title: Donor_5; 3uM SAHA

description:
Sample name: 5590177039_A
Donor_5


title: Donor_1; DMSO

status: Public on Aug 13 2015

type: RNA

city: La Jolla

first: Brian

last: Reardon

state: CA

address: 9500 Gilman Drive

department: Medicine

country: USA

institute: UCSD

description:
Sample name: 5590177038_L
Donor_1

hyb_protocol: Standard Illumina hybridization protocol; conducted by Asuragen, Inc

scan_protocol: Standard Illumina scanning protocol; conducted by Asuragen, Inc.

data_processing: Expression data were extracted with GenomeStudio software (Illumina); genes with undetectable expression were excluded from analysis.  The lumi package [12] in bioconductor was used to transform (variance-stabilizing) and normalize (robust spline) the raw expression data.  Genes significantly modulated across SAHA doses were identified using a likelihood ratio test (LRT) in the R package Isogene GX [13].  The family wise error rate was controlled using Bonferroni-adjusted p-values (p < 0.05).

molecule: total RNA

organism: Homo sapiens

source_name: CD4+ T cells; DMSO

label_protocol: Biotinylated cRNA were prepared by Asuragen, Inc using standard Illumina protocols

growth_protocol: Human peripheral blood was drawn according to institutional review board approved protocols from 9 healthy HIV-seronegative donors by venipuncture and collected into sodium heparin containing tubes.  Peripheral blood mononuclear cells (PBMCs) were collected from fresh whole blood by centrifugation.   Primary CD4+ T cells were isolated from PBMCs with Rosette Sep CD4+ Isolation Kits according to the manufacturers protocol (Stem Cell Technologies, Inc.).  CD4+ T cells were incubated at 37°C, 5% CO2 overnight in fresh media (5% human serum AB in RPMI 1640).  CD4+ T cell purity and activation were assessed with flow cytometry.  All CD4+ T cell samples included in microarray analysis had >95% purity with fewer than 10% activated cells (i.e., <10% expressing HLA-DR).

extract_protocol: RNA was extracted from treated cells using Qiagen RNeasy RNA isolation kits according to manufacturer’s protocols.  RNA integrity numbers (RINs) were determined with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc).  RNA samples submitted for microarray analysis (N=6) had RINs between 7.9 and 9.0 with an average RIN of 8.5.  cRNA was generated and hybridized to IlluminaHT-12 v3 BeadChips (48,803 probes).

treatment_protocol: CD4+ T cells were counted and aliquoted into 6-well plates; 5 million cells per well at a concentration of 2.5 million cells per mL of media (RPMI 1640 with 5% human serum AB).  Wells containing CD4+ T cells were treated with SAHA (Merck) at 0.34 μM, 1 μM, 3 μM, or 10 μM in 0.1% DMSO, or with only 0.1% DMSO.  Treated cells were incubated at 37°C, 5% CO2 for 24 hours.

tag: individual

value: Donor 1

tag: tissue

value: peripheral blood

tag: cell type

value: CD4+ T cells

tag: agent

value: DMSO

tag: dose

value: control

tag: rin


title: Donor_6; 0.34uM SAHA

description:
Sample name: 5590177038_A
Donor_6

source_name: CD4+ T cells; 0.34uM SAHA

value: Donor 6

value: SAHA


title: Donor_6; 3uM SAHA

description:
Sample name: 5590177014_F
Donor_6

source_name: CD4+ T cells; 3uM SAHA


title: Donor_4; 1uM SAHA

description:
Sample name: 5590177038_H
Donor_4

source_name: CD4+ T cells; 1uM SAHA

value: Donor 4


title: Donor_5; 10uM SAHA

description:
Sample name: 5590177014_G
Donor_5

source_name: CD4+ T cells; 10uM SAHA

value: Donor 5


title: Donor_3; 0.34uM SAHA

description:
Sample name: 5590177014_D
Donor_3

value: Donor 3


title: Donor_4; DMSO

description:
Sample name: 5590177014_B
Donor_4


title: Donor_1; 10uM SAHA

description:
Sample name: 5590177014_A
Donor_1


title: Multiple myeloma, TT3, relapse, 120

city: Little Rock

first: Joshua

last: Epstein

department: Myeloma Institute for Research and Therapy

institute: University of Arkansas for Medical Sciances

description: Gene expression data from multiple myeloma plasma cells at relapse.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133-Plus-2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

label: biotin

source_name: Multiple myeloma plasma cells, TT3, relapse

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

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

value: multiple myeloma plasma cells

tag: treatment

tag: time of testing

value: relapse


title: Multiple myeloma, TT3, relapse, 121


title: Multiple myeloma, TT3, relapse, 119


title: JJ-45, human PDAC tissue

city: Gainesville

first: Thomas

last: Schmittgen

state: FL - FLORIDA

address: 2033 Mowry Road

department: Pharmacy

institute: Univ of Florida

description: Gene expression data from human PDACc tisssue

hyb_protocol: Labeled cRNA targets were hybridized to Affymetrix GeneChip® Human Genome U133 Plus 2.0array for 16 h at 45 °C rotating at 60rpm.  The arrays were washed and stained using the Fluidics Station 450

scan_protocol: GeneChips were scanned using the the Affymetrix GeneChip Scanner 3000.

data_processing:
Gene expression raw data from Affymetric microarrays were processed and normalized using  'affy' R package (v.2.0.0) from Bioconductor (PMID:14960456). Normalization was done using RMA algorithm (PMID:12925520).
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.28061

source_name: Tissue from PDAC patients

label_protocol: A 2ug aliquot of total RNA was linearly amplified and labeled using the BioArray High Yield RNA Transcript labeling kit (Enzo Life Sciences).  Then, 15ug of labeled cRNA was frageneted following the manufacturer's instructions.

extract_protocol: RNA of normal pancreatic specimens were purchased commercially. Trizol extraction of total RNA was performed on PDAC specimens according to the manufacturer's instructions.

tag: subject status

value: pancreatic ductal adenocarcinoma (PDAC) patient

value: pancrea

tag: tissue subtype

value: PDAC


title: JJ-39, human PDAC tissue


title: JJ-47, human PDAC tissue


title: JJ-32, human PDAC tissue


title: JJ-29, human PDAC tissue


title: JJ-31, human PDAC tissue


title: JJ-27, human PDAC tissue

description: Gene expression data from human normal pancreatic tisssue


title: Donor_4; 0.34uM SAHA

description:
Sample name: 5590177039_F
Donor_4


title: JJ-50, human PDAC tissue


title: JJ-43, human PDAC tissue


title: JJ-49, human PDAC tissue


title: JJ-4, human normal pancreatic tissue

source_name: human normal pancreatic tissue

value: Normal

value: normal pancreatic tissue

tag: rna vendor

value: Ambion

tag: rna cat. #


title: JJ-6, human normal pancreatic tissue

value: Stratagen


title: JJ-7, human normal pancreatic tissue


title: JJ-1, human normal pancreatic tissue


title: JJ-44, human PDAC tissue


title: JJ-46, human PDAC tissue


title: JJ-2, human normal pancreatic tissue


title: JJ-26, human PDAC tissue


title: JJ-3, human normal pancreatic tissue


title: JJ-5, human normal pancreatic tissue

value: Clontech


title: Multiple myeloma, TT3, relapse, 115


title: Multiple myeloma, TT3, relapse, 117


title: Donor_2; DMSO

description:
Sample name: 5590177038_F
Donor_2

value: Donor 2

value: peripheral blood

value: CD4+ T cells

value: DMSO


title: Multiple myeloma, TT3, relapse, 118


title: JJ-8, human normal pancreatic tissue


title: Donor_5; 1uM SAHA

description:
Sample name: 5590177014_E
Donor_5

value: SAHA


title: Multiple myeloma, TT3, relapse, 110


title: Multiple myeloma, TT3, relapse, 114


title: Multiple myeloma, TT3, relapse, 112


title: Multiple myeloma, TT3, relapse, 104


title: Multiple myeloma, TT3, relapse, 108


title: Multiple myeloma, TT3, relapse, 106


title: Multiple myeloma, TT3, relapse, 109


title: Multiple myeloma, TT3, relapse, 116


title: Multiple myeloma, TT3, relapse, 103


title: Multiple myeloma, TT3, relapse, 107


title: Multiple myeloma, TT3, relapse, 101


title: Multiple myeloma, TT3, relapse, 113


title: Multiple myeloma, TT3, relapse, 105


title: Multiple myeloma, TT3, relapse, 111


title: Multiple myeloma, TT3, baseline, 433

description: Gene expression data from multiple myeloma plasma cells at baseline.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on an HG-U133-Plus-2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Multiple myeloma plasma cells, TT3, baseline

value: baseline


title: Multiple myeloma, TT3, baseline, 428


title: Multiple myeloma, TT3, baseline, 426


title: Multiple myeloma, TT3, relapse, 102


title: Multiple myeloma, TT3, baseline, 431


title: Multiple myeloma, TT2, baseline, 179

source_name: Multiple myeloma plasma cells, TT2, baseline


title: Multiple myeloma, TT3, baseline, 429


title: Multiple myeloma, TT3, baseline, 430


title: Multiple myeloma, TT3, baseline, 432


title: Multiple myeloma, TT3, baseline, 421


title: Multiple myeloma, TT2, baseline, 77


title: Multiple myeloma, TT3, baseline, 423


title: Multiple myeloma, TT3, baseline, 420


title: Multiple myeloma, TT3, baseline, 425


title: Multiple myeloma, TT2, baseline, 80


title: Multiple myeloma, TT3, baseline, 422


title: Multiple myeloma, TT3, baseline, 427


title: Multiple myeloma, TT3, baseline, 424


title: Multiple myeloma, TT3, baseline, 419


title: Multiple myeloma, TT3, baseline, 416


title: Multiple myeloma, TT3, baseline, 413


title: Multiple myeloma, TT3, baseline, 417


title: Multiple myeloma, TT3, baseline, 404


title: Multiple myeloma, TT3, baseline, 406


title: Multiple myeloma, TT3, baseline, 405


title: Multiple myeloma, TT3, baseline, 407


title: Multiple myeloma, TT3, baseline, 412


title: Multiple myeloma, TT3, baseline, 415


title: Multiple myeloma, TT3, baseline, 403


title: Multiple myeloma, TT3, baseline, 418


title: Multiple myeloma, TT3, baseline, 402


title: Multiple myeloma, TT3, baseline, 397


title: Multiple myeloma, TT3, baseline, 411


title: Multiple myeloma, TT3, baseline, 391


title: Multiple myeloma, TT3, baseline, 396


title: Multiple myeloma, TT3, baseline, 392


title: Multiple myeloma, TT3, baseline, 414


title: Multiple myeloma, TT3, baseline, 399


title: Multiple myeloma, TT3, baseline, 401


title: Multiple myeloma, TT3, baseline, 394


title: Multiple myeloma, TT3, baseline, 400


title: Multiple myeloma, TT3, baseline, 409


title: Multiple myeloma, TT3, baseline, 398


title: Multiple myeloma, TT3, baseline, 390


title: Multiple myeloma, TT3, baseline, 395


title: Multiple myeloma, TT3, baseline, 393


title: Multiple myeloma, TT3, baseline, 408


title: Multiple myeloma, TT3, baseline, 410


title: Multiple myeloma, TT3, baseline, 389


title: Multiple myeloma, TT3, baseline, 384


title: Multiple myeloma, TT3, baseline, 386


title: Multiple myeloma, TT3, baseline, 388


title: Multiple myeloma, TT3, baseline, 382


title: Multiple myeloma, TT3, baseline, 383


title: Multiple myeloma, TT3, baseline, 381


title: Multiple myeloma, TT3, baseline, 385


title: Multiple myeloma, TT3, baseline, 387


title: Multiple myeloma, TT3, baseline, 380


title: Multiple myeloma, TT3, baseline, 375


title: Multiple myeloma, TT3, baseline, 377


title: Multiple myeloma, TT3, baseline, 373


title: Multiple myeloma, TT3, baseline, 376


title: Multiple myeloma, TT3, baseline, 378


title: Multiple myeloma, TT3, baseline, 372


title: Multiple myeloma, TT3, baseline, 374


title: Multiple myeloma, TT3, baseline, 364


title: Multiple myeloma, TT3, baseline, 379


title: Multiple myeloma, TT3, baseline, 371


title: Multiple myeloma, TT3, baseline, 366


title: Multiple myeloma, TT3, baseline, 363


title: Multiple myeloma, TT3, baseline, 365


title: Multiple myeloma, TT3, baseline, 367


title: Multiple myeloma, TT3, baseline, 362


title: Multiple myeloma, TT3, baseline, 361


title: Multiple myeloma, TT3, baseline, 370


title: Multiple myeloma, TT3, baseline, 352


title: Multiple myeloma, TT3, baseline, 369


title: Multiple myeloma, TT3, baseline, 368


title: Multiple myeloma, TT3, baseline, 358


title: Multiple myeloma, TT3, baseline, 359


title: Multiple myeloma, TT3, baseline, 354


title: Multiple myeloma, TT3, baseline, 355


title: Multiple myeloma, TT3, baseline, 353


title: Multiple myeloma, TT3, baseline, 360


title: Multiple myeloma, TT3, baseline, 357


title: Multiple myeloma, TT3, baseline, 356


title: Multiple myeloma, TT3, baseline, 344


title: Multiple myeloma, TT3, baseline, 349


title: Multiple myeloma, TT3, baseline, 348


title: Multiple myeloma, TT3, baseline, 345


title: Multiple myeloma, TT3, baseline, 346


title: Multiple myeloma, TT3, baseline, 347


title: Multiple myeloma, TT3, baseline, 343


title: Multiple myeloma, TT3, baseline, 350


title: Multiple myeloma, TT3, baseline, 351


title: Multiple myeloma, TT3, baseline, 336


title: Multiple myeloma, TT3, baseline, 337


title: Multiple myeloma, TT3, baseline, 342


title: Multiple myeloma, TT3, baseline, 339


title: Multiple myeloma, TT3, baseline, 338


title: Multiple myeloma, TT3, baseline, 340


title: Multiple myeloma, TT3, baseline, 335


title: Multiple myeloma, TT3, baseline, 341


title: Multiple myeloma, TT3, baseline, 334


title: Multiple myeloma, TT3, baseline, 332


title: Multiple myeloma, TT3, baseline, 333


title: Multiple myeloma, TT3, baseline, 330


title: Multiple myeloma, TT3, baseline, 331


title: Multiple myeloma, TT3, baseline, 326


title: Multiple myeloma, TT3, baseline, 329


title: Multiple myeloma, TT3, baseline, 325


title: Multiple myeloma, TT3, baseline, 320


title: Multiple myeloma, TT3, baseline, 323


title: Multiple myeloma, TT3, baseline, 324


title: Multiple myeloma, TT3, baseline, 328


title: Multiple myeloma, TT3, baseline, 316


title: Multiple myeloma, TT3, baseline, 321


title: Multiple myeloma, TT3, baseline, 313


title: Multiple myeloma, TT3, baseline, 315


title: Multiple myeloma, TT3, baseline, 314


title: Multiple myeloma, TT3, baseline, 319


title: Multiple myeloma, TT3, baseline, 317


title: Multiple myeloma, TT3, baseline, 322


title: Multiple myeloma, TT3, baseline, 312


title: Multiple myeloma, TT3, baseline, 327


title: Multiple myeloma, TT3, baseline, 318


title: Multiple myeloma, TT3, baseline, 304


title: Multiple myeloma, TT3, baseline, 308


title: Multiple myeloma, TT3, baseline, 309


title: Multiple myeloma, TT3, baseline, 306


title: Multiple myeloma, TT3, baseline, 305


title: Multiple myeloma, TT3, baseline, 307


title: Multiple myeloma, TT3, baseline, 311


title: Multiple myeloma, TT3, baseline, 310


title: Multiple myeloma, TT3, baseline, 302


title: Multiple myeloma, TT3, baseline, 301


title: Multiple myeloma, TT3, baseline, 300


title: Multiple myeloma, TT3, baseline, 293


title: Multiple myeloma, TT3, baseline, 292


title: Multiple myeloma, TT3, baseline, 291


title: Multiple myeloma, TT3, baseline, 294


title: Multiple myeloma, TT3, baseline, 295


title: Multiple myeloma, TT3, baseline, 297


title: Multiple myeloma, TT3, baseline, 296


title: Multiple myeloma, TT3, baseline, 298


title: Multiple myeloma, TT3, baseline, 287


title: Multiple myeloma, TT3, baseline, 290


title: Multiple myeloma, TT3, baseline, 289


title: Multiple myeloma, TT3, baseline, 299


title: Multiple myeloma, TT3, baseline, 288


title: Multiple myeloma, TT3, baseline, 303


title: Multiple myeloma, TT3, baseline, 285


title: Multiple myeloma, TT3, baseline, 282


title: Multiple myeloma, TT3, baseline, 286


title: Multiple myeloma, TT3, baseline, 275


title: Multiple myeloma, TT3, baseline, 272


title: Multiple myeloma, TT3, baseline, 281


title: Multiple myeloma, TT3, baseline, 277


title: Multiple myeloma, TT3, baseline, 274


title: Multiple myeloma, TT3, baseline, 284


title: Multiple myeloma, TT3, baseline, 283


title: Multiple myeloma, TT3, baseline, 273


title: Multiple myeloma, TT3, baseline, 264


title: Multiple myeloma, TT3, baseline, 261


title: Multiple myeloma, TT3, baseline, 278


title: Multiple myeloma, TT3, baseline, 276


title: Multiple myeloma, TT3, baseline, 271


title: Multiple myeloma, TT3, baseline, 259


title: Multiple myeloma, TT3, baseline, 257


title: Multiple myeloma, TT3, baseline, 265


title: Multiple myeloma, TT3, baseline, 263


title: Multiple myeloma, TT3, baseline, 256


title: Multiple myeloma, TT3, baseline, 260


title: Multiple myeloma, TT3, baseline, 268


title: Multiple myeloma, TT3, baseline, 269


title: Multiple myeloma, TT3, baseline, 267


title: Multiple myeloma, TT3, baseline, 279


title: Multiple myeloma, TT3, baseline, 266


title: Multiple myeloma, TT3, baseline, 270


title: Multiple myeloma, TT3, baseline, 250


title: Multiple myeloma, TT3, baseline, 253


title: Multiple myeloma, TT3, baseline, 246


title: Multiple myeloma, TT3, baseline, 255


title: Multiple myeloma, TT3, baseline, 254


title: Multiple myeloma, TT3, baseline, 251


title: Multiple myeloma, TT3, baseline, 245


title: Multiple myeloma, TT3, baseline, 248


title: Multiple myeloma, TT3, baseline, 244


title: Multiple myeloma, TT3, baseline, 247


title: Multiple myeloma, TT3, baseline, 238


title: Multiple myeloma, TT3, baseline, 235


title: Multiple myeloma, TT3, baseline, 258


title: Multiple myeloma, TT3, baseline, 233


title: Multiple myeloma, TT3, baseline, 234


title: Multiple myeloma, TT3, baseline, 249


title: Multiple myeloma, TT3, baseline, 243


title: Multiple myeloma, TT3, baseline, 232


title: Multiple myeloma, TT3, baseline, 241


title: Multiple myeloma, TT3, baseline, 236


title: Multiple myeloma, TT3, baseline, 240


title: Multiple myeloma, TT3, baseline, 239


title: Multiple myeloma, TT3, baseline, 230


title: Multiple myeloma, TT3, baseline, 231


title: Multiple myeloma, TT3, baseline, 242


title: Multiple myeloma, TT3, baseline, 237


title: Multiple myeloma, TT3, baseline, 252


title: Multiple myeloma, TT3, baseline, 229


title: Multiple myeloma, TT3, baseline, 228


title: Multiple myeloma, TT3, baseline, 224


title: Multiple myeloma, TT3, baseline, 226


title: Multiple myeloma, TT3, baseline, 225


title: Multiple myeloma, TT3, baseline, 280


title: Multiple myeloma, TT3, baseline, 220


title: Multiple myeloma, TT3, baseline, 212


title: Multiple myeloma, TT3, baseline, 214


title: Multiple myeloma, TT3, baseline, 215


title: Multiple myeloma, TT3, baseline, 211


title: Multiple myeloma, TT3, baseline, 204


title: Multiple myeloma, TT3, baseline, 216


title: Multiple myeloma, TT3, baseline, 209


title: Multiple myeloma, TT3, baseline, 227


title: Multiple myeloma, TT3, baseline, 202


title: Multiple myeloma, TT3, baseline, 219


title: Multiple myeloma, TT3, baseline, 208


title: Multiple myeloma, TT3, baseline, 223


title: Multiple myeloma, TT3, baseline, 210


title: Multiple myeloma, TT3, baseline, 221


title: Multiple myeloma, TT3, baseline, 206


title: Multiple myeloma, TT3, baseline, 218


title: Multiple myeloma, TT3, baseline, 205


title: Multiple myeloma, TT3, baseline, 207


title: Multiple myeloma, TT3, baseline, 213


title: Multiple myeloma, TT3, baseline, 201


title: Multiple myeloma, TT3, baseline, 222


title: Multiple myeloma, TT3, baseline, 262


title: Multiple myeloma, TT3, baseline, 203


title: Multiple myeloma, TT3, baseline, 197


title: Multiple myeloma, TT3, baseline, 199


title: Multiple myeloma, TT3, baseline, 195


title: Multiple myeloma, TT3, baseline, 196


title: Multiple myeloma, TT3, baseline, 198


title: Multiple myeloma, TT3, baseline, 188


title: Multiple myeloma, TT3, baseline, 183


title: Multiple myeloma, TT3, baseline, 185


title: Multiple myeloma, TT3, baseline, 190


title: Multiple myeloma, TT3, baseline, 200


title: Multiple myeloma, TT3, baseline, 187


title: Multiple myeloma, TT3, baseline, 192


title: Multiple myeloma, TT3, baseline, 179


title: Multiple myeloma, TT3, baseline, 177


title: Multiple myeloma, TT3, baseline, 189


title: Multiple myeloma, TT3, baseline, 181


title: Multiple myeloma, TT3, baseline, 182


title: Multiple myeloma, TT3, baseline, 184


title: Multiple myeloma, TT3, baseline, 178


title: Multiple myeloma, TT3, baseline, 186


title: Multiple myeloma, TT3, baseline, 191


title: Multiple myeloma, TT3, baseline, 180


title: Multiple myeloma, TT3, baseline, 175


title: Multiple myeloma, TT3, baseline, 194


title: Multiple myeloma, TT3, baseline, 193


title: Multiple myeloma, TT3, baseline, 217


title: Multiple myeloma, TT3, baseline, 176


title: Multiple myeloma, TT3, baseline, 172


title: Multiple myeloma, TT3, baseline, 174


title: Multiple myeloma, TT3, baseline, 169


title: Multiple myeloma, TT3, baseline, 170


title: Multiple myeloma, TT3, baseline, 171


title: Multiple myeloma, TT3, baseline, 167


title: Multiple myeloma, TT3, baseline, 168


title: Multiple myeloma, TT3, baseline, 164


title: Multiple myeloma, TT3, baseline, 162


title: Multiple myeloma, TT3, baseline, 163


title: Multiple myeloma, TT3, baseline, 158


title: Multiple myeloma, TT3, baseline, 161


title: Multiple myeloma, TT3, baseline, 155


title: Multiple myeloma, TT3, baseline, 165


title: Multiple myeloma, TT3, baseline, 157


title: Multiple myeloma, TT3, baseline, 173


title: Multiple myeloma, TT3, baseline, 159


title: Multiple myeloma, TT3, baseline, 156


title: Multiple myeloma, TT3, baseline, 151


title: Multiple myeloma, TT3, baseline, 147


title: Multiple myeloma, TT3, baseline, 153


title: Multiple myeloma, TT3, baseline, 148


title: Multiple myeloma, TT3, baseline, 154


title: Multiple myeloma, TT3, baseline, 152


title: Multiple myeloma, TT3, baseline, 149


title: Multiple myeloma, TT3, baseline, 145


title: Multiple myeloma, TT3, baseline, 146


title: Multiple myeloma, TT3, baseline, 160


title: Multiple myeloma, TT3, baseline, 150


title: Multiple myeloma, TT3, baseline, 138


title: Multiple myeloma, TT3, baseline, 139


title: Multiple myeloma, TT3, baseline, 166


title: Multiple myeloma, TT3, baseline, 140


title: Multiple myeloma, TT3, baseline, 141


title: Multiple myeloma, TT3, baseline, 142


title: Multiple myeloma, TT3, baseline, 143


title: Multiple myeloma, TT3, baseline, 144


title: Multiple myeloma, TT3, baseline, 137


title: Multiple myeloma, TT3, baseline, 136


title: Multiple myeloma, TT3, baseline, 130


title: Multiple myeloma, TT3, baseline, 135


title: Multiple myeloma, TT3, baseline, 134


title: Multiple myeloma, TT3, baseline, 128


title: Multiple myeloma, TT3, baseline, 126


title: Multiple myeloma, TT3, baseline, 120


title: Multiple myeloma, TT3, baseline, 133


title: Multiple myeloma, TT3, baseline, 115


title: Multiple myeloma, TT3, baseline, 129


title: Multiple myeloma, TT3, baseline, 118


title: Multiple myeloma, TT3, baseline, 113


title: Multiple myeloma, TT3, baseline, 111


title: Multiple myeloma, TT3, baseline, 131


title: Multiple myeloma, TT3, baseline, 127


title: Multiple myeloma, TT3, baseline, 124


title: Multiple myeloma, TT3, baseline, 125


title: Multiple myeloma, TT3, baseline, 132


title: Multiple myeloma, TT3, baseline, 108


title: Multiple myeloma, TT3, baseline, 119


title: Multiple myeloma, TT3, baseline, 109


title: Multiple myeloma, TT3, baseline, 121


title: Multiple myeloma, TT3, baseline, 116


title: Multiple myeloma, TT3, baseline, 110


title: Multiple myeloma, TT3, baseline, 122


title: Multiple myeloma, TT3, baseline, 117


title: Multiple myeloma, TT3, baseline, 114


title: Multiple myeloma, TT3, baseline, 123


title: Multiple myeloma, TT3, baseline, 107


title: Multiple myeloma, TT3, baseline, 106


title: Multiple myeloma, TT3, baseline, 102


title: Multiple myeloma, TT3, baseline, 101


title: Multiple myeloma, TT3, baseline, 95


title: Multiple myeloma, TT3, baseline, 93


title: Multiple myeloma, TT3, baseline, 88


title: Multiple myeloma, TT3, baseline, 97


title: Multiple myeloma, TT3, baseline, 104


title: Multiple myeloma, TT3, baseline, 105


title: Multiple myeloma, TT3, baseline, 92


title: Multiple myeloma, TT3, baseline, 100


title: Multiple myeloma, TT3, baseline, 91


title: Multiple myeloma, TT3, baseline, 84


title: Multiple myeloma, TT3, baseline, 99


title: Multiple myeloma, TT3, baseline, 85


title: Multiple myeloma, TT3, baseline, 89


title: Multiple myeloma, TT3, baseline, 81


title: Multiple myeloma, TT3, baseline, 96


title: Multiple myeloma, TT3, baseline, 94


title: Multiple myeloma, TT3, baseline, 90


title: Multiple myeloma, TT3, baseline, 98


title: Multiple myeloma, TT3, baseline, 80


title: Multiple myeloma, TT3, baseline, 83


title: Multiple myeloma, TT3, baseline, 87


title: Multiple myeloma, TT3, baseline, 86


title: Multiple myeloma, TT3, baseline, 82


title: Multiple myeloma, TT3, baseline, 79


title: Multiple myeloma, TT3, baseline, 77


title: Multiple myeloma, TT3, baseline, 112


title: Multiple myeloma, TT3, baseline, 70


title: Multiple myeloma, TT3, baseline, 75


title: Multiple myeloma, TT3, baseline, 73


title: Multiple myeloma, TT3, baseline, 76


title: Multiple myeloma, TT3, baseline, 74


title: Multiple myeloma, TT3, baseline, 65


title: Multiple myeloma, TT3, baseline, 67


title: Multiple myeloma, TT3, baseline, 69


title: Multiple myeloma, TT3, baseline, 68


title: Multiple myeloma, TT3, baseline, 64


title: Multiple myeloma, TT3, baseline, 66


title: Multiple myeloma, TT3, baseline, 71


title: Multiple myeloma, TT3, baseline, 63


title: Multiple myeloma, TT3, baseline, 78


title: Multiple myeloma, TT3, baseline, 62


title: Multiple myeloma, TT3, baseline, 60


title: Multiple myeloma, TT3, baseline, 57


title: Multiple myeloma, TT3, baseline, 72


title: Multiple myeloma, TT3, baseline, 55


title: Multiple myeloma, TT3, baseline, 51


title: Multiple myeloma, TT3, baseline, 56


title: Multiple myeloma, TT3, baseline, 42


title: Multiple myeloma, TT3, baseline, 47


title: Multiple myeloma, TT3, baseline, 46


title: Multiple myeloma, TT3, baseline, 53


title: Multiple myeloma, TT3, baseline, 54


title: Multiple myeloma, TT3, baseline, 45


title: Multiple myeloma, TT3, baseline, 49


title: Multiple myeloma, TT3, baseline, 48


title: Multiple myeloma, TT3, baseline, 38


title: Multiple myeloma, TT3, baseline, 52


title: Multiple myeloma, TT3, baseline, 58


title: Multiple myeloma, TT3, baseline, 44


title: Multiple myeloma, TT3, baseline, 37


title: Multiple myeloma, TT3, baseline, 39


title: Multiple myeloma, TT3, baseline, 103


title: Multiple myeloma, TT3, baseline, 34


title: Multiple myeloma, TT3, baseline, 50


title: Multiple myeloma, TT3, baseline, 36


title: Multiple myeloma, TT3, baseline, 33


title: Multiple myeloma, TT3, baseline, 41


title: Multiple myeloma, TT3, baseline, 35


title: Multiple myeloma, TT3, baseline, 43


title: Multiple myeloma, TT3, baseline, 32


title: Multiple myeloma, TT3, baseline, 40


title: Multiple myeloma, TT3, baseline, 31


title: Multiple myeloma, TT3, baseline, 30


title: Multiple myeloma, TT3, baseline, 20


title: Multiple myeloma, TT3, baseline, 27


title: Multiple myeloma, TT3, baseline, 13


title: Multiple myeloma, TT3, baseline, 28


title: Multiple myeloma, TT3, baseline, 29


title: Multiple myeloma, TT3, baseline, 18


title: Multiple myeloma, TT3, baseline, 19


title: Multiple myeloma, TT3, baseline, 23


title: Multiple myeloma, TT3, baseline, 24


title: Multiple myeloma, TT3, baseline, 26


title: Multiple myeloma, TT3, baseline, 21


title: Multiple myeloma, TT3, baseline, 17


title: Multiple myeloma, TT3, baseline, 12


title: Multiple myeloma, TT3, baseline, 25


title: Multiple myeloma, TT3, baseline, 16


title: Multiple myeloma, TT3, baseline, 22


title: Multiple myeloma, TT3, baseline, 9


title: Multiple myeloma, TT3, baseline, 14


title: Multiple myeloma, TT3, baseline, 15


title: Multiple myeloma, TT3, baseline, 6


title: Multiple myeloma, TT3, baseline, 10


title: Multiple myeloma, TT3, baseline, 5


title: Multiple myeloma, TT3, baseline, 61


title: Multiple myeloma, TT3, baseline, 8


title: Multiple myeloma, TT3, baseline, 4


title: Multiple myeloma, TT3, baseline, 11


title: Multiple myeloma, TT3, baseline, 59


title: Multiple myeloma, TT3, baseline, 7


title: Multiple myeloma, TT3, baseline, 2


title: Multiple myeloma, TT3, baseline, 3


title: Multiple myeloma, TT3, baseline, 1


title: Multiple myeloma, TT2, baseline, 347


title: Multiple myeloma, TT2, baseline, 344


title: Multiple myeloma, TT2, baseline, 340


title: Multiple myeloma, TT2, baseline, 345


title: Multiple myeloma, TT2, baseline, 330


title: Multiple myeloma, TT2, baseline, 331


title: Multiple myeloma, TT2, baseline, 333


title: Multiple myeloma, TT2, baseline, 338


title: Multiple myeloma, TT2, baseline, 339


title: Multiple myeloma, TT2, baseline, 342


title: Multiple myeloma, TT2, baseline, 335


title: Multiple myeloma, TT2, baseline, 332


title: Multiple myeloma, TT2, baseline, 341


title: Multiple myeloma, TT2, baseline, 337


title: Multiple myeloma, TT2, baseline, 325


title: Multiple myeloma, TT2, baseline, 329


title: Multiple myeloma, TT2, baseline, 336


title: Multiple myeloma, TT2, baseline, 328


title: Multiple myeloma, TT2, baseline, 334


title: Multiple myeloma, TT2, baseline, 343


title: Multiple myeloma, TT2, baseline, 346


title: Multiple myeloma, TT2, baseline, 323


title: Multiple myeloma, TT2, baseline, 324


title: Multiple myeloma, TT2, baseline, 326


title: Multiple myeloma, TT2, baseline, 327


title: Multiple myeloma, TT2, baseline, 322


title: Multiple myeloma, TT2, baseline, 319


title: Multiple myeloma, TT2, baseline, 321


title: Multiple myeloma, TT2, baseline, 317


title: Multiple myeloma, TT2, baseline, 316


title: Multiple myeloma, TT2, baseline, 318


title: Multiple myeloma, TT2, baseline, 314


title: Multiple myeloma, TT2, baseline, 315


title: Multiple myeloma, TT2, baseline, 306


title: Multiple myeloma, TT2, baseline, 310


title: Multiple myeloma, TT2, baseline, 313


title: Multiple myeloma, TT2, baseline, 304


title: Multiple myeloma, TT2, baseline, 312


title: Multiple myeloma, TT2, baseline, 302


title: Multiple myeloma, TT2, baseline, 303


title: Multiple myeloma, TT2, baseline, 308


title: Multiple myeloma, TT2, baseline, 311


title: Multiple myeloma, TT2, baseline, 294


title: Multiple myeloma, TT2, baseline, 307


title: Multiple myeloma, TT2, baseline, 296


title: Multiple myeloma, TT2, baseline, 291


title: Multiple myeloma, TT2, baseline, 297


title: Multiple myeloma, TT2, baseline, 300


title: Multiple myeloma, TT2, baseline, 299


title: Multiple myeloma, TT2, baseline, 301


title: Multiple myeloma, TT2, baseline, 293


title: Multiple myeloma, TT2, baseline, 295


title: Multiple myeloma, TT2, baseline, 298


title: Multiple myeloma, TT2, baseline, 305


title: Multiple myeloma, TT2, baseline, 290


title: Multiple myeloma, TT2, baseline, 309


title: Multiple myeloma, TT2, baseline, 320


title: Multiple myeloma, TT2, baseline, 287


title: Multiple myeloma, TT2, baseline, 292


title: Multiple myeloma, TT2, baseline, 288


title: Multiple myeloma, TT2, baseline, 286


title: Multiple myeloma, TT2, baseline, 285


title: Multiple myeloma, TT2, baseline, 289


title: Multiple myeloma, TT2, baseline, 281


title: Multiple myeloma, TT2, baseline, 272


title: Multiple myeloma, TT2, baseline, 274


title: Multiple myeloma, TT2, baseline, 262


title: Multiple myeloma, TT2, baseline, 278


title: Multiple myeloma, TT2, baseline, 261


title: Multiple myeloma, TT2, baseline, 283


title: Multiple myeloma, TT2, baseline, 276


title: Multiple myeloma, TT2, baseline, 275


title: Multiple myeloma, TT2, baseline, 259


title: Multiple myeloma, TT2, baseline, 279


title: Multiple myeloma, TT2, baseline, 277


title: Multiple myeloma, TT2, baseline, 284


title: Multiple myeloma, TT2, baseline, 282


title: Multiple myeloma, TT2, baseline, 264


title: Multiple myeloma, TT2, baseline, 265


title: Multiple myeloma, TT2, baseline, 280


title: Multiple myeloma, TT2, baseline, 271


title: Multiple myeloma, TT2, baseline, 270


title: Multiple myeloma, TT2, baseline, 260


title: Multiple myeloma, TT2, baseline, 273


title: Multiple myeloma, TT2, baseline, 256


title: Multiple myeloma, TT2, baseline, 269


title: Multiple myeloma, TT2, baseline, 266


title: Multiple myeloma, TT2, baseline, 267


title: Multiple myeloma, TT2, baseline, 257


title: Multiple myeloma, TT2, baseline, 258


title: Multiple myeloma, TT2, baseline, 268


title: Multiple myeloma, TT2, baseline, 249


title: Multiple myeloma, TT2, baseline, 252


title: Multiple myeloma, TT2, baseline, 251


title: Multiple myeloma, TT2, baseline, 231


title: Multiple myeloma, TT2, baseline, 240


title: Multiple myeloma, TT2, baseline, 255


title: Multiple myeloma, TT2, baseline, 246


title: Multiple myeloma, TT2, baseline, 253


title: Multiple myeloma, TT2, baseline, 243


title: Multiple myeloma, TT2, baseline, 236


title: Multiple myeloma, TT2, baseline, 247


title: Multiple myeloma, TT2, baseline, 241


title: Multiple myeloma, TT2, baseline, 239


title: Multiple myeloma, TT2, baseline, 250


title: Multiple myeloma, TT2, baseline, 248


title: Multiple myeloma, TT2, baseline, 242


title: Multiple myeloma, TT2, baseline, 234


title: Multiple myeloma, TT2, baseline, 238


title: Multiple myeloma, TT2, baseline, 232


title: Multiple myeloma, TT2, baseline, 235


title: Multiple myeloma, TT2, baseline, 244


title: Multiple myeloma, TT2, baseline, 233


title: Multiple myeloma, TT2, baseline, 229


title: Multiple myeloma, TT2, baseline, 237


title: Multiple myeloma, TT2, baseline, 245


title: Multiple myeloma, TT2, baseline, 227


title: Multiple myeloma, TT2, baseline, 228


title: Multiple myeloma, TT2, baseline, 230


title: Multiple myeloma, TT2, baseline, 254


title: Multiple myeloma, TT2, baseline, 226


title: Multiple myeloma, TT2, baseline, 223


title: Multiple myeloma, TT2, baseline, 221


title: Multiple myeloma, TT2, baseline, 222


title: Multiple myeloma, TT2, baseline, 224


title: Multiple myeloma, TT2, baseline, 225


title: Multiple myeloma, TT2, baseline, 263


title: Multiple myeloma, TT2, baseline, 212


title: Multiple myeloma, TT2, baseline, 220


title: Multiple myeloma, TT2, baseline, 207


title: Multiple myeloma, TT2, baseline, 213


title: Multiple myeloma, TT2, baseline, 209


title: Multiple myeloma, TT2, baseline, 210


title: Multiple myeloma, TT2, baseline, 219


title: Multiple myeloma, TT2, baseline, 204


title: Multiple myeloma, TT2, baseline, 208


title: Multiple myeloma, TT2, baseline, 211


title: Multiple myeloma, TT2, baseline, 217


title: Multiple myeloma, TT2, baseline, 215


title: Multiple myeloma, TT2, baseline, 214


title: Multiple myeloma, TT2, baseline, 216


title: Multiple myeloma, TT2, baseline, 218


title: Multiple myeloma, TT2, baseline, 202


title: Multiple myeloma, TT2, baseline, 205


title: Multiple myeloma, TT2, baseline, 200


title: Multiple myeloma, TT2, baseline, 206


title: Multiple myeloma, TT2, baseline, 198


title: Multiple myeloma, TT2, baseline, 199


title: Multiple myeloma, TT2, baseline, 203


title: Multiple myeloma, TT2, baseline, 196


title: Multiple myeloma, TT2, baseline, 195


title: Multiple myeloma, TT2, baseline, 197


title: Multiple myeloma, TT2, baseline, 201


title: Multiple myeloma, TT2, baseline, 194


title: Multiple myeloma, TT2, baseline, 192


title: Multiple myeloma, TT2, baseline, 184


title: Multiple myeloma, TT2, baseline, 193


title: Multiple myeloma, TT2, baseline, 187


title: Multiple myeloma, TT2, baseline, 191


title: Multiple myeloma, TT2, baseline, 189


title: Multiple myeloma, TT2, baseline, 181


title: Multiple myeloma, TT2, baseline, 173


title: Multiple myeloma, TT2, baseline, 182


title: Multiple myeloma, TT2, baseline, 177


title: Multiple myeloma, TT2, baseline, 183


title: Multiple myeloma, TT2, baseline, 174


title: Multiple myeloma, TT2, baseline, 167


title: Multiple myeloma, TT2, baseline, 178


title: Multiple myeloma, TT2, baseline, 190


title: Multiple myeloma, TT2, baseline, 186


title: Multiple myeloma, TT2, baseline, 188


title: Multiple myeloma, TT2, baseline, 172


title: Multiple myeloma, TT2, baseline, 180


title: Multiple myeloma, TT2, baseline, 176


title: Multiple myeloma, TT2, baseline, 185


title: Multiple myeloma, TT2, baseline, 171


title: Multiple myeloma, TT2, baseline, 164


title: Multiple myeloma, TT2, baseline, 169


title: Multiple myeloma, TT2, baseline, 170


title: Multiple myeloma, TT2, baseline, 168


title: Multiple myeloma, TT2, baseline, 166


title: Multiple myeloma, TT2, baseline, 175


title: Multiple myeloma, TT2, baseline, 163


title: Multiple myeloma, TT2, baseline, 165


title: Multiple myeloma, TT2, baseline, 162


title: Multiple myeloma, TT2, baseline, 161


title: Multiple myeloma, TT2, baseline, 160


title: Multiple myeloma, TT2, baseline, 157


title: Multiple myeloma, TT2, baseline, 149


title: Multiple myeloma, TT2, baseline, 150


title: Multiple myeloma, TT2, baseline, 152


title: Multiple myeloma, TT2, baseline, 148


title: Multiple myeloma, TT2, baseline, 139


title: Multiple myeloma, TT2, baseline, 143


title: Multiple myeloma, TT2, baseline, 151


title: Multiple myeloma, TT2, baseline, 153


title: Multiple myeloma, TT2, baseline, 156


title: Multiple myeloma, TT2, baseline, 141


title: Multiple myeloma, TT2, baseline, 138


title: Multiple myeloma, TT2, baseline, 144


title: Multiple myeloma, TT2, baseline, 136


title: Multiple myeloma, TT2, baseline, 158


title: Multiple myeloma, TT2, baseline, 147


title: Multiple myeloma, TT2, baseline, 145


title: Multiple myeloma, TT2, baseline, 134


title: Multiple myeloma, TT2, baseline, 137


title: Multiple myeloma, TT2, baseline, 135


title: Multiple myeloma, TT2, baseline, 146


title: Multiple myeloma, TT2, baseline, 140


title: Multiple myeloma, TT2, baseline, 133


title: Multiple myeloma, TT2, baseline, 159


title: Multiple myeloma, TT2, baseline, 142


title: Multiple myeloma, TT2, baseline, 154


title: Multiple myeloma, TT2, baseline, 132


title: Multiple myeloma, TT2, baseline, 128


title: Multiple myeloma, TT2, baseline, 130


title: Multiple myeloma, TT2, baseline, 155


title: Multiple myeloma, TT2, baseline, 125


title: Multiple myeloma, TT2, baseline, 131


title: Multiple myeloma, TT2, baseline, 127


title: Multiple myeloma, TT2, baseline, 124


title: Multiple myeloma, TT2, baseline, 123


title: Multiple myeloma, TT2, baseline, 121


title: Multiple myeloma, TT2, baseline, 126


title: Multiple myeloma, TT2, baseline, 113


title: Multiple myeloma, TT2, baseline, 122


title: Multiple myeloma, TT2, baseline, 114


title: Multiple myeloma, TT2, baseline, 117


title: Multiple myeloma, TT2, baseline, 116


title: Multiple myeloma, TT2, baseline, 118


title: Multiple myeloma, TT2, baseline, 120


title: Multiple myeloma, TT2, baseline, 110


title: Multiple myeloma, TT2, baseline, 106


title: Multiple myeloma, TT2, baseline, 129


title: Multiple myeloma, TT2, baseline, 111


title: Multiple myeloma, TT2, baseline, 108


title: Multiple myeloma, TT2, baseline, 107


title: Multiple myeloma, TT2, baseline, 104


title: Multiple myeloma, TT2, baseline, 105


title: Multiple myeloma, TT2, baseline, 109


title: Multiple myeloma, TT2, baseline, 112


title: Multiple myeloma, TT2, baseline, 103


title: Multiple myeloma, TT2, baseline, 102


title: Multiple myeloma, TT2, baseline, 101


title: Multiple myeloma, TT2, baseline, 115


title: Multiple myeloma, TT2, baseline, 94


title: Multiple myeloma, TT2, baseline, 85


title: Multiple myeloma, TT2, baseline, 93


title: Multiple myeloma, TT2, baseline, 92


title: Multiple myeloma, TT2, baseline, 96


title: Multiple myeloma, TT2, baseline, 90


title: Multiple myeloma, TT2, baseline, 89


title: Multiple myeloma, TT2, baseline, 100


title: Multiple myeloma, TT2, baseline, 88


title: Multiple myeloma, TT2, baseline, 83


title: Multiple myeloma, TT2, baseline, 91


title: Multiple myeloma, TT2, baseline, 84


title: Multiple myeloma, TT2, baseline, 95


title: Multiple myeloma, TT2, baseline, 79


title: Multiple myeloma, TT2, baseline, 86


title: Multiple myeloma, TT2, baseline, 78


title: Multiple myeloma, TT2, baseline, 72


title: Multiple myeloma, TT2, baseline, 76


title: Multiple myeloma, TT2, baseline, 97


title: Multiple myeloma, TT2, baseline, 75


title: Multiple myeloma, TT2, baseline, 81


title: Multiple myeloma, TT2, baseline, 74


title: Multiple myeloma, TT2, baseline, 73


title: Multiple myeloma, TT2, baseline, 87


title: Multiple myeloma, TT2, baseline, 82


title: Multiple myeloma, TT2, baseline, 99


title: Multiple myeloma, TT2, baseline, 98


title: Multiple myeloma, TT2, baseline, 71


title: Multiple myeloma, TT2, baseline, 119


title: Multiple myeloma, TT2, baseline, 66


title: Multiple myeloma, TT2, baseline, 63


title: Multiple myeloma, TT2, baseline, 65


title: B149_bleo_5d_bleoskin, bleomycin treated

city: Hanover

first: Michael

last: Whitfield

state: New Hampshire

address: 710 Remsen 74 College Street

department: Genetics

institute: Geisel School of Medicine at Dartmouth

description: 5-day post bleomycin treatment

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Mouse Genome microarrays

scan_protocol: Scanned on Axon scanner

data_processing: Images were quantified using GenePixPro

organism: Mus musculus

source_name: Cell line

label_protocol: 200ng of total RNA was reversed transcribed using Agilent Quick-Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Skin total RNA was extracted using Qiagen Rneasy mini fibrous kit

tag: cell line

value: UMR

source_name: Skin

value: Skin

value: 5-day post bleomycin treatment


title: Multiple myeloma, TT2, baseline, 67

value: multiple myeloma plasma cells


title: Multiple myeloma, TT2, baseline, 61


title: B153_PBS_21d_bleoskin, PBS treated

description: 21-day post PBS treatment

value: 21-day post PBS treatment


title: B156_bleo_21d_bleoskin, bleomycin treated

description: 21-day post bleomycin treatment

value: 21-day post bleomycin treatment


title: B154_PBS_21d_bleoskin, PBS treated

description: 21-day post PBS treatment


title: B146_bleo_5d_bleoskin, bleomycin treated

description: 5-day post bleomycin treatment


title: Multiple myeloma, TT2, baseline, 68


title: Multiple myeloma, TT2, baseline, 58


title: Multiple myeloma, TT2, baseline, 55


title: Multiple myeloma, TT2, baseline, 60


title: B145_bleo_5d_bleoskin, bleomycin treated

description: 5-day post bleomycin treatment


title: Multiple myeloma, TT2, baseline, 62


title: B158_bleo_21d_bleoskin, bleomycin treated

description: 21-day post bleomycin treatment


title: Multiple myeloma, TT2, baseline, 59


title: B149a_bleo_5d_bleoskin, bleomycin treated

description: 5-day post bleomycin treatment


title: B159_bleo_21d_bleoskin, bleomycin treated

description: 21-day post bleomycin treatment


title: Multiple myeloma, TT2, baseline, 69


title: B155_bleo_21d_bleoskin, bleomycin treated

description: 21-day post bleomycin treatment


title: Multiple myeloma, TT2, baseline, 56


title: Multiple myeloma, TT2, baseline, 64


title: Multiple myeloma, TT2, baseline, 57


title: B148_bleo_5d_bleoskin, bleomycin treated

description: 5-day post bleomycin treatment


title: B157_bleo_21d_bleoskin, bleomycin treated

description: 21-day post bleomycin treatment


title: Multiple myeloma, TT2, baseline, 54


title: Multiple myeloma, TT2, baseline, 53


title: B144_PBS_5d_bleoskin, PBS treated

description: 5-day post PBS treatment

value: 5-day post PBS treatment


title: Multiple myeloma, TT2, baseline, 49


title: Multiple myeloma, TT2, baseline, 51


title: Multiple myeloma, TT2, baseline, 50


title: B151_PBS_21d_bleoskin, PBS treated

description: 21-day post PBS treatment


title: B143_PBS_5d_bleoskin, PBS treated

description: 5-day post PBS treatment


title: Tsk2 transgenic 4month old TSK2_4month_9869-1

description: Tsk2 mouse skin, 4month of age

tag: genotype/variation

tag: skin age

value: 4 month


title: Tsk2 transgenic 4month old TSK2_4month_9919-1 (rep1)

description: Tsk2 mouse skin, 4month of age


title: B150_PBS_21d_bleoskin, PBS treated

description: 21-day post PBS treatment


title: B152_PBS_21d_bleoskin, PBS treated

description: 21-day post PBS treatment


title: Multiple myeloma, TT2, baseline, 48


title: Tsk2 transgenic 4month old TSK2_4month_9919-2

description: Tsk2 mouse skin, 4month of age


title: Multiple myeloma, TT2, baseline, 42


title: Multiple myeloma, TT2, baseline, 44


title: B140_PBS_5d_bleoskin, PBS treated

description: 5-day post PBS treatment


title: B142_PBS_5d_bleoskin, PBS treated

description: 5-day post PBS treatment


title: Tsk2 transgenic 4month old TSK2_4month_9920-1

description: Tsk2 mouse skin, 4month of age


title: Multiple myeloma, TT2, baseline, 52


title: Tsk2 transgenic 4month old TSK2_4month_9919-1

description: Tsk2 mouse skin, 4month of age


title: Tsk2 transgenic 1month old TSK2_1month_10121-2

description: Tsk2 mouse skin, 1 month of age

value: 1 month


title: Multiple myeloma, TT2, baseline, 41


title: B141_PBS_5d_bleoskin, PBS treated

description: 5-day post PBS treatment


title: Multiple myeloma, TT2, baseline, 47


title: Multiple myeloma, TT2, baseline, 43


title: Multiple myeloma, TT2, baseline, 45


title: Multiple myeloma, TT2, baseline, 46


title: Multiple myeloma, TT2, baseline, 40


title: Multiple myeloma, TT2, baseline, 70


title: Tsk2 transgenic 1month old TSK2_1month_10121-1

description: Tsk2 mouse skin, 1 month of age


title: Multiple myeloma, TT2, baseline, 39


title: Multiple myeloma, TT2, baseline, 37


title: Multiple myeloma, TT2, baseline, 35


title: Tsk2 transgenic 1month old TSK2_1month_10120-2

description: Tsk2 mouse skin, 1 month of age


title: Tsk2 transgenic 1month old TSK2_1month_10120-1

description: Tsk2 mouse skin, 1 month of age


title: Multiple myeloma, TT2, baseline, 33


title: K8PIK TU-4

city: Bruxelles

first: Alexandra

last: Van Keymeulen

address: 808, route de Lennik CP602

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

description: Gene expression of tumor cells of K8CREERT2/PIK3CA-H1047R/RosaYFP mice , replicate 4

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix MG-430 PM arrays  according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: The data were analyzed with R (version 2.14.0) Bioconductor fRMA (version 1.6) package with default analysis settings.

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent).  All following steps were carried out at the IRB Functional Genomic Core (Barcelona) according to the manufacturers protocol (Affymetrix)

growth_protocol: Mice were maintained in a certified animal house according to European guidelines

extract_protocol: Qiagen Rneasy Micro

treatment_protocol: Female mice were injected with 3 times with 5 mg of tamoxifen every three days starting at age of 4-5 week. Mice were sacrified at the indicated time point and mammary gland was digested in Collagenase+hyaluronidase. Single cells were stained with the appropriate antibodies and FACS sorted before RNA extraction.

value: Mouse mammary gland FACS purified tumour cells


title: Tsk1 transgenic, TSK1_2-2

description: Tsk1/+ mouse skin


title: Tsk1 transgenic, TSK1_1-1

description: Tsk1/+ mouse skin


title: K8PIK TU-7

description: Gene expression of tumor cells of K8CREERT2/PIK3CA-H1047R/RosaYFP mice , replicate 7


title: Tsk1 transgenic, TSK1_2-1

description: Tsk1/+ mouse skin


title: Tsk1 transgenic, TSK1_1-2

description: Tsk1/+ mouse skin


title: K8PIK TU-5

description: Gene expression of tumor cells of K8CREERT2/PIK3CA-H1047R/RosaYFP mice , replicate 5


title: Multiple myeloma, TT2, baseline, 36


title: Multiple myeloma, TT2, baseline, 30


title: K8PIK TU-1

description: Gene expression of tumor cells of K8CREERT2/PIK3CA-H1047R/RosaYFP mice , replicate 1


title: K8PIK TU-2

description: Gene expression of tumor cells of K8CREERT2/PIK3CA-H1047R/RosaYFP mice , replicate 2


title: Multiple myeloma, TT2, baseline, 29


title: Multiple myeloma, TT2, baseline, 32


title: Multiple myeloma, TT2, baseline, 26


title: Multiple myeloma, TT2, baseline, 34


title: K8PIK TU-6

description: Gene expression of tumor cells of K8CREERT2/PIK3CA-H1047R/RosaYFP mice , replicate 6


title: Multiple myeloma, TT2, baseline, 31


title: Multiple myeloma, TT2, baseline, 24


title: K8PIK TU-3

description: Gene expression of tumor cells of K8CREERT2/PIK3CA-H1047R/RosaYFP mice , replicate 3


title: Multiple myeloma, TT2, baseline, 38


title: Multiple myeloma, TT2, baseline, 28


title: Multiple myeloma, TT2, baseline, 27


title: Multiple myeloma, TT2, baseline, 25


title: K8PIKp53 TU-1

description: Gene expression of tumor cells of K8CREERT2/PIK3CA-H1047R/p53flox/flox/RosaYFP mice , replicate 1


title: K5PIK TU-3

description: Gene expression of tumor cells of K5CREERT2/PIK3CA-H1047R/RosaYFP mice , replicate 3


title: Multiple myeloma, TT2, baseline, 23


title: Multiple myeloma, TT2, baseline, 22


title: Basal-K5PIK-10m-1

description: Gene expression of YFP+basal cells of K5CREERT2/PIK3CA-H1047R/RosaYFP mice 10m following tamoxifen administration, replicate 1

value: Mouse mammary gland FACS purified basal cells


title: K5PIK TU-2

description: Gene expression of tumor cells of K5CREERT2/PIK3CA-H1047R/RosaYFP mice , replicate 2


title: K5PIK TU-1

description: Gene expression of tumor cells of K5CREERT2/PIK3CA-H1047R/RosaYFP mice , replicate 1


title: Multiple myeloma, TT2, baseline, 21


title: Basal-K8PIK-8w-2

description: Gene expression of YFP+ basal cells of K8CREERT2/PIK3CA-H1047R/RosaYFP mice 8w following tamoxifen administration, replicate 2


title: Multiple myeloma, TT2, baseline, 19


title: Luminal-K5PIK-10m-2

description: Gene expression of YFP+ luminal cells of K5CREERT2/PIK3CA-H1047R/RosaYFP mice 10m following tamoxifen administration, replicate 2

value: Mouse mammary gland FACS purified luminal cells


title: Basal-K5PIK-10m-2

description: Gene expression of YFP+ basal cells of K5CREERT2/PIK3CA-H1047R/RosaYFP mice 10m following tamoxifen administration, replicate 2


title: Multiple myeloma, TT2, baseline, 20


title: Basal-K8PIK-8w-1

description: Gene expression of YFP+ basal cells of K8CREERT2/PIK3CA-H1047R/RosaYFP mice 8w following tamoxifen administration, replicate 1


title: Multiple myeloma, TT2, baseline, 16

description: Gene expression data from multiple myeloma plasma cells at baseline.


title: Multiple myeloma, TT2, baseline, 17


title: K8PIKp53 TU-2

description: Gene expression of tumor cells of K8CREERT2/PIK3CA-H1047R/p53flox/flox/RosaYFP mice , replicate 2


title: Multiple myeloma, TT2, baseline, 13


title: Luminal-K8PIK-8w-2

description: Gene expression of YFP+ luminal cells of K8CREERT2/PIK3CA-H1047R/RosaYFP mice 8w following tamoxifen administration, replicate 2


title: Multiple myeloma, TT2, baseline, 15


title: Multiple myeloma, TT2, baseline, 11


title: Luminal-K8PIK-8w-1

description: Gene expression of YFP+ luminal cells of K8CREERT2/PIK3CA-H1047R/RosaYFP mice 8w following tamoxifen administration, replicate 1


title: Multiple myeloma, TT2, baseline, 9


title: Basal-K5YFP-10m-2

description: Gene expression of YFP+ basal cells of K5CREERT2/RosaYFP mice 10m following tamoxifen administration, replicate 2


title: Multiple myeloma, TT2, baseline, 18


title: Basal-K5YFP-10m-1

description: Gene expression of YFP+ basal cells of K5CREERT2/RosaYFP mice 10m following tamoxifen administration, replicate 1


title: Luminal-K5PIK-10m-1

description: Gene expression of YFP+ luminal cells of K5CREERT2/PIK3CA-H1047R/RosaYFP mice 10m following tamoxifen administration, replicate 1


title: Luminal-K8YFP-10m-2

description: Gene expression of YFP+ luminal cells of K8CREERT2/RosaYFP mice 10m following tamoxifen administration, replicate 2


title: Multiple myeloma, TT2, baseline, 12


title: Multiple myeloma, TT2, baseline, 14


title: Multiple myeloma, TT2, baseline, 10


title: Luminal-K8YFP-10m-1

description: Gene expression of YFP+ luminal cells of K8CREERT2/RosaYFP mice 10m following tamoxifen administration, replicate 1


title: Multiple myeloma, TT2, baseline, 7


title: Multiple myeloma, TT3, relapse, 15

description: Gene expression data from multiple myeloma plasma cells at relapse.

value: relapse


title: Multiple myeloma, TT2, baseline, 4


title: Multiple myeloma, TT2, baseline, 8


title: Multiple myeloma, TT3, relapse, 12


title: Multiple myeloma, TT3, relapse, 13


title: Tsk2 transgenic 1month old TSK2_1month_10120-1 (rep1)

description: Tsk2 mouse skin, 1 month of age


title: Multiple myeloma, TT3, relapse, 10


title: Multiple myeloma, TT3, relapse, 11


title: Multiple myeloma, TT2, baseline, 1


title: Multiple myeloma, OtherTreatments, relapse, 98

source_name: Multiple myeloma plasma cells, other treatments, relapse

value: other


title: Multiple myeloma, TT3, relapse, 18


title: Multiple myeloma, TT2, baseline, 5


title: Multiple myeloma, TT3, relapse, 8


title: Multiple myeloma, TT2, baseline, 2


title: Multiple myeloma, TT3, relapse, 16


title: Multiple myeloma, OtherTreatments, relapse, 91


title: Multiple myeloma, OtherTreatments, relapse, 94


title: Multiple myeloma, TT2, baseline, 3


title: Multiple myeloma, TT3, relapse, 14


title: Multiple myeloma, OtherTreatments, relapse, 95


title: Multiple myeloma, TT2, baseline, 6


title: Multiple myeloma, OtherTreatments, relapse, 96


title: Multiple myeloma, OtherTreatments, relapse, 93


title: Multiple myeloma, OtherTreatments, relapse, 97


title: Multiple myeloma, TT3, relapse, 7


title: Multiple myeloma, TT3, relapse, 3


title: Multiple myeloma, OtherTreatments, relapse, 92


title: Multiple myeloma, TT3, relapse, 2


title: Multiple myeloma, OtherTreatments, relapse, 78


title: Multiple myeloma, OtherTreatments, relapse, 90


title: Multiple myeloma, OtherTreatments, relapse, 85


title: Multiple myeloma, OtherTreatments, relapse, 89


title: Multiple myeloma, OtherTreatments, relapse, 74


title: Multiple myeloma, OtherTreatments, relapse, 79


title: Multiple myeloma, OtherTreatments, relapse, 77


title: Multiple myeloma, OtherTreatments, relapse, 87


title: Multiple myeloma, OtherTreatments, relapse, 75


title: Multiple myeloma, OtherTreatments, relapse, 76


title: Multiple myeloma, OtherTreatments, relapse, 73


title: Multiple myeloma, OtherTreatments, relapse, 68


title: Multiple myeloma, OtherTreatments, relapse, 71


title: Multiple myeloma, OtherTreatments, relapse, 82


title: Multiple myeloma, OtherTreatments, relapse, 83


title: Multiple myeloma, OtherTreatments, relapse, 81


title: sk

city: guangzhou

first: Li

last: Changpeng

address: kai yuan road

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: This sample is of wild-type HCC cancer cell

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol.

scan_protocol: Scanning performed by using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.

source_name: liver cancer

label_protocol: For Cy3 labeling, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA).

growth_protocol: sk-hep-1 and sk-hep-1-shEZH2 were obtained from the American Type Culture Collection (Manassas, VA, USA) and cultured in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS; HyClone Laboratories).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen).RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: genotype

value: Wild-type


title: Multiple myeloma, OtherTreatments, relapse, 88


title: Multiple myeloma, OtherTreatments, relapse, 72


title: sks

description: This sample is of  HCC cancer cell with EZH2 knocked down

value: EZH2 knocked down


title: Multiple myeloma, OtherTreatments, relapse, 69


title: Multiple myeloma, OtherTreatments, relapse, 70


title: Multiple myeloma, OtherTreatments, relapse, 66


title: Multiple myeloma, OtherTreatments, relapse, 65


title: Multiple myeloma, OtherTreatments, relapse, 63


title: Multiple myeloma, OtherTreatments, relapse, 62


title: Multiple myeloma, OtherTreatments, relapse, 58


title: Multiple myeloma, OtherTreatments, relapse, 61


title: Multiple myeloma, OtherTreatments, relapse, 60


title: Multiple myeloma, OtherTreatments, relapse, 53


title: Multiple myeloma, OtherTreatments, relapse, 51


title: Multiple myeloma, OtherTreatments, relapse, 52


title: Multiple myeloma, OtherTreatments, relapse, 84


title: Multiple myeloma, OtherTreatments, relapse, 50


title: Multiple myeloma, OtherTreatments, relapse, 57


title: Multiple myeloma, OtherTreatments, relapse, 49


title: Multiple myeloma, OtherTreatments, relapse, 46


title: Multiple myeloma, OtherTreatments, relapse, 42


title: Multiple myeloma, OtherTreatments, relapse, 44


title: Multiple myeloma, OtherTreatments, relapse, 54


title: Multiple myeloma, OtherTreatments, relapse, 56


title: Multiple myeloma, OtherTreatments, relapse, 43


title: Multiple myeloma, OtherTreatments, relapse, 47


title: Multiple myeloma, OtherTreatments, relapse, 41


title: Multiple myeloma, OtherTreatments, relapse, 86


title: Multiple myeloma, OtherTreatments, relapse, 39


title: Multiple myeloma, OtherTreatments, relapse, 38


title: Multiple myeloma, OtherTreatments, relapse, 45


title: Multiple myeloma, OtherTreatments, relapse, 48


title: Multiple myeloma, OtherTreatments, relapse, 59


title: Multiple myeloma, OtherTreatments, relapse, 80


title: Multiple myeloma, OtherTreatments, relapse, 64


title: Multiple myeloma, OtherTreatments, relapse, 34


title: Multiple myeloma, OtherTreatments, relapse, 36


title: Multiple myeloma, OtherTreatments, relapse, 23


title: Multiple myeloma, OtherTreatments, relapse, 32


title: Multiple myeloma, OtherTreatments, relapse, 27


title: Multiple myeloma, OtherTreatments, relapse, 25


title: Multiple myeloma, OtherTreatments, relapse, 40


title: Multiple myeloma, OtherTreatments, relapse, 35


title: Multiple myeloma, OtherTreatments, relapse, 67


title: Multiple myeloma, OtherTreatments, relapse, 18


title: Multiple myeloma, OtherTreatments, relapse, 16


title: Multiple myeloma, OtherTreatments, relapse, 33


title: Multiple myeloma, OtherTreatments, relapse, 17


title: Multiple myeloma, OtherTreatments, relapse, 29


title: Multiple myeloma, OtherTreatments, relapse, 26


title: Multiple myeloma, OtherTreatments, relapse, 14


title: Multiple myeloma, OtherTreatments, relapse, 22


title: SSEA1- sorted fraction of porcine fetal fibroblasts - replicate 5

city: Frederiksberg C

first: Vanessa

last: Hall

address: Grønnegårdsvej 7

country: Denmark

institute: University of Copenhagen

description:
Gene expression data from porcine fetal fibroblasts sorted based on SSEA1 expression
SSEA1-R5

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: RMA normalization

organism: Sus scrofa

source_name: porcine fetal fibroblasts from day 24 Danish Landrace/Yorkshire x Duroc embryos

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from >23 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Porcine fetal fibroblasts were cultured in DMEM+10%FCS containing 1% penicillin/streptomycin and on 0.1% gelatin-coated dishes

extract_protocol: Total RNA was extracted using the Rneasy Microkit (Qiagen).

treatment_protocol: Fibroblasts were subjected to magnetic activated cell sorting according to manufacturer's instrunctions.

tag: breed

value: Danish Landrace/Yorkshire x Duroc

tag: age

value: fetal day 24

value: fetal tissue minus the head

value: fetal fibroblast

tag: sorted cell fraction


title: Multiple myeloma, OtherTreatments, relapse, 31

tag: cell type

value: multiple myeloma plasma cells


title: SSEA1- sorted fraction of porcine fetal fibroblasts - replicate 4

description:
Gene expression data from porcine fetal fibroblasts sorted based on SSEA1 expression
SSEA1-R4

tag: tissue


title: Multiple myeloma, OtherTreatments, relapse, 21


title: Multiple myeloma, OtherTreatments, relapse, 24


title: Multiple myeloma, OtherTreatments, relapse, 37


title: Multiple myeloma, OtherTreatments, relapse, 15


title: Multiple myeloma, OtherTreatments, relapse, 28


title: Multiple myeloma, OtherTreatments, relapse, 30


title: DLD-1 treated with MEK inhibitor

type: protein

city: Seoul

first: Dong-Hoon

last: Jin

address: 88 Olympicro-43gil, Songpa-gu

country: South Korea

institute: Asan Medical Center

description: protein from cells

hyb_protocol: Biotin labeled extract was hybridized with antibody-spotted slide for 2hr at room temperature. After hybridization, slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water. Detection Buffer including Cy3-Streptavidin (fullmoon Bio) was treated for 20min at room temperature. And slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water.

scan_protocol: Scanned on an Axon 4000B scanner.

data_processing: GenePix Software (v 6.1) was used for data extraction and Genowiz software (v 4.0.5.6) was used for global normalization.

molecule: protein

source_name: DLD-1 treated with MEK inhibitor

label_protocol: 50ug of cells extract was labeled with Biotin and label buffer (Fullmoon Bio).

growth_protocol: Cells were grown on RPMI1640 contained 10%FBS and 1% penicillin/streptomycin.

extract_protocol: 10~40mg of cells were washed with cold 1X PBS. And samples were homogenized with Extracting buffer (Fullmoon Bio). Debris was removed from cell extract with centrifuge.

treatment_protocol: Cells were seeded and then treated with MEK inhibitor (AZD6244) or not for 24 hrs.

value: colon cancer


title: DLD-1 control

description: protein from cells

source_name: DLD-1 control


title: Multiple myeloma, OtherTreatments, relapse, 19


title: Bacteroides thetaiotaomicron genomic DNA 2

type: genomic

city: Stanford

first: Justin

middle: L

last: Sonnenburg

address: Fairchild D315

department: Microbiology and Immunology

institute: Stanford University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The sample was used as genomic DNA control to determine whether the genomic DNA correctly bound to the probes and thus, was not included in data processing (i.e no processed/normalized data).

label: Biotin

molecule: genomic DNA

organism: Bacteroides thetaiotaomicron

source_name: bacterial

label_protocol: Enzo Biochemicals Bioarray terminal labeling kit

growth_protocol: Inoulation into germ-free mice. Cecal contents were removed and kept at -80C before extraction.

extract_protocol: Qiagen Rneasy mini column extraction, Ambion DNA free treatment

treatment_protocol: Qiagen RNA protect

tag: strain

value: Strain VPI-5482

value: in vitro culture


title: SW620 treated with MEK inhibitor

description: protein from cells

source_name: SW620 treated with MEK inhibitor


title: SW620 control

description: protein from cells

source_name: SW620 control


title: Multiple myeloma, OtherTreatments, relapse, 13


title: Bacteroides thetaiotaomicron genomic DNA 1


title: SSEA1- sorted fraction of porcine fetal fibroblasts - replicate 1

description:
Gene expression data from porcine fetal fibroblasts sorted based on SSEA1 expression
SSEA1-R1


title: Clostridium difficile genomic DNA 2

organism: Clostridioides difficile

value: Strain 630


title: Multiple myeloma, OtherTreatments, relapse, 12


title: Multiple myeloma, OtherTreatments, relapse, 9


title: Clostridium difficile genomic DNA 1


title: SSEA1- sorted fraction of porcine fetal fibroblasts - replicate 2

description:
Gene expression data from porcine fetal fibroblasts sorted based on SSEA1 expression
SSEA1-R2


title: Multiple myeloma, OtherTreatments, relapse, 10


title: SSEA1- sorted fraction of porcine fetal fibroblasts - replicate 3

description:
Gene expression data from porcine fetal fibroblasts sorted based on SSEA1 expression
SSEA1-R3


title: SSEA1+ sorted fraction of porcine fetal fibroblasts - replicate 1

description:
Gene expression data from porcine fetal fibroblasts sorted based on SSEA1 expression
SSEA1+R1


title: Multiple myeloma, OtherTreatments, relapse, 11


title: SSEA1+ sorted fraction of porcine fetal fibroblasts - replicate 2

description:
Gene expression data from porcine fetal fibroblasts sorted based on SSEA1 expression
SSEA1+R2


title: Multiple myeloma, OtherTreatments, relapse, 6


title: SSEA1+ sorted fraction of porcine fetal fibroblasts - replicate 3

description:
Gene expression data from porcine fetal fibroblasts sorted based on SSEA1 expression
SSEA1+R3


title: Flag leaves, heat stress, rep1

city: Beijing

first: zhenshan

last: liu

address: NO.2 Yuanmingyuan Xi Road,Haidian District

institute: China Agricultural University

description: wheat flag leaf of 10DAP under heat stress for 1 hour

hyb_protocol: Twenty micrograms of cRNA samples were fragmented and hybridized for 16 hours at 45°C to the Affymetrix Wheat Genome Array (Santa Clara, CA, USA) and then washing using the Genechip® Fluidics Station 450.

scan_protocol: The arrays were scanned using the Genechip® 3000 Scanner that is located in the Bioinformatics Center at China Agricultural University.

data_processing: Cell intensity (CEL) files for the Wheat Genome Array were normalized using Affymetrix Expression Console software (version 1.1) with the MAS 5.0 method.

organism: Triticum aestivum

source_name: wheat flag leaf, heat stress 1h

label_protocol: The biotin-labeled cRNA was made using the GeneChip® IVT Labelling Kit (Affymetrix, CA, USA).

growth_protocol: Wheat cultivar ‘TAM 107’ plants growing in the field were transferred to pots about one week before flowering and cultivated under normal condition.

treatment_protocol: Heat stress was applied by transferring the plants to a growth chamber with the temperature raised to 40℃ at ~10 DAP (Days After Pollination).

value: flag leaf

tag: cultivar

value: 10 DAP


title: Clostridium difficile response in cecum of Bt-monoassociated mice fed polysaccharide deficient diet 3

data_processing: The raw data were RMA-MS normalized using R-2.9.1. and log2 transformed, excluding other species present on chip.


title: Multiple myeloma, OtherTreatments, relapse, 4

tag: treatment


title: Multiple myeloma, OtherTreatments, relapse, 8

tag: time of testing


title: Multiple myeloma, OtherTreatments, relapse, 7


title: SSEA1+ sorted fraction of porcine fetal fibroblasts - replicate 5

description:
Gene expression data from porcine fetal fibroblasts sorted based on SSEA1 expression
SSEA1+R5


title: SSEA1+ sorted fraction of porcine fetal fibroblasts - replicate 4

description:
Gene expression data from porcine fetal fibroblasts sorted based on SSEA1 expression
SSEA1+R4


title: Multiple myeloma, OtherTreatments, relapse, 5


title: Multiple myeloma, OtherTreatments, relapse, 1


title: Flag leaves, control, rep2

description: wheat flag leaf of 10DAP under normal growth condition

source_name: wheat flag leaf, normal condition


title: Clostridium difficile response in cecum of Bt-monoassociated mice fed polysaccharide deficient diet 4


title: pH 6_7_U1_2

city: Zurich

first: Cheryl

last: de Valliere

address: Steinwartstrasse 14

country: Switzerland

institute: University Hospital Zurich

hyb_protocol: Array hybridization and washing were performed on a Gene Atlas Instrument according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual (Rev. 2).

scan_protocol: Arrays were scanned with Affymetrix's Gene Atlas Instrument (Control Software Version 1.0)

data_processing: Data was summarized with RMA using R/bioconductor (R version 2.15.2 and Bioconductor version 2.11)

source_name: OGR1 stable overexpressing pH 6.7

growth_protocol: Caco-2 cells were cultured in RPMI 1640, 10% FCS

extract_protocol: Qiagen Rneasy mini kit, DNase treatment followed by high-capacity reverse cDNA transcription (Applied Biosystems)

treatment_protocol: 24hrs at acidic (6.7) or control (7.8) pH

value: colon adenoma cell line

value: overexpressing OGR1 (U1)


title: Clostridium difficile response in cecum of Bt-monoassociated mice fed polysaccharide deficient diet 2


title: pH 6_7_U1_3


title: Multiple myeloma, OtherTreatments, relapse, 3

value: relapse


title: Flag leaves, heat stress, rep2


title: Multiple myeloma, TT2, relapse, 127

source_name: Multiple myeloma plasma cells, TT2, relapse


title: Multiple myeloma, TT2, relapse, 126


title: Multiple myeloma, OtherTreatments, relapse, 2

value: other


title: Flag leaves, control, rep1


title: Multiple myeloma, OtherTreatments, relapse, 20


title: pH 7_8_U1_3

source_name: OGR1 stable overexpressing pH 7.8


title: Multiple myeloma, TT2, relapse, 125


title: Clostridium difficile response in cecum of germ-free mice fed polysaccharide deficient diet 4


title: pH 7_8_U1_2


title: Clostridium difficile response in cecum of germ-free mice fed polysaccharide deficient diet 1


title: Clostridium difficile response in cecum of Bt-monoassociated mice fed standard, polysaccharide rich diet 4


title: Clostridium difficile response in cecum of Bt-monoassociated mice fed standard, polysaccharide rich diet 3


title: Clostridium difficile response in cecum of germ-free mice fed polysaccharide deficient diet 2


title: Clostridium difficile response in cecum of germ-free mice fed polysaccharide deficient diet 3


title: Clostridium difficile response in cecum of Bt-monoassociated mice fed standard, polysaccharide rich diet 2


title: Multiple myeloma, TT2, relapse, 123


title: Clostridium difficile response in cecum of germ-free mice fed standard, polysaccharide rich diet 4


title: pH 6_7_U1_1


title: Multiple myeloma, TT2, relapse, 119


title: Clostridium difficile response in cecum of Bt-monoassociated mice fed standard, polysaccharide rich diet 1


title: pH 7_8_U1_1


title: Multiple myeloma, TT2, relapse, 121


title: Multiple myeloma, TT2, relapse, 124


title: Multiple myeloma, TT2, relapse, 117


title: pH 7_8_VC_3

source_name: vector control pH 7.8

value: vector control (VC)


title: Multiple myeloma, TT2, relapse, 122


title: Multiple myeloma, TT2, relapse, 116


title: Multiple myeloma, OtherTreatments, relapse, 55


title: pH 6_7_VC_3

source_name: vector control pH 6.7


title: Multiple myeloma, TT2, relapse, 118


title: pH 6_7_VC_2


title: Multiple myeloma, TT2, relapse, 120


title: pH 6_7_VC_1


title: pH 7_8_VC_2


title: Clostridium difficile response in cecum of germ-free mice fed standard, polysaccharide rich diet 3


title: Clostridium difficile response in cecum of germ-free mice fed standard, polysaccharide rich diet 2


title: Clostridium difficile response in cecum of germ-free mice fed standard, polysaccharide rich diet 1


title: pH 7_8_VC_1


title: Multiple myeloma, TT2, relapse, 114


title: Multiple myeloma, TT2, relapse, 115


title: Multiple myeloma, TT2, relapse, 113


title: Multiple myeloma, TT2, relapse, 112


title: Multiple myeloma, TT2, relapse, 109


title: Multiple myeloma, TT2, relapse, 107


title: Clostridium difficile response in cecum of Bt-monoassociated mice fed polysaccharide deficient diet 1


title: Multiple myeloma, TT2, relapse, 108


title: Multiple myeloma, TT2, relapse, 110


title: Multiple myeloma, TT2, relapse, 106


title: Multiple myeloma, TT2, relapse, 104


title: Multiple myeloma, TT2, relapse, 102


title: HCT116 wildtype

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

country: Netherlands

institute: University Medical Center Utrecht

description: Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a iScan (Illumina).

data_processing: Data processing was done using GenomeStudio (Illumina)

label: Biotin (C, G), DNP (A,T)

source_name: DNA from cultured cells

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (MSM) and primer/neutralization mix (MA1-MA2-0.1N NaOH). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

value: Human colon cancer cells

tag: transferred chromosome

value: not applicable

tag: ploidy

value: diploid


title: Multiple myeloma, TT2, relapse, 100


title: Multiple myeloma, TT2, relapse, 105


title: Multiple myeloma, TT2, relapse, 103


title: Multiple myeloma, TT2, relapse, 99


title: RPE1 wildtype

value: Human retinal pigment epithelial cells


title: HCT116 H2B-GFP chr 8/3 clone 26


title: Multiple myeloma, TT2, relapse, 101


title: Multiple myeloma, TT2, relapse, 97


title: HCT116 H2B-GFP chr 8/3 clone 16


title: HCT116 H2B-GFP chr 8/3 clone 12


title: Multiple myeloma, TT2, relapse, 96


title: Multiple myeloma, TT2, relapse, 95


title: HCT116 H2B-GFP chr 8/3 clone 27


title: Multiple myeloma, TT2, relapse, 94


title: HCT116 H2B-GFP chr 5/3 clone 17


title: Multiple myeloma, TT2, relapse, 98


title: HCT116 H2B-GFP chr 8/3 clone 14


title: HCT116 H2B-GFP chr 8/3 clone 13


title: Multiple myeloma, TT2, relapse, 111


title: HCT116 H2B-GFP chr 8/3 clone 19


title: HCT116 H2B-GFP chr 5/3 clone 19


title: HCT116 H2B-GFP chr 8/3 clone 15


title: RPE1 H2B-GFP chr 3/3 clone 2


title: RPE1 H2B-GFP chr 21/3 clone 2


title: HCT116 H2B-GFP chr 5/3 clone 18


title: HCT116 H2B-GFP chr 8/3 clone 11


title: RPE1 chr 5/3 clone 3


title: RPE1 chr 5/3 clone 7


title: Multiple myeloma, TT2, relapse, 88


title: Multiple myeloma, TT2, relapse, 86


title: Multiple myeloma, TT2, relapse, 89


title: Multiple myeloma, TT2, relapse, 87


title: row pool 16_long arm of chromosome 5A

city: Fiorenzuola d'Arda

first: Delfina

last: Barabaschi

address: Via San Protaso 302

country: Italy

institute: CRA-Genomics Research Centre

description:
raw data file: chip15_680.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.

hyb_protocol: After a cooling step on ice of 3 min, non-reacted ULS-Cy3 were removed through KREApureTM columns (Kreatech Biotechnology) and the yield and degree of labeling was evaluated by the Nanodrop ND-1000. Hybridizations and washing were performed as recommended (Agilent Oligonucleotide Array-Based cgh for Genomic DNA Analysis v3.4).

scan_protocol: Scanning was performed on a Axon GenePix 4000A scanner.

data_processing: Data extraction was carried out using the GenePix Pro 7 software.

source_name: 3D-pool of BAC clones of chromosome 5A

label_protocol: Briefly, 450 ng of DNA polymerase amplified DNA of each pool was fragmented for 10 min at 95°C and then labeled with Cy3 using the Genomic DNA ULS Labeling Kit according to manufacturer instructions (Agilent Technologies).

growth_protocol: BAC clones colonies (5,412 for 5AS and 8,709 for 5AL) were individually growth in 2YT media supplemented with 12.5 μg/mL chloramphenicol. The plate pools (PPs), column pools (CPs) and row pools (RPs) (15, 24, 16 for 5AS and 23, 24,16 for 5AL respectively) were obtained by mixing 10 μl of each bacterial culture, then adding 1 mL of fresh medium and growing for 16 h at 37°C.

extract_protocol: DNA from each pool was obtained employing the phi29 DNA polymerase rolling circle amplification (GenomiPhi V2 DNA Polymerase Kit, GE Healthcare, Dean et al, 2001). Briefly, 1 μl of each BAC pool was denatured in 9 μl sample buffer at 95°C for 5 min and then cooled on ice for 5 min. The denatured samples were mixed with 1 μl GenomiPhi phi29 DNA polymerase and 9 μl reaction buffer, and then incubated at 30°C for 2 hours; reaction was terminated at 65°C for 10 min.

value: Chinese spring

tag: chromosome arm

value: long arm


title: Multiple myeloma, TT2, relapse, 93

description: Gene expression data from multiple myeloma plasma cells at relapse.

value: multiple myeloma plasma cells


title: row pool 15_long arm of chromosome 5A

description:
raw data file: chip13_650.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HCT116 H2B-GFP chr 5/3 clone 14


title: Multiple myeloma, TT2, relapse, 90


title: Multiple myeloma, TT2, relapse, 91


title: HCT116 H2B-GFP chr 5/3 clone 11


title: row pool 14_long arm of chromosome 5A

description:
raw data file: chip15_680.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 92


title: 3832-TSI vs 3832-T

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

description:
3832-T = control siRNA
3832-TSI = IE siRNA

hyb_protocol: Hybridization protocol II. Prehybridization 1. Prepare Prehybridization Solution (Fresh Each Time) **this volume is based on a glass dish with a base measurement of 11x8cm. This dish allows for a pre-hyb of 1-4 slides. Adjust volume accordingly based on size of dish and/or number of slides. 106.0ml dH2O 3.0g BSA 1.2ml 10%SDS 2. Add Prehybridization solution to a glass slide-staining dish and place post-processed slides array side up into solution. Make sure there are no bubbles on the surfaces of the slides. 3. Place the staining jar containing the Prehybridization solution and slides into a waterbath and hybridize for 1 hour at 42oC. 4. Take the prehybridized slides out of the Prehybridization solution and place into a slide holder submerged in a slide-washing tray containing nuclease-free water. Wash slides for 2 minutes with constant shaking up and down. 5. Transfer slide rack to a slide washing tray containing isopropanol and wash for 2 minutes with constant shaking up and down. 6. Take the slides in the isopropanol bath to the centrifuge to keep the slides wet until you can dry them rapidly. Spin at 600 RPM in a 50ml conical for 3 minutes to dry. **Complete this step within one hour of hybridization III. Hybridization 1. Add the following to the 4.5µl labeled sample. 0.5µl 10 mg/ml tRNA 0.5ul 10mg/ml Salmon Sperm DNA 1.0µl 20X SSC 2.5ul Formamide 1.0µl 1% SDS 2. Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg. Let cool for 5 min. 3. Pipette cooled 10µl hybridization solution on microarray. Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate). 4. OPTIONAL: Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement. This step is recommended if your waterbath is not perfectly level. 5. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath **Bubbles (esp. large ones) can be troublesome for your arrays since they can cause areas of non-hybridization. To avoid bubbles, do not use the blowout feature of the pipette when adding the probe to the slide. Also, clean your coverslips with alcohol and lint-free wipes before placing over probe. IV. Post Hyb washes (next day) 1. Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking. 2. Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking. 3. Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry. Scan immediately.

scan_protocol: After washing, the arrays were scanned with a GenePix4200AL scanner (Molecular Devices, Sunnyvale, CA). The images were processed using GenePix 6.1 and the resulting text files were exported to Microsoft Excel.

data_processing: A normalization factor was calculated using 36 human control genes by dividing the median intensity of the Cy5 signal by the median intensity of Cy3 signal of the controls. The data were normalized by multiplying the Cy3 signal of each spot by the normalization factor. The ratio of the Cy5 median intensity over the Cy3 median intensity was determined for each spot and the average ratio determined for the replicate spots.

source_name: Primary Human Glioblastoma surgical resection

label_protocol: I. Synthesis and Labeling of cDNA:  (1) Bring 1.5µg of RNA to a volume of 11µl (in a PCR tube) with nucleotide-free water and add 2.2µl (2mg/ml) random primers (pulse spin to collect contents).   (2) Heat 2 min at 98oC, snap cool on ice.  (3) (Keep on ice) and add 11.1µl of the following reaction mix: 5.0µl 5X First-Strand buffer 2.5µl 100 mM DTT 2.3µl low dTdNTP mix (5mM A,G,C and 0.2mM T stock) 1.5ul Cy3 or Cy5 Then add 1.2ul Superscript, vortex to mix and spin to collect contents.    (4) Incubate 10 min at 25oC followed by 90 min at 42oC in PCR machine. **Can freeze or leave at 4oC overnight if necessary.   (5) Prime an Amicon Ultra 10K column (Ultracel-10K from Millipore) with 400µl of 25% TE and spin for 5 min at 14,000 Xg.  Empty flow-through from collection tube and return primed column.  Add another 400ul of 25% TE followed by both reactions (cy3 and cy5) to column and centrifuge at 14,000 Xg for 7 min.  Empty flow-through, and add yet another 400ul of 25% TE, centrifuge at 14,000 Xg for 7 min.  Empty flow-through once more, add 400ul of 25% TE and centrifuge at 14,000 Xg for 12 min.  Empty the flow-through.  (6) Recover cDNA by inverting Amicon filter into the same collection tube and centrifuge at 1,000 Xg for 2 min.  (7) Using a speedvac, concentrate sample to 4.5ul.

growth_protocol: Primary GBM lines were grown as neurospheres in Neural Basal Media + 20ng/ml FGF and EGF.

extract_protocol: RNA was extracted using the Qiagen Rneasy kit, according to the manufacturer's instructions

treatment_protocol: 40 nM final concentration of control siRNA and IE1 siRNA (2 duplexes)+ 6 ul Lipofectamine was added to triplicate wells and RNA was harvested 48-72h later

value: Brain Tumor

value: glioblastoma


title: row pool 13_long arm of chromosome 5A

description:
raw data file: chip15_680.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HCT116 H2B-GFP chr 5/3 clone 12


title: row pool 12_long arm of chromosome 5A

description:
raw data file: chip11_640.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: 0609-TSI vs 0609-T

description:
0609-T = control siRNA
0609-TSI = IE siRNA


title: Multiple myeloma, TT2, relapse, 84


title: Multiple myeloma, TT2, relapse, 83


title: row pool 10_long arm of chromosome 5A

description:
raw data file: 254552110007_660.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: row pool 11_long arm of chromosome 5A

description:
raw data file: chip15_680.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 81


title: Multiple myeloma, TT2, relapse, 85


title: row pool 9_long arm of chromosome 5A

description:
raw data file: chip15_680.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: row pool 8_long arm of chromosome 5A

description:
raw data file: chip15_680.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: row pool 6_long arm of chromosome 5A

description:
raw data file: 254552110008_620.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 78


title: row pool 5_long arm of chromosome 5A

description:
raw data file: chip15_680.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 79


title: RPE1 chr 3/3 clone 1


title: HCT116 H2B-GFP chr 3/3 clone 13


title: Multiple myeloma, TT2, relapse, 82


title: Multiple myeloma, TT2, relapse, 80


title: row pool 4_long arm of chromosome 5A

description:
raw data file: chip14_680.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: row pool 3_long arm of chromosome 5A

description:
raw data file: chip14_680.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 76


title: row pool 2_long arm of chromosome 5A

description:
raw data file: chip14_680.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: RPE1 H2B-GFP chr 21/3

description: Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.


title: Multiple myeloma, TT2, relapse, 75

description: Gene expression data from multiple myeloma plasma cells at relapse.


title: row pool 1_long arm of chromosome 5A

description:
raw data file: chip14_680.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 24_long arm of chromosome 5A

description:
raw data file: chip12_680(II).txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HCT116 H2B-GFP chr 5/3 clone 16


title: HCT116 H2B-GFP chr 8/3 clone 8


title: Multiple myeloma, TT2, relapse, 73


title: HCT116 H2B-GFP chr 3/3 clone 11


title: Multiple myeloma, TT2, relapse, 70


title: column pool 22_long arm of chromosome 5A

description:
raw data file: chip14_680.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HCT116 H2B-GFP chr 8/3 clone 7


title: column pool 21_long arm of chromosome 5A

description:
raw data file: chip13_650.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 20_long arm of chromosome 5A

description:
raw data file: chip11_640.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: row pool 7_long arm of chromosome 5A

description:
raw data file: chip15_680.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HCT116 H2B-GFP wildtype


title: column pool 23_long arm of chromosome 5A

description:
raw data file: chip13_650.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 19_long arm of chromosome 5A

description:
raw data file: chip13_650.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HCT116 H2B-GFP chr 5/3 clone 13


title: HCT116 H2B-GFP chr 3/3 clone 14


title: HCT116 H2B-GFP chr 8/3 clone 6


title: HCT116 5/4


title: Multiple myeloma, TT2, relapse, 69


title: column pool 18_long arm of chromosome 5A

description:
raw data file: chip13_650.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 17_long arm of chromosome 5A

description:
raw data file: chip12_680(II).txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 72


title: Multiple myeloma, TT2, relapse, 71


title: column pool 15_long arm of chromosome 5A

description:
raw data file: chip11_640.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 16_long arm of chromosome 5A

description:
raw data file: chip11_640.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 13_long arm of chromosome 5A

description:
raw data file: chip11_640.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 65


title: Multiple myeloma, TT2, relapse, 66


title: Multiple myeloma, TT2, relapse, 67


title: HCT116 H2B-GFP chr 8/3 clone 5


title: column pool 14_long arm of chromosome 5A

description:
raw data file: chip11_640.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 68


title: Multiple myeloma, TT2, relapse, 77


title: column pool 11_long arm of chromosome 5A

description:
raw data file: chip13_570.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 12_long arm of chromosome 5A

description:
raw data file: chip13_650.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 64

description: Gene expression data from multiple myeloma plasma cells at relapse.


title: Multiple myeloma, TT2, relapse, 74


title: Multiple myeloma, TT2, relapse, 63


title: column pool 10_long arm of chromosome 5A

description:
raw data file: chip12_680(II).txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 8_long arm of chromosome 5A

description:
raw data file: chip12_680(II).txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 9_long arm of chromosome 5A

description:
raw data file: 254552110007_660.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 61


title: column pool 7_long arm of chromosome 5A

description:
raw data file: chip12_680(II).txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 58


title: column pool 5_long arm of chromosome 5A

description:
raw data file: 254552110007_660.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 4_long arm of chromosome 5A

description:
raw data file: chip12_680(II).txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 62


title: column pool 6_long arm of chromosome 5A

description:
raw data file: 254552110008_620.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 3_long arm of chromosome 5A

description:
raw data file: chip12_680(II).txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 59


title: column pool 1_long arm of chromosome 5A

description:
raw data file: 254552110008_620.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 60


title: Multiple myeloma, TT2, relapse, 56


title: plate pool 23_long arm of chromosome 5A

description:
raw data file: chip11_640.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 53


title: Multiple myeloma, TT2, relapse, 52


title: Multiple myeloma, TT2, relapse, 54


title: Multiple myeloma, TT2, relapse, 55


title: Multiple myeloma, TT2, relapse, 57


title: plate pool 22_long arm of chromosome 5A

description:
raw data file: chip11_640.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 50


title: Multiple myeloma, TT2, relapse, 49


title: plate pool 20_long arm of chromosome 5A

description:
raw data file: chip6_640.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 2_long arm of chromosome 5A

description:
raw data file: chip12_530.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Hippocampus, control rat-rep1

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

institute: ETH Zurich

description:
Gene expression data of hippocampi dissected out from 16 month-old male Wistar control rats.
Rat-control-1

hyb_protocol: For hybridization, 15 μg of fragmented, biotin-labeled cRNA were incubated with the gene chip (Affymetrix GeneChip Rat Genome 230. 2.0 Array) in 200 μl of the hybridization solution in a hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual.

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

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v. 1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 300.

organism: Rattus norvegicus

source_name: Hippocampi from 16 month-old male Wistar control rats

label_protocol: Biotin-labeled cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual).

growth_protocol: The study was performed with 16 month-old male Wistar rats, which had been subjected to the chronic unpredictable mild stress battery for four weeks. The age-matched control group was housed under standard conditions and had free access to food and water. At an age of 16 months, hippocampi were dissected out on ice and processed for whole genome microarray gene expression profiling.

extract_protocol: Total hippocampal RNA was isolated with the RNeasy Mini kit according to the protocol of the manufacturer (Qiagen).

treatment_protocol: The study was performed with hippocampi dissected out from two groups of male Wistar rats, i.e. (i) 16 month-old rats, which had been subjected to the chronic unpredictable mild stress battery for four weeks, and (ii) 16 month-old rats, which were housed under standard conditions and had free access to food and water.

value: Wistar

tag: gender

value: male

tag: stress

value: control

value: 16 months old

value: hippocampus


title: plate pool 19_long arm of chromosome 5A

description:
raw data file: chip6_640.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Hippocampus, stressed rat-rep2

description:
Gene expression data of hippocampi dissected out from 16 month-old male Wistar rats after four weeks of chronic unpredictable mild stress.
Rat-stressed-2

source_name: Hippocampi from 16 month-old male Wistar rats after 4 weeks of chronic unpredictable mild stress

value: 4 weeks of chronic unpredictable mild stress.


title: Multiple myeloma, TT2, relapse, 46

description: Gene expression data from multiple myeloma plasma cells at relapse.

value: relapse


title: plate pool 18_long arm of chromosome 5A

description:
raw data file: chip6_640.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 17_long arm of chromosome 5A

description:
raw data file: chip14_680.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 16_long arm of chromosome 5A

description:
raw data file: 254552110007_660.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 21_long arm of chromosome 5A

description:
raw data file: chip6_640.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.