample 58


title: Normal genomic DNA from sample 45


title: Normal genomic DNA from sample 46


title: Normal genomic DNA from sample 40


title: Normal genomic DNA from sample 44


title: Normal genomic DNA from sample 49


title: Normal genomic DNA from sample 50


title: Normal genomic DNA from sample 55


title: Normal genomic DNA from sample 53


title: Normal genomic DNA from sample 41


title: Normal genomic DNA from sample 37


title: Normal genomic DNA from sample 38


title: Normal genomic DNA from sample 35


title: Normal genomic DNA from sample 31


title: Normal genomic DNA from sample 33


title: Normal genomic DNA from sample 34


title: Normal genomic DNA from sample 32


title: Normal genomic DNA from sample 42


title: Normal genomic DNA from sample 28


title: Normal genomic DNA from sample 29


title: Normal genomic DNA from sample 43


title: Normal genomic DNA from sample 36


title: Normal genomic DNA from sample 25


title: Patient genomic DNA from sample 23


title: Patient genomic DNA from sample 30


title: Normal genomic DNA from sample 21


title: Patient genomic DNA from sample 24


title: Normal genomic DNA from sample 19


title: Normal genomic DNA from sample 20


title: Normal genomic DNA from sample 16


title: Normal genomic DNA from sample 27


title: Normal genomic DNA from sample 26


title: Normal genomic DNA from sample 15


title: Normal genomic DNA from sample 14


title: Normal genomic DNA from sample 17


title: Nod-LCO control 6h roots biological replicate 1

status: Public on May 31 2012

type: RNA

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

country: Germany

institute: Leibniz Universität Hannover

description: Gene expression data from Medicago truncatula plantlet roots treated with control solution

hyb_protocol: 12.5 ug of fragmented aRNA was added to a 250 ul cocktail also containing hybridization controls. 200 ul of the mixture was hybridized on GeneChips for 16 h at 45C. Standard post hybridization wash and double-stain protocols (FS450_0001; GeneChip HWS kit; Affymetrix, Santa Clara, CA, USA) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Cel files obtained from Medicago GeneChip hybridizations were analysed using the Robin software (http://mapman.gabipd.org/web/guest/robin). Normalization was performed using the Robust Multichip Average (RMA) algorithm. Intensity values calculated for each probe set were log2-transformed and averaged across all three biological replicates. Log2 differences between the conditions studied were evaluated statistically via Students t-tests implemented in Robin.

label: biotin

molecule: total RNA

organism: Medicago truncatula

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Medicago Genome Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA with by a RIN number (Agilent 2100 Bioanalyzer, Agilent, Böblingen, Germany) of at least 9.0 containing spiked-in poly-A+ RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After secondstrand synthesis, double-stranded cDNA was used in a 16 h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of in vitro transcribed aRNA and fragmented aRNA, respectively, was assessed via an Agilent 2100 Bioanalyzer, using an RNA 6000 Nano Assay.

growth_protocol: Medicago truncatula Gaertn cv Jemalong genotype A17 seeds were surface-sterilized and scarified. Plates with M. truncatula seeds were incubated for 24 hours in the climate chamber (humidity: 70 %; photosynthetic photon flux: 150 μmol m-2 s-1) at a 16 h light (23 °C) and 8 h dark (18 °C) regime. Subsequently, seedlings were moisturized with sterile water (pH 7.0) to allow careful removal of seed coats. In each case, eight seedlings were put on the upper quarter of a 2.5 % (w/v) phytoagar (Duchefa Biochemie, Haarlem, The Netherlands) slant plate (120 x 120 mm; DoctorLab, Jena, Germany). Seedlings used for treatment with Myc-LCOs and corresponding controls were put on plates with half-strength Hoagland´s solution (Arnon and Hoagland, 1940) set to pH 6.5 with KOH, whereas seedlings treated with Nod-LCOs and corresponding controls were grown on slant agar plates with an N-free nutrient solution of pH 7.5 as described in Baier et al. (2007), further on referred to as NH-mix. An approximately one cm strap of Whatman paper (Schleicher & Schuell, Dassel, Germany) soaked with appropriate nutrient solutions as described above was used to fix the seedlings on the plates beneath the cotyledons. Three plates at a time were sealed with transparent wrapping foil, which was cut at the upper side to allow gas exchange. The lower half of each plate stack was wrapped with aluminium foil for light protection to allow normal root development (Figure 1 E). Each triple pack of plates was placed in an approximately 70° angle in the climate chamber for five days.

extract_protocol: Ten root fragments per biological relicate were pooled and ground using lysing matrix D tubes (MP Biomedicals, Illkirch, France) in a FastPrep (MP Biomedicals, Illkirch, France) prior to RNA extraction. Total RNA isolation and DNaseI on-column digestion was performed via RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA preparations were quality-checked both via spectrophotometry (NanoDrop ND-1000, Peqlab, Erlangen, Germany) and capillary electrophoresis (RNA Nano chips, Agilent Bioanalyzer, Agilent, Böblingen, Germany), as recommended by the manufacturers.

treatment_protocol: Plantlets were carefully removed from slant agar plates and placed in 13 mL tubes wrapped with aluminium foil that were cut off at the 8 mL mark, using 20 plantlets per tube (Sarstedt, Nürnbrecht, Germany). Each tube contained 5 mL of the following solutions: sulphated Myc-LCO solution (half-strength Hoagland´s solution of pH 6.5 containing 10-8 M sulphated Myc-LCOs), non-sulphated Myc-LCO solution (half-strength Hoagland´s solution of pH 6.5 containing 10-7 M non-sulphated Myc-LCOs), mixed sulphated and non-sulphated Myc-LCO solution (half-strength Hoagland´s solution of pH 6.5 containing 10-8 M sulphated and 10-7 M non-sulphated Myc-LCOs), Myc control solution (half-strength Hoagland´s solution of pH 6.5), Nod-LCO solution (NH-mix of pH 7.5 containing 10-8 M Nod-LCOs), and Nod control solution (NH-mix of pH 7.5). After 6 h of incubation in the climate chamber, 10 plantlets per batch were removed from the treatment or control solutions and harvested, while the other 10 remained in the respective solutions for a total of 24 h.

tag: time

tag: treatment

value: control

tag: tissue

value: Root

tag: genotype

value: Jemalong A17

value: 10 days


title: Normal genomic DNA from sample 12


title: Patient genomic DNA from sample 22


title: Normal genomic DNA from sample 18


title: Normal genomic DNA from sample 9


title: Normal genomic DNA from sample 10


title: Nod-LCOs 6h roots biological replicate 3

description: Gene expression data from Medicago truncatula plantlet roots treated with symbiotic LCOs

value: Nod-LCOs


title: Normal genomic DNA from sample 13


title: Nod-LCOs 6h roots biological replicate 2

source_name: Medicago truncatula plantlet roots treated with symbiotic LCOs


title: Nod-LCOs 6h roots biological replicate 1


title: Normal genomic DNA from sample 11


title: MDA-MB-231 Control-shRNA 1

status: Public on Feb 01 2012

city: La Jolla

first: suping

last: zhang

state: CA

address: 8955 health science Dr

department: Medical school

country: USA

institute: UCSD

description: Each microarray contains 30,275 oligonucleotides: 29,187 human genome probes, and 1,088 experimental control probes.

hyb_protocol: Mix 2 μg of aRNA sample with 1 μl 10x Fragmentation Reagent, and incubate at 70C for 15 minutes.Add the Hybridization Buffer solution to the target array. Heat the mixture to 95°C for 5 minutes. Place the entire labeled target plus the microarray set-up into a closable, chambered box that is humidified by 2X SSPE buffer in the 50°C oven for14 to 16 hours. http://www.phalanxbiotech.com/tech_support/HOAv5_UserGuide.pdf

scan_protocol: Raw intensity signals for each microarray are captured using a Molecular Dynamics™ Axon 4100A scanner, measured using GenePixPro™ Software. http://www.phalanxbiotech.com/tech_support/HOAv5_UserGuide.pdf

data_processing: After removing experimental control probes, the intensities of 30968 probes were quantile normalized to have similar distributions across all 4 arrays.  The normalized intensity of probes derived from the same gene was collapsed into a single NCBI Entrez gene by the maximal value in each sample

source_name: Breast Caner Cell Line

label_protocol: 20ug RNA were labled using commercial available Kit. http://www.phalanxbiotech.com/tech_support/HOAv5_UserGuide.pdf

extract_protocol: Total RNA was prepared from cells using RNeasy Mini kit (Qiagen, Valencia, CA)

tag: cell line

tag: protocol

value: Control-shRNA tranduced


title: MDA-MB-231 Control-shRNA 2


title: MDA-MB-231 ROR1-shRNA 1

value: ROR1-shRNA tranduced


title: Aspergillus nidulans 18h Vs 24h biological replicate 2

status: Public on May 01 2008

city: Norwich

first: Andrew

last: Breakspear

address: Norwich Research Park

country: United Kingdom

institute: John Innes Centre

description: Technical ‘dye swap’ replicates were carried out for each biological replicate and normalized as a pair of files.  Image analysis and normalization were done using the TIGR TM4 Microarray Software Suite (http://www.tm4.org/).

hyb_protocol: The resulting labeled cDNA was hybridized according to the standard TIGR protocol (SOP #: M008; http://pfgrc.tigr.org/protocols/protocols).

scan_protocol: The slides were scanned at 10um resolution and 85% laser power using a PerkinElmer ScanArray microarray scanner.

data_processing: The resulting tiff images were imported into TIGR Spotfinder (version 3.1.1).  Raw intensities were calculated for each detectable spot using the Otsu method and quality control filtering used to eliminate values from spots with poor morphology or low signal to noise ratios.  Resulting intensities were then imported into TIGR MIDAS (version 2.20) and those with values of less than 10000 removed from the data set using the low intensity filter.  Normalization was done using the LOWESS (Locfit) algorithm (global mode; 0.33 smoothing parameter) and print-tip bias addressed using standard deviation regularization. The dye swap consistency filter was used to remove data for genes with inconsistent expression levels between dye swap replicates.  The in-slide replicate function was used to average the normalized intensity values representing replicate spots on the array.  Finally, Log2 ratios (channel 2/channel 1) were calculated for all the remaining data.

organism: Aspergillus nidulans

source_name: 18h cells biological replicate 2

label_protocol: cDNA synthesis and indirect Cy dye incorporation was performed using the standard TIGR protocol (SOP #: M007; http://pfgrc.tigr.org/protocols/protocols) with the following modifications:  5 µg total RNA was used in the 1st strand cDNA reaction with a 3:1 aminoallyl-dUTP to dTTP ratio.  Dried aminoallyl-labeled cDNA was resuspended in 9 µl 0.05 M sodium carbonate pH 9.0 and added directly to the appropriate dye vial from the Amersham CyDye Post-Labeling Reactive Dye Pack (RPN5661).

growth_protocol: Flasks of 300 ml complete medium plus uracil and uridine (CMUU; medium described in Momany et al., 1999) were inoculated with 10 to the power of 8 conidia and grown with continual shaking (250 rpm) for 18h at 42°C (undifferentiated vegetative hyphae).  Following incubation cells were harvested using a Steritop filter (Millipore) and the resulting cells frozen and ground in liquid nitrogen.

extract_protocol: RNA was purified using TRIzol according to the manufacturer’s instructions (Invitrogen).

tag: Strain

source_name: 42h cells biological replicate 2

growth_protocol: Flasks of 300 ml complete medium plus uracil and uridine (CMUU; medium described in Momany et al., 1999) were inoculated with 10 to the power of 8 conidia and grown with continual shaking (250 rpm) for 18h at 42°C.  Cultures were  transferred to filters and incubated on solid CMUU medium for 24h at 42°C (synchronously conidiating cultures).  Following incubation cells were frozen and ground in liquid nitrogen.


title: Patient genomic DNA from sample 8

value: PBL


title: Nod-LCO control 6h roots biological replicate 2

source_name: Medicago truncatula plantlet roots treated with control solution


title: Aspergillus nidulans 0h Vs 3h biological replicate 1

source_name: 0h cells biological replicate 1

growth_protocol: Isolated dormant conidia were frozen and ground in liquid nitrogen.

source_name: 3h cells biological replicate 1

growth_protocol: Flasks of 300 ml complete medium plus uracil and uridine (CMUU; medium described in Momany et al., 1999) were inoculated with 10 ml spore stock and incubated for 3 hours at 42°C with constant shaking (250 rpm).  Microscopic inspection revealed 100% of spores lacked germ tubes (n=200).  Following incubation cells were harvested using a Steritop filter (Millipore) and the resulting cells frozen and ground in liquid nitrogen.


title: Aspergillus nidulans 0h Vs 3h biological replicate 2

source_name: 0h cells biological replicate 2

source_name: 3h cells biological replicate 2


title: Aspergillus nidulans 18h Vs 42h biological replicate 1

source_name: 18h cells biological replicate 1

source_name: 42h cells biological replicate 1


title: MDA-MB-231 ROR1-shRNA 2


title: Nod-LCO control 6h roots biological replicate 3


title: Patient genomic DNA from sample 7

value: rheumatoid arthritis


title: E. histolytica clinical isolate replicate 2

status: Public on Mar 01 2007

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

description: Isolated in Bangladesh, 3 week growth in xenic culture

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: GCOS scaling only- target 500

organism: Entamoeba histolytica

source_name: recent clinical isolate

label_protocol: Affymetrix 2 rounds amplification

tag: Media

value: Robinson's

tag: Clinical isolate


title: E. histolytica clinical isolate replicate 3

description: Isolated in Bangladesh, 8 week growth in xenic culture


title: Normal genomic DNA from sample 39

value: f


title: E. histolytica strain CBA replicate 1

description: Grown 1 day in mouse colon

source_name: in vivo trophozoites

label_protocol: SPIA

value: HM1:IMSS mouse adapted

value: grown in vivo

tag: Recovered from mouse colon


title: Aspergillus nidulans 3h Vs 5h biological replicate 1

source_name: 3h cells

source_name: 5h cells

growth_protocol: Flasks of 300 ml complete medium plus uracil and uridine (CMUU; medium described in Momany et al., 1999) were inoculated with 10 ml spore stock and incubated for 5 hours at 42°C with constant shaking (250 rpm).  Microscopic inspection revealed 90% of spores had early germ tubes (n=200).  Following incubation cells were harvested using a Steritop filter (Millipore) and the resulting cells frozen and ground in liquid nitrogen.


title: Aspergillus nidulans 3h Vs 5h biological replicate 2

source_name: 5h cells biological replicate 2


title: E. histolytica strain CBA replicate 2

description: Grown 1 day in mouse colon


title: E. histolytica strain Ap replicate 1

description: Trophozoites after long term axenic growth. Isolated mid-log phase

source_name: Mouse-adapted trophozoites

value: TYI

tag: Mouse adapted


title: E. histolytica clinical isolate replicate 1

description: Isolated in Bangladesh, 1 week growth in xenic culture


title: E. histolytica strain CBA replicate 5

description: Grown 29 days in mouse colon

source_name: in vivo trohozoites


title: Patient genomic DNA from sample 2

source_name: PBL

tag: cell type

value: Patient

value: current


title: E. histolytica strain CBA replicate 4

description: Grown 29 days in mouse colon


title: E. histolytica strain 200:NIH LG 1

source_name: Trophozoites grown in TYI-low glucose

label_protocol: Affymetrix single amplification

value: TYI-LG

tag: Long term axenic growth


title: E. histolytica strain CBA replicate 3

description: Grown 1 day in mouse colon


title: E. histolytica strain 200:NIH LG2


title: E. histolytica strain Ap replicate 2


title: Patient genomic DNA from sample 5

tag: disease state

tag: subject

value: never


title: Patient genomic DNA from sample 6

tag: age

tag: gender


title: Patient genomic DNA from sample 1

tag: smoking status


title: Patient genomic DNA from sample 4


title: Patient genomic DNA from sample 3

value: ex