title: 427_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 426_lcl-trisomy21

status: Public on Jan 30 2017

type: genomic

city: Atlanta

first: Benjamin

last: Rambo-Martin

state: Georgia

address: 1600 Clifton Road

country: USA

institute: Centers for Disease Contol and Prevention

description: Custom Agilent 8x60k targeting chr21

hyb_protocol: Default: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells or Tissues with Covaris sonicated fracturing.  Version 6.3 - October 2010

scan_protocol: Default: Agilent SureScan High-Resolution Microarray Scanner

data_processing: Default: Agilent Feature Extraction Software version 10.7

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: Genomic DNA extraction protocol not provided.

tag: Sex

value: male

tag: ethnicity

value: Caucasian

tag: omim

source_name: lcl-trisomy21_reference individual

value: female


title: 411_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

label_protocol: Default: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells or Tissues with Covaris sonicated fracturing.  Version 6.3 - October 2010


title: 420_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 424_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 430_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 415_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 414_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 425_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 413_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 428_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 419_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 412_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 409_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 416_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 423_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 417_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 421_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 418_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 392_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 406_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 402_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 385_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 407_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 410_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 393_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 388_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 383_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 391_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 390_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 398_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 403_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 389_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 404_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 395_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 397_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 408_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 384_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 382_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 396_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 401_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 381_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 400_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 387_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 399_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 394_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 386_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 405_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 379_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 378_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 376_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 377_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 375_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 380_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 369_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 365_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 370_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 372_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 366_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 374_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 364_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 363_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 368_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 373_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 361_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 362_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 371_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 356_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 367_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 358_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 353_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 357_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 355_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 351_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 350_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 354_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 360_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 359_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 343_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 349_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 344_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 348_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 335_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 347_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 345_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 340_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 346_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 334_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 341_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 329_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 330_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 333_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 331_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 332_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 336_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 326_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 338_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 337_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 327_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 339_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 328_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 352_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 342_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 319_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 324_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 317_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 322_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 325_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 312_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 315_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 321_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 313_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 320_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 314_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 318_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 310_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 306_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 298_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 303_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 302_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 308_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 305_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 311_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 309_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 299_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 316_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 300_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 301_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 307_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 297_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 304_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 323_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 291_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 293_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 287_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 295_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 288_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 281_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 292_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 290_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 296_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 286_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 283_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 279_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 294_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 280_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 289_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 284_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 275_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 277_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 278_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 268_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 267_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 270_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 271_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 282_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 269_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 285_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 272_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 276_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 273_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 266_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 274_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 264_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 265_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 263_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 254_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 258_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 255_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 260_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 257_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 249_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 251_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 253_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 248_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 256_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 244_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 247_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 246_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 239_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 242_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 232_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 262_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 243_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 250_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 225_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 252_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 259_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 245_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 241_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 229_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 237_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 224_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 234_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 223_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 230_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 228_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 235_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 240_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 236_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 221_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 238_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 227_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 216_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 233_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 222_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 218_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 220_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 217_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 215_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 261_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 212_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 211_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 213_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 210_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 214_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 231_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 206_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 226_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 207_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 208_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 219_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 209_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 204_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 201_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 202_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 205_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 199_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 203_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 193_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 196_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 195_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 198_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 194_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 200_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 187_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 192_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 189_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 186_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 184_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 188_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 191_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 190_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 179_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 180_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 182_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 178_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 175_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 183_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 174_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 177_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 181_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 185_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 176_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 173_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 170_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 169_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 166_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 167_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 172_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 197_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 171_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 168_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 165_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 158_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 164_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 161_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 159_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 151_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 162_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 148_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 163_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 157_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 160_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 149_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 156_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 146_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 142_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 155_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 152_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 154_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 153_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 150_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 141_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 145_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 143_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 147_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-C-089-TT

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

description:
HB
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0

hyb_protocol: Affymetrix Genome-Wide Human SNP Array 6.0, Affymetrix adapters using T4 DNA ligase

scan_protocol: GAP laboratory at the Broad Institute using Affymetrix Power Tools

data_processing: Partek Genomics Suite 6: Allele specific Intensity, Probe Sequence correction

label: biotin

source_name: Hepatoblastoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was digested with NspI and StyI enzymes

treatment_protocol: washed and stained with streptavidin-phycoerythrin (Invitrogen).

tag: tissue

value: Hepatoblastoma

tag: age (yrs)

value: F

tag: race

value: Hispanic

tag: histology

value: Epithelial hepatoblastoma


title: SNP_TLT-C-087-TT

value: M

tag: Stage


title: SNP_TLT-C-091-TT

value: Epithelial, embryonal, nesting pattern (small cell)


title: SNP_TLT-C-093-TT

value: Epithelial, embryonal and  small cell (minor)


title: SNP_TLT-C-081-TT


title: SNP_TLT-C-082-TT

value: Epithelial hepatoblastoma, mitotically active fetal


title: SNP_TLT-C-079-TT

value: Epithelial hepatoblastoma, embryonal and fetal


title: SNP_TLT-C-083-TT

value: African American

value: Normal liver


title: SNP_TLT-C-062-TT

value: Epithelial hepatoblastoma, embryonal


title: 136_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-C-084-TT


title: 138_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-C-060-TT

value: Other


title: SNP_TLT-C-074-TT

value: Epithelial hepatoblastoma, fetal


title: 137_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: male


title: SNP_TLT-C-060-LV

description:
NL
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0

source_name: Normal liver


title: 140_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: Caucasian


title: 139_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: female


title: 134_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 144_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 131_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 132_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 135_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 129_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 128_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-C-059-TT

value: Hepatoblastoma


title: SNP_TLT-C-059-LV


title: 127_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 126_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-C-086-TT


title: SNP_TLT-C-058-TT

value: F

value: Epithelial, hepatoblastoma embryonal, fetal, some anaplastia, telangiectatic


title: SNP_TLT-C-058-LV


title: 130_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-D-056-LV


title: SNP_TLT-C-057-LV


title: SNP_TLT-C-057-TT

value: Epithelial hepatoblastoma fetal and blastemal. Small foci of small cell


title: SNP_TLT-C-053-TT

value: Mixed epithelial and mesenchymal, fetal (60%), embryonal (20%), stromal (10%), blastema (5%) and small cell (2%)


title: SNP_TLT-C-046-LV


title: SNP_TLT-C-045-LV

value: M

value: Native American


title: SNP_TLT-C-044-TT

value: Epithelial hepatoblastoma , fetal (50%), embryonal (50%)


title: SNP_TLT-C-045-TT

value: Epithelial hepatoblastoma, fetal (60%) and embryonal (40%)


title: SNP_TLT-C-044-LV


title: SNP_TLT-C-042-TT

value: Asian

value: Epithelial hepatoblastoma, embryonal (65%) and fetal (15%)


title: SNP_TLT-D-056-TT

value: Epithelial hepatoblastoma


title: SNP_TLT-C-042-LV

value: Normal liver


title: SNP_TLT-C-040-TT

value: Epithelial hepatoblastoma, fetal (20%), embryonal (70%) and small cell (10%)


title: SNP_TLT-C-053-LV


title: SNP_TLT-C-040-LV


title: 133_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 124_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-P-033-TT

value: Mixed hepatoblastoma, predominately meshenchymal, 14% fetal  and 1% embryonal


title: 118_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: male

value: Caucasian


title: 125_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: female


title: 123_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 122_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-P-033-LV

value: F


title: 119_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 121_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-P-032-TT

value: Hepatoblastoma

value: Epithelial hepatoblastoma, mostly embryonal, small foci of fetal and rare small cell elements


title: 120_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: CD14+ monocytes from peripheral blood (healthy control HC-8)

type: RNA

city: Måløv

first: Klaus Stensgaard

last: Frederiksen

address: Novo Nordisk Park F9.1.07

department: Molecular Genetics

country: Denmark

institute: Novo Nordisk A/S

hyb_protocol: Affymetrix EukGE-WS2v5

scan_protocol: Affymetrix cel analysis

data_processing: Bioconductor/R RMA

molecule: total RNA

source_name: CD14+ monocytes from peripheral blood

label_protocol: Affymetrix in vitro transcription

extract_protocol: Total RNA was isolated using the standard TRIzol protocol (Invitrogen, Carlsbad, CA), but with subsequent RNA clean-up of the water phase using the RNeasy Qiagen MinElute kit (Qiagen, Germantown, MD). The quality of the RNA was confirmed on the Agilent Bioanalyzer using RNA Nano chips (Agilent Technologies, Santa Clara, CA).

tag: disease state

value: control

tag: individual

value: peripheral blood

tag: cell type

value: CD14+ monocyte


title: SNP_TLT-P-031-TT

value: M

value: Epithelial hepatoblastoma, mitotically active fetal


title: SNP_TLT-P-032-LV


title: SNP_TLT-P-031-LV


title: SNP_TLT-P-028-TT

value: Epithelial hepatoblastoma, predominately embryonal


title: SNP_TLT-P-024-BL

description:
BL
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0

source_name: Blood

value: Blood


title: SNP_TLT-P-023-LV


title: SNP_TLT-P-024-TT

value: Mixed epithelial and mesenchymal hepatoblastoma


title: SNP_TLT-P-028-LV

value: Normal liver


title: SNP_TLT-P-019-LV


title: SNP_TLT-P-019-TT

value: Mixed hepatoblastoma 40% mesenchymal with prominent ostteoid component, 60% epithelial ( fetal and embryonal)


title: SNP_TLT-P-021-TT

value: Other

value: Mixed hepatoblastoma, predominately epithelial (fetal and embryonal), small area of osteoid


title: SNP_TLT-P-021-BL


title: SNP_TLT-P-023-TT

value: Caucasian

value: Epithelial hepatoblastoma, embryonal and fetal


title: SNP_TLT-P-018-TT

value: F

value: Hispanic

value: Epithelial hepatoblastoma, fetal and embryonal


title: SNP_TLT-P-018-BL


title: SNP_TLT-P-017-TT

value: Hepatoblastoma

value: African American

value: Well differentiated fetal hepatoblastoma, small foci of embryonal and cholangioblastic differentiation


title: 111_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: female


title: CD14+ monocytes from peripheral blood (healthy control HC-2)

value: control

value: peripheral blood

value: CD14+ monocyte


title: CD14+ monocytes from peripheral blood (healthy control HC-3)


title: 113_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: male


title: CD14+ monocytes from peripheral blood (healthy control HC-1)


title: SNP_TLT-P-016-TT

value: M

value: Epithelial hepatoblastoma, embryonal, fetal and minor small cell


title: 116_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: CD14+ monocytes from peripheral blood (healthy control HC-4)


title: SNP_TLT-P-016-BL

value: Blood


title: SNP_TLT-P-015-TT


title: SNP_TLT-P-015-BL


title: SNP_TLT-P-014-BL


title: CD14+ monocytes from synovial fluid (patient RA8)

source_name: CD14+ monocytes from synovial fluid

value: RA

value: synovial fluid


title: 114_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: Caucasian


title: 112_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 108_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 109_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 107_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-P-013-TT

value: F

value: Well differentiated pure fetal hepatoblastoma; lack of mitotic activity


title: CD14+ monocytes from synovial fluid (patient RA13)


title: CD14+ monocytes from peripheral blood (healthy control HC-5)


title: SNP_TLT-P-014-TT

value: Epithelial hepatoblastoma, mixed fetal and small cell


title: SNP_TLT-P-013-LV

value: Normal liver

value: Hispanic


title: CD14+ monocytes from synovial fluid (patient RA7)


title: 117_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: CD14+ monocytes from peripheral blood (healthy control HC-6)


title: 106_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: CD14+ monocytes from synovial fluid (patient RA5)


title: 105_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 115_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-P-012-TT

value: Hepatoblastoma

value: Mixed epithelial and mesenchymal hepatoblastoma


title: CD14+ monocytes from peripheral blood (healthy control HC-7)

value: control


title: 104_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: female


title: CD14+ monocytes from synovial fluid (patient RA3)

value: CD14+ monocyte


title: CD14+ monocytes from synovial fluid (patient RA15)


title: CD14+ monocytes from synovial fluid (patient RA4)


title: CD14+ monocytes from synovial fluid (patient RA2)


title: 110_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 103_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 102_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-P-011-TT

value: Epithelial hepatoblastoma predominantly fetal and embryonal


title: SNP_TLT-P-011-LV


title: SNP_TLT-D-009-TT

value: Hepatocellular neoplasm, NOS


title: SNP_TLT-D-009-LV


title: SNP_TLT-P-007-BL

value: M


title: SNP_TLT-P-007-TT

value: Epithelial hepatoblastoma, fetal and embryonal


title: SNP_TLT-P-012-LV


title: SNP_TLT-P-006-TT

value: Asian Islander


title: SNP_TLT-P-006-BL

value: Blood


title: SNP_TLT-P-005-LV


title: SNP_TLT-P-005-TT


title: SNP_TLT-P-004-TT

value: Caucasian


title: CD14+ monocytes from synovial fluid (patient RA1)

value: RA

value: synovial fluid


title: SNP_TLT-P-004-LV


title: SNP_TLT-P-003-TT

value: F

value: Epithelial hepatoblastoma mitotically active fetal and embryonal


title: SNP_TLT-P-003-LV

value: Normal liver


title: SNP_TLT-D-001-LV


title: 101_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: male


title: SNP_TLT-D-001-TT

value: Hepatoblastoma

value: Epithelial hepatoblastoma, fetal, embryonal and minor small cell


title: CD14+ monocytes from peripheral blood (patient RA13)

value: peripheral blood


title: 100_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: female


title: 99_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: CD14+ monocytes from peripheral blood (patient RA7)

value: CD14+ monocyte


title: CD14+ monocytes from peripheral blood (patient RA6)


title: 95_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 98_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: CD14+ monocytes from peripheral blood (patient RA3)


title: CD14+ monocytes from peripheral blood (patient RA15)


title: 94_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: CD14+ monocytes from peripheral blood (patient RA8)


title: 96_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: CD14+ monocytes from peripheral blood (patient RA5)


title: 97_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: CD14+ monocytes from peripheral blood (patient RA2)


title: 93_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-P-017-BL

value: African American


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17ex/ex_male_rep2

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

country: Germany

institute: Ludwig-Maximilians-University Munich

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalised using quantile normalisation and background substraction with Illumina BeadStudio.

organism: Mus musculus

source_name: primary macrophages

label_protocol: cRNA was prepared  using the TargetAmp- Nano Labeling Kit for Illumina Expression BeadChip (Epicentre Biotechnologies, Madison, WI, USA).

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

tag: strain

tag: adam17 genotype

value: ex/ex


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17ex/ex_female_rep4


title: P4-VB-CTR-36_3

city: San Juan de Alicante

first: Guillermina

last: López-Bendito

state: Alicante

address: Av. Ramón y Caja,Campus de San Juan

department: Instituto de Neurociencias CSIC

country: Spain

institute: Universidad Miguel Hernández

description: Lopez-Bendito_0213_P4VB_36_3_(Mouse430_2).CEL

hyb_protocol: biotinylated cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Array following the standard protocols

scan_protocol: Affymetrix standard

data_processing:
RMA Probes to Import: Interrogating Probes, Probe filtering: skip,Algorithm: RMA,Background Correction: RMA Background Correction,Normalization: Quantile Normalization,Log Probes using Base: 2,Probeset Summarization: Median Polish,Library files used during import: Mouse430_2.cdf, Mouse430_2.na31.annot.csv
The data were normalized using RMA and changes in gene expression > 1.5-fold with a p-value < 0.05 were considered to reflect a significant difference in expression.

label_protocol: small-scale protocol from Affymetrix (High Wycombe) was used for amplification and labelling > after the second amplification

growth_protocol: Wild type mice maintained on a C57BL/6 background were housed in a pathogen free Animal House under controlled temperature and light cycle

extract_protocol: RNA was extracted from the tissue collected using the RNeasy Mini Kit (Qiagen), including a DNaseI step. Complimentary RNAs (two rounds of amplification) were hybridized to Affymetrix GeneChip Mouse Genome arrays 430 v2, and the signal intensities were analyzed using Partek Genomics suites (Partek, St. Louis, MI, USA) and Matlab (The MathWorks Inc, Natick, MA, USA).

treatment_protocol: To collect tissue from the dLGN and VB nuclei at neonatal stages, animals were sacrificed and their brain was dissected out in RNase-free conditions to prevent RNA degradation. Vibratome sections (200μm) were obtained and collected in ice-cold oxygenated aCSF (117mM NaCl, 4.7mM KCl, 1.2mM MgCl2, 2.5mM CaCl2, 1.2mM NaH2PO4, 25mM NaHCO3 and 0.45% D-glucose), and the thalamic nucleus was rapidly microdissected under a microscope. The tissue was maintained overnight at 4 ºC in RNA-Later (Sigma) and stored at -80 ºC for subsequent RNA extraction.

tag: strain background

tag: age

tag: genotype/variation

value: controls (non-enucleated)

value: ventrobasal (VB) thalamic nucleus


title: 90_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 92_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17ex/ex_male_rep3


title: 87_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: CD14+ monocytes from peripheral blood (patient RA1)


title: P4-VB-CTR-40_1

description: Lopez-Bendito_0213_P4VB_40_1_(Mouse430_2).CEL


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17wt/wt_male_rep2

value: wt/wt


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17wt/wt_female_rep4


title: P4-VB-BE-36_2

description: Lopez-Bendito_0213_P4VB_36_2_(Mouse430_2).CEL

value: embryonically bilateral enucleated (embBE)


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17ex/ex_male_rep1


title: 91_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: Caucasian


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17wt/wt_male_rep1


title: 88_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17ex/ex_male_rep4


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17wt/wt_male_rep3


title: P4-VB-BE-40_3

description: Lopez-Bendito_0213_P4VB_40_3_(Mouse430_2).CEL


title: P4-VB-CTR-24_2

description: Lopez-Bendito_0213_P4VB_24_2_(Mouse430_2).CEL


title: P4-VB-BE-24_4

description: Lopez-Bendito_0213_P4VB_24_4_(Mouse430_2).CEL


title: 86_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17wt/wt_female_rep3


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17wt/wt_male_rep4


title: 89_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17wt/wt_female_rep1


title: 84_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17wt/wt_female_rep2


title: 85_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: mouse_aorta_B6.Ldlr-/-.Adam17wt/wt_male_rep4

source_name: aorta

extract_protocol: RNA was extracted with RNAqueous-Micro Kit (Ambion). Quality control was performed with Agilent Bioanalyzer.


title: mouse_aorta_B6.Ldlr-/-.Adam17wt/wt_male_rep3


title: 82_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: P0-VB-CTR-35_1

description: Lopez-Bendito_0213_P0VB_35_1_(Mouse430_2).CEL


title: P0-VB-CTR-39_5

description: Lopez-Bendito_0213_P0VB_39_5_(Mouse430_2).CEL


title: 81_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17ex/ex_female_rep3


title: 83_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 80_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17ex/ex_female_rep1


title: mouse_aorta_B6.Ldlr-/-.Adam17wt/wt_male_rep1


title: P4-dLGN-CTR-36_3

description: Lopez-Bendito_0213_P4dLGN_36_3_(Mouse430_2).CEL

value: dorsal lateral geniculate nucleus (dLGN) thalamic nucleus


title: mouse_primary macrophages_B6.Ldlr-/-.Adam17ex/ex_female_rep2


title: mouse_aorta_B6.Ldlr-/-.Adam17ex/ex_male_rep2


title: P4-dLGN-CTR-40_1

description: Lopez-Bendito_0213_P4dLGN_40_1_(Mouse430_2).CEL


title: mouse_aorta_B6.Ldlr-/-.Adam17ex/ex_male_rep4


title: 78_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: P0-VB-BE-35_3

description: Lopez-Bendito_0213_P0VB_35_3_(Mouse430_2).CEL


title: P0-VB-BE-39_3

description: Lopez-Bendito_0213_P0VB_39_3_(Mouse430_2).CEL


title: mouse_aorta_B6.Ldlr-/-.Adam17ex/ex_male_rep3


title: mouse_aorta_B6.Ldlr-/-.Adam17ex/ex_male_rep1


title: mouse_aorta_B6.Ldlr-/-.Adam17wt/wt_male_rep2


title: P0-VB-BE-39_4

description: Lopez-Bendito_0213_P0VB_39_4_(Mouse430_2).CEL


title: P0-VB-CTR-35_2

description: Lopez-Bendito_0213_P0VB_35_2_(Mouse430_2).CEL


title: 79_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: mouse_aorta_B6.Ldlr-/-.Adam17ex/ex_female_rep3


title: P4-dLGN-BE-36_2

description: Lopez-Bendito_0213_P4dLGN_36_2_(Mouse430_2).CEL


title: 75_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 74_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: P4-dLGN-BE-24_4

description: Lopez-Bendito_0213_P4dLGN_24_4_(Mouse430_2).CEL


title: P4-dLGN-CTR-24_2

description: Lopez-Bendito_0213_P4dLGN_24_2_(Mouse430_2).CEL


title: control replicate 8

city: Oxford

first: Ian

last: Tomlinson

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics, University of Oxford

description: Sample name: C8

hyb_protocol: Whole-Genome gene expression direct hybridization #11286340 from Illumina

scan_protocol: Illumina array scanning systems on iScan software version3 2011

data_processing: Raw signal intensities were exported from Illumina® GenomeStudio 2011 to R. Background correction and preprocessing using the VSN package from BioCondcutor were performed. Note that the dataset comprises 2 batches of samples hybridized at separate times so VSN was used to normalise (i) batch 1 samples (T1..T6, C1..C6) and (ii)  batch 2 samples (T7..T9, C7..C9) with reference to the first. Despite this, a strong batch effect remains in the normalised data and requires adjusting for in any downstream analysis

source_name: brain SVZ

label_protocol: Illumina TotalPrep96 RNA amplification kit # 4393543 from Life technologies

growth_protocol: Samples were frozen after the dissection and before the extraction

extract_protocol: RNA extracted from murine SVZ cells using Rneasy micro kit (QIAGEN)

treatment_protocol: Conditionally expressed Idh1R132H in the subventricular zone (SVZ) of adult mouse brain (to induce recombination of the mutant protein mice at 5-6 weeks of age received intraperitoneal daily tamoxifen injections  at 50mg/kg for five days)

value: brain

tag: brain region

value: subventricular zone

tag: genotype

value: control

tag: gender

tag: age (months)

tag: date of array hybridisation


title: mouse_aorta_B6.Ldlr-/-.Adam17wt/wt_female_rep3

tag: Sex


title: mouse_aorta_B6.Ldlr-/-.Adam17wt/wt_female_rep1


title: mouse_aorta_B6.Ldlr-/-.Adam17wt/wt_female_rep2


title: P0-dLGN-BE-35_3

description: Lopez-Bendito_0213_P0dLGN_35_3_(Mouse430_2).CEL

tag: tissue


title: 76_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

tag: ethnicity

tag: omim


title: P0-dLGN-BE-39_4

description: Lopez-Bendito_0213_P0dLGN_39_4_(Mouse430_2).CEL


title: control replicate 6

description: Sample name: C6

value: male


title: 71_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: mouse_aorta_B6.Ldlr-/-.Adam17ex/ex_female_rep2


title: 69_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: P0-dLGN-CTR-35_1

description: Lopez-Bendito_0213_P0dLGN_35_1_(Mouse430_2).CEL


title: 72_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: control replicate 7

description: Sample name: C7


title: mouse_aorta_B6.Ldlr-/-.Adam17ex/ex_female_rep4


title: mouse_aorta_B6.Ldlr-/-.Adam17ex/ex_female_rep1


title: P0-dLGN-CTR-39_5

description: Lopez-Bendito_0213_P0dLGN_39_5_(Mouse430_2).CEL


title: 73_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: control replicate 5

description: Sample name: C5


title: 70_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: control replicate 9

description: Sample name: C9


title: P0-dLGN-BE-39_2

description: Lopez-Bendito_0213_P0dLGN_39_2_(Mouse430_2).CEL


title: 68_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 77_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: P0-dLGN-BE-39_3

description: Lopez-Bendito_0213_P0dLGN_39_3_(Mouse430_2).CEL


title: 64_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 67_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 63_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 65_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Tam-Idh1-KI replicate 9

description: Sample name: T9


title: control replicate 4

description: Sample name: C4


title: control replicate 3

description: Sample name: C3


title: control replicate 2

description: Sample name: C2


title: 66_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 61_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Tam-Idh1-KI replicate 6

description: Sample name: T6


title: 62_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Tam-Idh1-KI replicate 4

description: Sample name: T4


title: Tam-Idh1-KI replicate 7

description: Sample name: T7


title: control replicate 1

description: Sample name: C1


title: 59_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Tam-Idh1-KI replicate 5

description: Sample name: T5


title: 58_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Tam-Idh1-KI replicate 3

description: Sample name: T3


title: Tam-Idh1-KI replicate 2

description: Sample name: T2


title: Tam-Idh1-KI replicate 8

description: Sample name: T8


title: 60_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 56_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 57_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Tam-Idh1-KI replicate 1

description: Sample name: T1


title: 50_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 55_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 53_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 52_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 54_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 49_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 45_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 51_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 48_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 47_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 44_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 39_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 42_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 35_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 33_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: P4-dLGN-BE-40_3

description: Lopez-Bendito_0213_P4dLGN_40_3_(Mouse430_2).CEL


title: 38_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 28_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 34_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 46_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 40_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 37_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 31_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 43_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 32_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 41_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 36_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 30_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 29_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 26_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 23_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 25_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 19_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 24_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 27_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 17_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 14_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 21_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 22_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 20_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 15_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Blood B cell-Control3-Rep1

city: weifang

first: yurong

last: fu

address: No.7166, Baotong Xi (Western) Street, Weicheng District, Department of Laboratory Medicine, Shandong Provincial Key Laboratory of Clinical Laboratory Diagnostics, Weifang Medical University

country: China

institute: weifang medical universtiy

description: Gene expression in peripheral blood B cells isolated from  healthy controls

hyb_protocol: Arraystar Human LncRNA Microarray V3.0 is designed for the global profiling of human LncRNAs and protein-coding transcripts, which is updated from the previous Microarray V2.0. About 30,586 LncRNAs and 26,109 coding transcripts can be detected by our third-generation LncRNA microarray.1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) .

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: Peripheral blood B cell, Control3(one of three control subjects),replicate 1

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: For RNA preparation, total RNA was isolated from purified B cells using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA) and further purified with RNeasy mini kit (Qiagen, Hilden, Germany). Quantification and quality check were performed with Nanodrop ND-1000 (NanoDrop Technologies,Wilmington, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies Europe, Waldbroon, Germany), respectively. RNA integrity was assessed by standard denaturing gel electrophoresis.

treatment_protocol: For preparation of B cells, fasting venous blood was drawn from each subject into a coded EDTA-anticoagulant tube. Peripheral blood mononuclear cells (PBMCs) were collected from venous blood using density gradient centrifugation. B cells were then isolated from obtained PBMCs by negative selection using B Cell Isolation Kit (R&D Systems, Minneapolis, MN, USA) according to the manufacturer’s instructions. Briefly, B cells were negatively selected by depletion of unwanted cells. Flow cytometric analysis was used to monitor purity of isolated B cells and only sample with purity over 90% was used for further analysis. Qualified samples were immediately stored in liquid nitrogen until further use.

value: B cell from peripheral blood


title: Blood B cell-Control1-Rep1

description: Gene expression in peripheral blood B cells isolated from healthy controls

source_name: Peripheral blood B cell, Control1(one of three control subjects),replicate 1


title: 18_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 10_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 13_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 7_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Blood B cell-Control2-Rep1

source_name: Peripheral blood B cell, Control2(one of three control subjects),replicate 1


title: 11_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Blood B cell-ATB2-Rep1

description: Gene expression in peripheral blood B cells isolated from patients with active TB

source_name: Peripheral blood B cell, ATB2(one of three active TB subjects),replicate 1


title: Blood B cell-ATB3-Rep1

source_name: Peripheral blood B cell, ATB3(one of three active TB subjects),replicate 1


title: 16_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Blood B cell-ATB1-Rep1

source_name: Peripheral blood B cell, ATB1(one of three active TB subjects),replicate 1


title: 6_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 8_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 12_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 9_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Crypts_Diabetes_16weeks_rep3

city: Guang-Zhou

first: Can-Ze

last: Huang

address: 107 Yan-Jiang Xi-Road

institute: Sun Yat-Sen Memorial Hospital

description:
Sample name: D3
It is the third of three db/db biological replicates used in this experimen.
meDIP-chip

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in NimbleGen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: From the normalized log2-ratio data, a sliding-window peak-finding algorithm provided by NimbleScan v2.5 (Roche-NimbleGen) was applied to find the enriched peaks with specified parameters (sliding window width: 1,500bp; mini probes per peak: 2; P-value minimum cutoff: 2; maximum spacing between nearby probes within peak: 500bp).

data_processing: We perform Median-centering, quantile normalization and linear smoothing in this analysis process by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data (*_ratio.gff file) was created for each sample, it can be used to further peak-finding analysis.

source_name: Promoter methylation DNA from intestinal crypts in 16 weeks old diabetic db/db mice

label_protocol: For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (NimbleGen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation.

growth_protocol: Mice were maintained under a 12 h light/12 h dark cycle in a specific pathogen-free animal facility.

extract_protocol: Genomic DNA (gDNA) was extracted from 6 samples using a DNeasy Blood & Tissue Kit (Qiagen, Fremont, CA). The purified gDNA was then quantified and quality assessed by nanodrop ND-1000. Genomic DNA of each sample was sonicated to ~200 – 1000 bp with a Bioruptor sonicator (Diagenode) on “Low” mode for 10 cycles of 30 seconds “ON” & 30 seconds “OFF”. The gDNA and each sheared DNA were aragrose analyzed.

treatment_protocol: Gene Lepr was mutated in single allele.

tag: background strain

value: BKS.Cg-Dock7m +/+ Leprdb/JNju

value: intestinal crypt

tag: antibody

value: 16 weeks

value: db/db

tag: phenotype

value: obese

tag: blood glucose value

value: ≥ 16.7 mmol/l

source_name: Input DNA from D3


title: 4_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: female

source_name: lcl-trisomy21_reference individual


title: 2_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: SNP_TLT-C-046-TT

description:
HB
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0

source_name: Hepatoblastoma

value: Hepatoblastoma

tag: age (yrs)

value: F

tag: race

tag: histology

value: Epithelial hepatoblastoma, mostly embryonal, nesting

tag: Stage


title: 5_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

value: Caucasian


title: Patient FSL1_replicate

status: Public on Jan 29 2017

city: Doha

first: Nico

last: Marr

address: Education City

country: Qatar

institute: Hamad Bin Khalifa University

description: replicate of sample 61 used for QC only

data_processing: Raw data were processed in R for quantile normalisation using the neqc function from the limma package. Fold changes (FC) in expression were calculated for each individual and set of stimulation conditions over the unstimulated sample of the same individual and within the same BeadChip (column: BeadChip ID) if the respective samples had passed the QC analysis.

source_name: Fibroblast

label_protocol: The cRNA was prepared using the Illumina® TotalPrepTM RNA Amplification Kit

growth_protocol: The fibroblasts were used to seed culture plates at a density of 2.5x10^5 cells/well and then cultured overnight.

extract_protocol: RNA was extracted using the ZR RNA MicroPrepZymo kit (Zymo Research) according to the manufacturer's instructions.

treatment_protocol: The next day, the cells were either left unstimulated or stimulated for 6 hours with PAM-2 (10 μg/ml), FSL-1 (1 μg/ml), LPS (10 μg/ml), MPLA (1 μg/ml), IL-1β (10 ng/ml) or TNF-α (20 ng/ml).

tag: beadchip id

tag: sample id

value: SAMPLE 72

tag: affected protein-coding gene(s)

value: IRAK1, MECP2, TMEM187

tag: in vitro stimulation condition


title: 3_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: Patient TNF-a

description: used for QC, downstream analysis

value: SAMPLE 65

value: TNF-a


title: MECP2Y/- LPS_replicate

description: replicate of sample 6 used for QC only

value: SAMPLE 68

value: MECP 2

value: LPS


title: Patient MPLA

description: used for QC, downstream analysis

value: SAMPLE 64

value: MPLA


title: Crypts_Diabetes_16weeks_rep1

description:
Sample name: D1
It is the first of three db/db biological replicates used in this experimen.
meDIP-chip

value: BKS.Cg-Dock7m +/+ Leprdb/JNju

value: intestinal crypt

tag: age

value: 16 weeks

tag: genotype

value: db/db

source_name: Input DNA from D1


title: IRAK4-/- IL-1b_replicate

description: replicate of sample 21 used for QC only

value: SAMPLE 69


title: IRAK4-/- LPS_replicate

description: replicate of sample 25 used for QC only

value: SAMPLE 70


title: Crypts_Diabetes_16weeks_rep2

description:
Sample name: D2
It is the second of three db/db biological replicates used in this experimen.
meDIP-chip

tag: tissue

value: obese

value: ≥ 16.7 mmol/l

source_name: Input DNA from D2


title: 1_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

tag: Sex

value: male

tag: ethnicity

value: Caucasian

value: female


title: Patient NS_replicate

description: replicate of sample 58, used for QC  and to calculate FC values for samples 61-65

value: SAMPLE 67

value: IRAK1, MECP2, TMEM187

value: not stimulated


title: Patient LPS

description: used for QC, downstream analysis

value: SAMPLE 63

value: LPS


title: C24 TNF-a

description: used for QC, downstream analysis

value: SAMPLE 56

value: healthy control

value: TNF-a


title: Patient NS

description: used for QC and to calculate FC values for samples 59-60

value: SAMPLE 58


title: Patient LTA

description: used for QC, downstream analysis

value: SAMPLE 62

value: LTA


title: Crypts_Control_16weeks_rep2

description:
Sample name: C3
It is the second of three db/+ biological replicates used in this experimen. The sample name C3 in this group was converted to C2 in the manuscript.
meDIP-chip

source_name: Promoter methylation DNA from intestinal crypts in 16 weeks old control db/+ mice

tag: background strain

value: BKS.Cg-Dock7m +/+ Leprdb/JNju

value: intestinal crypt

value: 16 weeks

value: db/+

value: normal

source_name: Input DNA from C3


title: Patient PAM-2

description: used for QC, downstream analysis

value: SAMPLE 60


title: Patient IL-1b

description: used for QC, downstream analysis

value: SAMPLE 59


title: C24 LPS

description: used for QC, downstream analysis

value: SAMPLE 54


title: Patient FSL1

description: used for QC, downstream analysis

value: SAMPLE 61

value: IRAK1, MECP2, TMEM187


title: C24 PAM-2

description: used for QC, downstream analysis

value: SAMPLE 51


title: C24 MPLA

description: used for QC, downstream analysis

value: SAMPLE 55

value: MPLA


title: Crypts_Control_16weeks_rep3

description:
Sample name: C4
It is the third of three db/+ biological replicates used in this experimen. The sample name C4 in this group was converted to C3 in the manuscript.
meDIP-chip

tag: antibody

source_name: Input DNA from C4


title: Crypts_Control_16weeks_rep1

description:
Sample name: C2
It is the first of three db/+ biological replicates used in this experimen. The sample name C2 in this group was converted to C1 in the manuscript.
meDIP-chip

tag: phenotype

source_name: Input DNA from C2


title: C24 IL-1b

description: used for QC, downstream analysis

value: SAMPLE 50

value: healthy control


title: C24 FSL1

description: used for QC, downstream analysis

value: SAMPLE 52


title: C24 LTA

description: used for QC, downstream analysis

value: SAMPLE 53

value: LTA


title: MyD88-/- LTA

description: used for QC, downstream analysis

value: SAMPLE 44


title: MyD88-/- MPLA

description: used for QC, downstream analysis

value: SAMPLE 46


title: MyD88-/- LPS

description: used for QC, downstream analysis

value: SAMPLE 45

value: LPS


title: MyD88-/- IL-1b

description: used for QC, downstream analysis

value: SAMPLE 41


title: MyD88-/- TNF-a

description: used for QC, downstream analysis

value: SAMPLE 47

value: TNF-a


title: MyD88-/- FSL1

description: used for QC, downstream analysis

value: SAMPLE 43


title: C23 MPLA

description: used for QC, downstream analysis

value: SAMPLE 36


title: MyD88-/- NS

description: used for QC and to calculate FC values for samples 41-47

value: SAMPLE 40

value: not stimulated


title: C23 NS

description: used for QC and to calculate FC values for samples 31-36

value: SAMPLE 30


title: C23 LPS

description: used for QC, downstream analysis

value: SAMPLE 35


title: C23 TNF-a

description: used for QC, downstream analysis

value: SAMPLE 37

value: healthy control


title: C24 NS

description: used for QC and to calculate FC values for samples 50-56

value: SAMPLE 49


title: C14 TNF-a

description: used for QC, downstream analysis

value: SAMPLE 17


title: IRAK4-/- TNF-a

description: used for QC, downstream analysis

value: SAMPLE 27


title: C23 LTA

description: used for QC, downstream analysis

value: SAMPLE 34

value: LTA


title: C23 FSL1

description: used for QC, downstream analysis

value: SAMPLE 33


title: IRAK4-/- NS_replicate

description: replicate of sample 20; used for QC and to calculate FC values for samples 21-27

value: SAMPLE 29


title: IRAK4-/- IL-1b

description: used for QC, downstream analysis

value: SAMPLE 21


title: IRAK4-/- LPS

description: used for QC, downstream analysis

value: SAMPLE 25

value: LPS


title: C23 IL-1b

description: used for QC, downstream analysis

value: SAMPLE 31


title: C14 MPLA

description: used for QC, downstream analysis

value: SAMPLE 16

value: MPLA


title: C14 LPS

description: used for QC, downstream analysis

value: SAMPLE 15


title: IRAK4-/- MPLA

description: used for QC, downstream analysis

value: SAMPLE 26


title: IRAK4-/- PAM-2

description: used for QC, downstream analysis

value: SAMPLE 22


title: IRAK4-/- NS

description: used for QC only and was excluded from downstream analysis because it did not pass QC criteria

value: SAMPLE 20

value: not stimulated


title: MyD88-/- PAM-2

description: used for QC, downstream analysis

value: SAMPLE 42


title: C23 NS_replicate

description: replicate of sample 30 used for QC only

value: SAMPLE 39

value: healthy control


title: IRAK4-/- LTA

description: used for QC, downstream analysis

value: SAMPLE 24

value: LTA


title: IRAK4-/- FSL1

description: used for QC, downstream analysis

value: SAMPLE 23


title: C14 NS_replicate

description: replicate of sample 10 used for QC and to calculate FC values for samples 13-19

value: SAMPLE 19


title: C23 PAM-2

description: used for QC, downstream analysis

value: SAMPLE 32


title: C14 FSL1

description: used for QC, downstream analysis

value: SAMPLE 13


title: C14 LTA

description: used for QC, downstream analysis

value: SAMPLE 14


title: MECP2-/Y MPLA

description: used for QC, downstream analysis

value: SAMPLE 7


title: NK-Cells_Ionmycin-vs-DMSO_REP2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

description: NK-Cells treated with Ionmycin compared against non treated (Replicate 2)

hyb_protocol: The whole genome transcriptional profile was determined by hybridization with the two color AGILENT human gene expression 4x44K v2 microarray kit (Agilent G4845A)

scan_protocol: The Agilent DNA Microarray Scanner was used for scanning all slides. Two-channel images were quantified with Agilent Feature Extraction software.

data_processing: Local background was corrected by normexp method with an offset of 50. Background corrected intensities were transformed to log scale (base 2) and normalized by loess for each array (Smyth and Speed, 2003). Finally, to have similar intensity distribution across all arrays, loess-normalized-intensity values were scaled by adjusting their quantiles (Bolstad et al., 2003).

source_name: Human NK cells

label_protocol: cDNA was synthesized and labeled with Cy3 or with Hyper5 Mono NHS ester (DMSO treated cells vs. ionomycin treated cells).

growth_protocol: NK cells were isolated from buffy coats, donated by healthy volunteers (Regional Blood Transfusion Centre, Madrid). NK cells were then isolated and purified from PBMCs by negative selection using a magnetic bead isolation kit (Human NK isolation kit, Miltenyi Biotech). After isolation, NK cells were expanded by culture in the presence of irradiated Daudi, RPMI-8866 and autologous PBMCs as feeder cells in RPMI 1640 medium (Lonza) supplemented with 10% FBS, 10% Human Serum (Sigma Aldrich), 4 mM L-glutamine, 0.1 mM non essential amino-acids, 10 mM HEPES, 1 mM sodium pyruvate, 100 U/mL penicillin, 100 U/mL streptomycin, 50 μM ß-mercaptoethanol and 50 U/mL rhIL-2 (Peprotech).

extract_protocol: Total RNA was isolated by TRIZOL reagent (Invitrogen) according to the manufacturer’s instructions, and then further purified using the RNeasy kit (Qiagen). A minimum of 4 μg of RNA was used for the gene expression analysis by microarrays. RNA quality was assessed using a Bioanalyzer2100.

treatment_protocol: NK cells were washed and resuspended at 1x10^6 cells/mL in RPMI 10% FBS (without human serum or IL-2). Cells were then treated with either 1 μM Ionomycin (Sigma) or DMSO (Sigma), as vehicle control, and cultured for 16 hours. Control and ionomycin-treated cells were then washed and allowed to rest for 24 hours at 2x106 cells/mL in RPMI 10% FBS. Where indicated, during this rest day, cell cultures were supplemented with 50 U/mL IL-2 (Peprotech), 10 ng/mL IL-12 (Peprotech), 10 ng/mL IL-18 (MBL),100/1000 U/mL IFN-α (Peprotech), 1000 U/mL IL-4 (Peprotech) or 10 ng/mL IL-15 (Peprotech)

tag: cell type

value: NK

tag: treatment

value: Treated with Ionomycin

value: DMSO


title: NK-Cells_Ionmycin-vs-DMSO_REP1

description: NK-Cells treated with Ionmycin compared against non treated (Replicate 1)


title: C14 PAM-2

description: used for QC, downstream analysis

value: SAMPLE 12


title: vitD:20215557

status: Public on Jan 28 2017

city: Tromso

first: Christopher

last: Fenton

state: Norge

address: MH bygget

department: GSCT

country: Norway

institute: Universiry of Tromso

hyb_protocol: standard as recommended by Illumina

scan_protocol: standard as recommended by Illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.26.4). It was log2 transformed and quantile normalized.

source_name: Blood

label_protocol: standard as recommended by Illumina

extract_protocol: standard as recommended by Illumina

tag: sampleID

value: blood

value: vitamin D

value: male

tag: calcium

tag: pth

tag: phosphate

tag: albumin

tag: height

tag: weight

tag: bmi

tag: smoke

tag: dbp

tag: dnaassay


title: MECP2-/Y FSL1

description: used for QC, downstream analysis

tag: beadchip id

tag: sample id

value: SAMPLE 4

tag: affected protein-coding gene(s)

tag: in vitro stimulation condition


title: NK-Cells_Ionmycin-vs-DMSO_REP4

description: NK-Cells treated with Ionmycin compared against non treated (Replicate 4)

tag: cell type


title: MECP2-/Y IL1b

description: used for QC, downstream analysis

value: SAMPLE 2


title: MECP2-/Y LPS

description: used for QC, downstream analysis

value: SAMPLE 6

value: LPS


title: vitD:20215552

tag: tissue

tag: treatment

value: Placebo

tag: Sex


title: MECP2-/Y PAM-2

description: used for QC, downstream analysis

value: SAMPLE 3


title: NK-Cells_Ionmycin-vs-DMSO_REP3

description: NK-Cells treated with Ionmycin compared against non treated (Replicate 3)


title: C14 NS

description: used for QC and to calculate FC values for samples 11 and 12

value: SAMPLE 10

value: healthy control

value: not stimulated


title: vitD:20215548

tag: sampleID

tag: calcium

tag: pth


title: MECP2-/Y TNF-a

description: used for QC, downstream analysis

value: SAMPLE 8

value: TNF-a


title: vitD:20215555

tag: phosphate

tag: albumin

tag: height


title: vitD:20215546

tag: weight

tag: bmi

tag: smoke


title: MECP2-/Y NS

description: used for QC and to calculate FC values for samples 2-8

tag: beadchip id

value: SAMPLE 1


title: C14 IL-1b

description: used for QC, downstream analysis

tag: sample id

value: SAMPLE 11


title: vitD:20215545

tag: dbp

tag: dnaassay


title: vitD:20215549


title: vitD:20215541


title: vitD:20215544


title: vitD:20215551


title: vitD:20215539


title: MECP2-/Y LTA

description: used for QC, downstream analysis

value: SAMPLE 5

tag: affected protein-coding gene(s)

tag: in vitro stimulation condition

value: LTA


title: vitD:20215528

tag: tissue

value: blood

tag: treatment


title: vitD:20215529

tag: sampleID

tag: Sex

value: male


title: vitD:20215524

tag: calcium

tag: pth


title: vitD:20215389

value: vitamin D

tag: phosphate

tag: albumin


title: vitD:20215482

tag: height

tag: weight


title: vitD:20215531

tag: bmi

tag: smoke


title: vitD:20215383

value: female


title: vitD:20215372


title: vitD:20215370


title: vitD:20215543


title: vitD:20215391


title: vitD:20215345


title: vitD:20215339


title: vitD:20215336


title: vitD:20215354


title: vitD:20215526


title: vitD:20215368


title: vitD:20215362


title: vitD:20215341


title: vitD:20215338


title: vitD:20215357


title: vitD:20215366


title: vitD:20215349


title: vitD:20215353


title: vitD:20215360


title: vitD:20215323


title: vitD:20215324


title: vitD:20215322


title: vitD:20215307


title: vitD:20215306


title: vitD:20215305


title: vitD:20215284


title: vitD:20215299


title: vitD:20215292


title: vitD:20215269


title: vitD:20215295


title: vitD:20215285


title: vitD:20215223


title: vitD:20215553


title: vitD:20215291


title: vitD:20215128


title: vitD:20215297


title: vitD:20215114


title: vitD:20215115


title: vitD:20215105


title: vitD:20215102


title: vitD:20215083


title: vitD:20215104


title: vitD:20215088


title: vitD:20215121


title: vitD:20215109


title: vitD:20215099


title: vitD:20215082


title: vitD:20215085


title: vitD:20215258


title: vitD:20215080


title: vitD:20215300


title: vitD:20215113


title: HiTCE_13d_rep3

city: Urbana

first: Yujie

last: Men

address: 205 N Mathews Ave

institute: University of Illinois at Urbana-Champaign

description:
HiTCE_13d-3
Gene expression data.

hyb_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

data_processing: Data analysis was performed using the MAS5 algorithm and R statistical program. Each microarray was normalized by scaling the signal intensities of spike-in controls to a value of 2500.

organism: Dehalococcoides mccartyi

source_name: HiTCE enrichment without B12 on 13d

label_protocol: One µg of cDNA was prepared for each microarray according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

growth_protocol: Three replicates of 100 mL dechlorinating enrichment cultures were grown with (HiTCEB12) and without vitamin B12 (HiTCE) for 13 days at 34 degC in dark. Cells of HiTCEB12 and HiTCE on day2, and cells of HiTCE on day9 and 13 were taken and collected by centrifugation.

extract_protocol: Total RNA was extracted using Phenol-Chloroform method. cDNA was synthesized according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

tag: culture type

value: without B12

tag: time point

value: day 13


title: HiTCE_13d_rep2

description:
HiTCE_13d-2
Gene expression data.

scan_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).


title: Heart border zone of minipig with MI and myoblast transplantation

city: Shanghai

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00‐0331‐220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00‐0079, Affymetrix, Santa Clara, CA, US) following the manufacturer's instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00‐00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).

organism: Sus scrofa

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3'IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) following the manufacturer's instructions to obtain biotin-labeled cRNA.

growth_protocol: The minipig were fed in specific pathogen-free conditions.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596‐018, Life Technologies, Carlsbad, CA, US) following the manufacturer's instructions Carlsbad, CA, US).

treatment_protocol: The minipig surgical model of myocardial infarction was constructed. Myoblasts were intramyocardially injected into the infarct and border zone of heart. The infarct and border zone heart tissues from minipigs treated with myoblast transplantation or untreated control (one sample for every group) were submitted for gene expression array analysis.

tag: disease state

value: myocardial infarction (MI)

value: heart

tag: zone

value: border

value: myoblast transplantation


title: HiTCE_13d_rep1

description:
HiTCE_13d-1
Gene expression data.


title: HiTCE_9d_rep3

description:
HiTCE_9d-3
Gene expression data.

source_name: HiTCE enrichment without B12 on 9d

value: day 9


title: Heart border zone of minipig with MI and untreated control


title: HiTCE_9d_rep2

description:
HiTCE_9d-2
Gene expression data.


title: vitD:20215073

value: Placebo

tag: dbp

tag: dnaassay


title: vitD:20215078

tag: tissue

tag: treatment


title: vitD:20215067

tag: sampleID

tag: Sex


title: Heart infarct zone of minipig with MI and untreated control

value: infarct


title: vitD:20215081

tag: calcium

tag: pth


title: vitD:20215077

tag: phosphate

tag: albumin


title: Heart infarct zone of minipig with MI and myoblast transplantation


title: HiTCE_9d_rep1

description:
HiTCE_9d-1
Gene expression data.


title: vitD:20215056

tag: height

tag: weight


title: HiTCE_2d_rep3

description:
HiTCE_2d-3
Gene expression data.

source_name: HiTCE enrichment without B12 on 2d

value: day 2


title: vitD:20215071

tag: bmi

tag: smoke


title: HiTCE_2d_rep2

description:
HiTCE_2d-2
Gene expression data.

tag: culture type

tag: time point


title: vitD:20215059


title: HiTCEB12_2d_rep3

description:
HiTCEB12_2d-3
Gene expression data.

source_name: HiTCEB12 enrichment with B12 on 2d


title: vitD:20215055


title: vitD:20215051


title: vitD:20215048


title: vitD:20215044


title: HiTCEB12_2d_rep2

description:
HiTCEB12_2d-2
Gene expression data.


title: vitD:20215369


title: HiTCE_2d_rep1

description:
HiTCE_2d-1
Gene expression data.


title: vitD:20215038


title: vitD:20215040


title: HiTCEB12_2d_rep1

description:
HiTCEB12_2d-1
Gene expression data.


title: vitD:20215335


title: vitD:20215037


title: vitD:20215035


title: vitD:20215027


title: vitD:20215036


title: vitD:20215022


title: vitD:20215018


title: Matrigel 1

city: Chapel Hill

first: Andrew

last: Wang

state: NC

address: 101 Manning Dr

department: Radiation Oncology

institute: University of North Carolina at Chapel Hill

description: Gene expression after HT29 cells formed 3D colonies when growing on matrigel

hyb_protocol: 5 ug of Cy3-labelled linearly amplified cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays (G4858A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with Gene Expression Wash buffer 2 (Agilent) at 37°C , then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan microarray scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Tiff file dynamic range is 20 bit, Dye channel is set to G (Green) and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F20101102) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HT-29 cells, colony, matrigel, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 250ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human colorectal cancer HT-29 cells were cultured in DMEM/F12 (Gibco, Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Gibco) and penicillin/streptomycin (Mediatech, Manassas, VA). The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2. HT-29 cells were grown on standard plastic culture dish (plastic), matrigel coated culture dish, liver biomatrix coated culture dish, or lung biomatrix coated dish. Liver or lung biomatrix were decellularized rat liver or lung after pulverization. For in vivo liver metastasis, HT-29 cells were intrasplenic injected into nude mice and tumors were harvested once liver metastasis was confirmed.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions from HT-29 cells .  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

tag: growth condition

value: matrigel


title: Liver Biomatrix 4

description: Gene expression after HT29 cells formed 3D colonies when growing on liver biomatrix

source_name: HT-29 cells, colony, liver biomatrix, replicate 4

value: liver biomatrix


title: Plastic 3

description: Gene expression from monolayer HT29 cells grown on plastic dish

source_name: HT-29 cells, monolayer cells, plastic culture dish, replicate 3

value: plastic


title: vitD:20215026

value: blood

tag: dbp

tag: dnaassay


title: Plastic 1

source_name: HT-29 cells, monolayer cells, plastic culture dish, replicate 1


title: vitD:20215010

tag: tissue

tag: treatment


title: vitD:20215019

tag: sampleID

tag: Sex

value: male


title: Lung Biomatrix 4

description: Gene expression after HT29 cells formed 3D colonies when growing on lung biomatrix

source_name: HT-29 cells, colony, lung biomatrix, replicate 4

value: lung biomatrix


title: Lung Biomatrix 3

source_name: HT-29 cells, colony, lung biomatrix, replicate 3


title: Plastic 4

source_name: HT-29 cells, monolayer cells, plastic culture dish, replicate 4


title: Lung Biomatrix 2

source_name: HT-29 cells, colony, lung biomatrix, replicate 2


title: In vivo metastasis 3

description: Gene expression after liver metastasis in Nude mice through intrasplenic injection with HT-29 cells

source_name: HT-29 cells, tumor, liver metastasis through intrasplenic injection, replicate 3


title: Matrigel 4

source_name: HT-29 cells, colony, matrigel, replicate 4


title: Liver Biomatrix 3

source_name: HT-29 cells, colony, liver biomatrix, replicate 3


title: Matrigel 3

source_name: HT-29 cells, colony, matrigel, replicate 3


title: Liver Biomatrix 2

source_name: HT-29 cells, colony, liver biomatrix, replicate 2


title: In vivo metastasis 4

source_name: HT-29 cells, tumor, liver metastasis through intrasplenic injection, replicate 4


title: Matrigel 2

source_name: HT-29 cells, colony, matrigel, replicate 2


title: Plastic 2

source_name: HT-29 cells, monolayer cells, plastic culture dish, replicate 2


title: Combinatorial scHi-C Library ML4

type: SRA

city: San Francisco

first: Vijay

last: Ramani

state: California

department: Biochemistry & Biophysics

institute: UCSF

library_source: genomic

data_processing:
Library strategy: Hi-C-seq
Reads were mapped to a combined Burrows-Wheeler reference of hg19 and mm10 using bowtie2. They were then filtered using custom Python scripts to generate validPairs files (see README)

organism:
Homo sapiens
Mus musculus

source_name: Cultured Cell Lines

growth_protocol: Cells are grown under standard tissue culture conditions (10 - 15% FBS, 5% CO2, DMEM or RPMI media, and 1X Pen-Strep) as the Coriell culture practices demand)

extract_protocol:
Cells are lysed using 0.2% NP-40; 10 mM NaCl; 10 mM Tris pH 8.0 in ddH2O
Combinatorial single-cell Hi-C is carried out using a similar protocol to the insitu Hi-C and in situ DNase protocols

treatment_protocol: Cells are fixed using 2% (HeLa, HAP1, GM12878, K562, MEF) or 2.5% (Patski) formaldehyde.

tag: cell lines

value: Contains HeLa S3 (human) and Patski (mouse) cell lines


title: Lung Biomatrix 1

source_name: HT-29 cells, colony, lung biomatrix, replicate 1


title: In vivo metastasis 2

source_name: HT-29 cells, tumor, liver metastasis through intrasplenic injection, replicate 2


title: Liver Biomatrix 1

source_name: HT-29 cells, colony, liver biomatrix, replicate 1


title: Specific memory CD8 from BAL, LBA 3

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
LBA 3
Gene expression data from specific memory CD8 from BAL.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST from Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomic Suite.

label: Biotin

source_name: CD8-specific memory T cells from BAL, IN immunization

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the GeneChip Whole Transcript (WT) Sense Target Labelling Assay kit, Affymetrix).

growth_protocol: Cells were extracted after prime and boost immunization by STxB-E7 vaccine.

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

treatment_protocol: The cells were sorted by FACS ARIA's specialist thanks to the T CD8 memory cells markers.

tag: strain/background

value: intranasal immunization with STxB-E7 vaccine

value: bronchoalveolar lavage (BAL)

tag: cell type

value: CD8 memory T cells


title: Specific memory CD8 from BAL, CD8_LBB1

description:
CD8_LBB1
Gene expression data from specific memory CD8 from BAL.


title: Combinatorial scHi-C Library PL2

data_processing:
Library strategy: Hi-C-seq
Reads were mapped to a combined Burrows-Wheeler reference of hg19 and mm10 using bowtie2. They were then filtered using custom Python scripts to generate validPairs files (see README file on series record).

value: Contains HeLa S3, HAP1, Patski, and primary MEF cells


title: In vivo metastasis 1

source_name: HT-29 cells, tumor, liver metastasis through intrasplenic injection, replicate 1


title: Combinatorial scHi-C Library PL1


title: Combinatorial scHi-C Library ML2


title: Combinatorial scHi-C Library ML1


title: Specific memory CD8 from spleen, CD44-4

description:
CD44-4
Gene expression data from specific memory CD8 from spleen.

source_name: CD8-specific memory T cells from spleen, IM immunization

value: intramuscular immunization with STxB-E7 vaccine

value: spleen


title: Specific memory CD8 from BAL, LBA 4

description:
LBA 4
Gene expression data from specific memory CD8 from BAL.


title: Specific memory CD8 from spleen, CD44-1

description:
CD44-1
Gene expression data from specific memory CD8 from spleen.


title: Tr1 cells at 2 hrs, biological replicate 2

status: Public on Jan 27 2017

city: Boston

first: Asaf

last: Madi

state: MA

address: 60 Fenwood Road, BTM 10016F

department: Neurology

institute: BWH

description:
Gene expression from Tr1 cells activated for 2 hrs
Tr1_2hd

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix microarray HT_MG-430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default

source_name: Naïve CD4+ T cells, activated with anti-CD3/CD28 for 2 hrs in the presence of IL-27 and anti-TGFb1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).

growth_protocol: Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter. Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.

extract_protocol: Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.

treatment_protocol: For Tr1 differentiation: 25ng/ml rmIL-27 with anti-TGFb1. Cells were cultured for 2 hours

value: spleen and lymph node

tag: time (hr)

value: IL27 + anti-TGFb1


title: Specific memory CD8 from spleen, CD44-3

description:
CD44-3
Gene expression data from specific memory CD8 from spleen.


title: Th0 cells at 2 hrs, biological replicate 1

description:
Gene expression from Th0 cells activated for 2 hrs
Ctrl_2h

source_name: Naïve CD4+ T cells, activated with anti-CD3/CD28 for 2 hrs


title: Sponge BMP2 DRG 7d rep2

city: Bethesda

first: Clifton

middle: Lee

last: Dalgard

state: Maryland

address: 4301 Jones Bridge Road B2038

department: Anatomy Physiology & Genetics

institute: Uniformed Services University

description:
replicate 2
B2 DRG6

data_processing: Background subtraction and quantile normalization in Illumina GenomeStudio

organism: Rattus norvegicus

source_name: Rat dorsal root gangion

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Labeling Kit kit for Illumina MouseRef-8 v2.0 Expression BeadChips

extract_protocol: Dorsal root gangion tissue was stablized by snap freezing before homogenization in Trizol reagent and isolation using Qiagen Rneasy Mini Kit.  RNA integiry was assessed using Bio-Rad RNA HighSens Chips on an Experion Automated Electrophores Station.

tag: strain

value: Sasco/Sprague-Dawley

value: Dorsal root Ganglion

tag: age

value: 13 weeks

value: Sponge with BMP2

value: 7 day


title: No Sponge DRG 7d rep4

description:
replicate 4
B12 DRG28


title: Sponge Vehicle DRG 7d rep3

description:
replicate 3
B7 DRG20

value: Sponge


title: Sponge BMP2 DRG 7d rep1

description:
replicate 1
B1 DRG4


title: Specific memory CD8 from spleen, CD44-2

description:
CD44-2
Gene expression data from specific memory CD8 from spleen.


title: Sponge Vehicle DRG 7d rep1

description:
replicate 1
B3 DRG8


title: Tr1 cells at 2 hrs, biological replicate 1

description:
Gene expression from Tr1 cells activated for 2 hrs
Tr1_2h


title: No Sponge DRG 7d rep3

description:
replicate 3
B11 DRG27


title: Sponge Vehicle DRG 7d rep4

description:
replicate 4
B8 DRG24


title: Sponge Vehicle DRG 3d rep2

description:
replicate 2
D3-7

value: 3 day


title: Sponge Vehicle DRG 3d rep1

description:
replicate 1
D3-6


title: Th0 cells at 2 hrs, biological replicate 2

description:
Gene expression from Th0 cells activated for 2 hrs
Ctrl_2hd


title: Sponge BMP2 DRG 7d rep3

description:
replicate 3
B4 DRG10


title: Sponge Vehicle DRG 3d rep3

description:
replicate 3
D3-8


title: No Sponge DRG 3d rep2

description:
replicate 2
D3-2


title: No Sponge DRG 7d rep2

description:
replicate 2
B10 DRG26


title: Sponge BMP2 DRG 3d rep2

description:
replicate 2
D3-11


title: Sponge BMP2 DRG 7d rep4

description:
replicate 4
B6 DRG18


title: No Sponge DRG 3d rep1

description:
replicate 1
D3-1


title: Sponge Vehicle DRG 7d rep2

description:
replicate 2
B5 DRG12


title: No Sponge DRG 7d rep1

description:
replicate 1
B9 DRG25


title: No Sponge DRG 3d rep3

description:
replicate 3
D3-4


title: Sponge BMP2 DRG 3d rep1

description:
replicate 1
D3-9


title: Sponge BMP2 DRG 3d rep3

description:
replicate 3
D3-12


title: Sponge BMP2 DRG 1d rep4

description:
replicate 4
D-12

value: 1 day


title: Sponge BMP2 DRG 1d rep3

description:
replicate 3
D-11


title: Sponge Vehicle DRG 1d rep3

description:
replicate 3
D-7


title: Sponge BMP2 DRG 1d rep1

description:
replicate 1
D-9


title: No Sponge DRG 1d rep4

description:
replicate 4
D-4


title: No Sponge DRG 1d rep3

description:
replicate 3
D-3


title: Sponge BMP2 DRG 1d rep2

description:
replicate 2
D-10


title: Sponge Vehicle DRG 1d rep1

description:
replicate 1
D-5


title: Sponge Vehicle DRG 1d rep2

description:
replicate 2
D-6


title: No Sponge DRG 1d rep2

description:
replicate 2
D-2


title: Sponge Vehicle DRG 1d rep4

description:
replicate 4
D-8


title: MCF10A shLATS1B ctrl cDNA replicate 2

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: Hybridization was carried out with 2.55 μg of biotinylated target, which was incubated with a GeneChip human Gene 1.0 ST Array (Affymetrix) at 45°C for 16 h.  Following hybridization, non-specifically bound nucleotides were removed by washing and specifically bound target detected using a GeneChip Hybridization, Wash and Stain kit and a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix) and CEL files acquired using GeneChip Command Console Software (Affymetrix).

data_processing: Arrays were normalized and probeset-level expression values calculated with R/Bioconductor's (v2.1415.3/v2.11) 'affy' package using the justRMA() function

source_name: MCF10A shLATS1B ctrl cDNA replicate 2

label_protocol: 100 ng  total RNA were processed with the Ambion WT Expression Kit (Thermo Fischer Scientific) and 2.75 μg of the resulting cDNA were fragmented and labeled with the Affymetrix GeneChip WT Terminal Labeling and Hybridization kit (Affymetrix).

growth_protocol: MCF10A cells were routinely cultured as described in the methods section, for the experiment, they were cultured in M5 estrogen containing medium.

extract_protocol: RNeasy Plus Mini Kit was used according to the manufacture's protocol

treatment_protocol: MCF10A cells were infected at an MOI of 5 with either with the pLKO non-targeting shRNA control lentivirus (shNT), lentivirus targeting LATS1 (shLATS1B) or lentivirus targeting LATS1 and LATS2 (shLATS1+2). Cells were selected with Puromycin at 1.5µg / ml for 4days. The medium was exchanged and the cells were allowed to recover for at least 7days. They were then transiently transfected with cDNA vectors according to the Lipofectamine2000 protocol and cultured in M5 for 5 days before lysis and RNA extraction (Quiagen).

value: mammary epithelial cell


title: MCF10A shLATS1+2 ctrl cDNA replicate 1

source_name: MCF10A shLATS1+2 ctrl cDNA replicate 1


title: MCF10A shLATS1+2 ctrl cDNA replicate 3

source_name: MCF10A shLATS1+2 ctrl cDNA replicate 3


title: MCF10A shNT ESR1 cDNA replicate 2

source_name: MCF10A shNT ESR1 cDNA replicate 2


title: MCF10A shNT YAP/TAZ ESR1 cDNA replicate 3


title: MCF10A shNT ESR1 cDNA replicate 3

source_name: MCF10A shNT ESR1 cDNA replicate 3


title: MCF10A shLATS1+2 ctrl cDNA replicate 2

source_name: MCF10A shLATS1+2 ctrl cDNA replicate 2


title: MCF10A shNT ctrl cDNA replicate 3

source_name: MCF10A shNT ctrl cDNA replicate 3


title: MCF10A shLATS1B ctrl cDNA replicate 1

source_name: MCF10A shLATS1B ctrl cDNA replicate 1


title: No Sponge DRG 1d rep1

description:
replicate 1
D-1