title: ade16 ade17 knock-out mutant vs ade16 ade17 ade8 his1 knock-out mutant (dye swap)

description: Technical replicate 2 of 2 (dye swap).

source_name: Total RNA extracted from ade16 ade17 knock-out mutant strain labeled with Cyanine-5 (red).

source_name: Total RNA extracted from ade16 ade17 ade8 his1 knock-out mutant strain labeled with Cyanine-3 (green).

tag: ade16 ade17 ade8 his1 knock-out mat alpha ade16

value: :KanMX4 ade17::KanMX4 ade8::KanMX4 his1::KanMX4 his3D1 leu2D0 ura3D0 strain


title: PCL-011

status: Public on Apr 14 2009

type: RNA

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data from human plasma cell leukemia patient PCL-011

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HG-U133A arrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix).

data_processing: The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization, and log2 transformed.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human multiple myeloma patient PCL-011

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: legend

value: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); N:Normal donor sample; MGUS:Monoclonal Gammopathy of Undetermined Significance sample; PCL:Plasma Cell Leukemia sample.

tag: cell type

value: purified plasma cells (PCs)

tag: sample type

value: PCL


title: ade16 ade17 knock-out mutant vs WT

status: Public on May 15 2009

city: PARIS

first: sophie

last: lemoine

address: 46 rue d'Ulm

department: Biologie

country: France

institute: Ecole Normale Supérieure

description: Technical replicate 1 of 2.

hyb_protocol: 2µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37°C. The array slides are then air dried and ready for scanning.

scan_protocol: Scanned on a genepix 4000B scanner (Axon)

data_processing:
Scanning software: GenePix Pro 6.1
Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/
Genepix flags are removed from the analysis. Spots are considered as saturating spot above 60000 and removed. Background is not subtracted from the main signal. Global Lowess normalisation method.

organism: Saccharomyces cerevisiae

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

growth_protocol: Cell growth 24 hours at 30°C in SD medium (Casaminoacid 0.2%, Adenin 300µM, Uracil 200µM, Tryptophan 200µM) to an OD = 0.5

extract_protocol: Hot phenol extract procedure followed by RNEasy Mini Kit purification step (Quiagen)

tag: ade16 ade17 knock-out mat alpha ade16

value: :KanMX4 ade17::KanMX4 his3D1 leu2D0 ura3D0 strain

source_name: Total RNA extracted from WT strain labeled with Cyanine-3 (green).

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy3. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

tag: WT Mat alpha his3D1 leu2D0 ura3D0 strain


title: PCL-006_5

description: Gene expression profiling data from human plasma cell leukemia patient PCL-006

source_name: Human multiple myeloma patient PCL-006


title: PCL-005_5

description: Gene expression profiling data from human plasma cell leukemia patient PCL-005

source_name: Human multiple myeloma patient PCL-005


title: ade16 ade17 ade8 his1 knock-out mutant vs ade16 ade17 knock-out mutant

description: Technical replicate 1 of 2.

source_name: Total RNA extracted from ade16 ade17 ade8 his1 knock-out mutant strain labeled with Cyanine-5 (red).

source_name: Total RNA extracted from ade16 ade17 knock-out mutant strain labeled with Cyanine-3 (green).


title: PCL-009_5

description: Gene expression profiling data from human plasma cell leukemia patient PCL-009

source_name: Human multiple myeloma patient PCL-009


title: PCL-007_5

description: Gene expression profiling data from human plasma cell leukemia patient PCL-007

source_name: Human multiple myeloma patient PCL-007


title: PCL-004_5

description: Gene expression profiling data from human plasma cell leukemia patient PCL-004

source_name: Human multiple myeloma patient PCL-004


title: MM-069_5

description: Gene expression profiling data from human multiple myeloma patient MM-069

source_name: Human multiple myeloma patient MM-069


title: PCL-001_5

description: Gene expression profiling data from human plasma cell leukemia patient PCL-001

source_name: Human multiple myeloma patient PCL-001


title: MM-004_5

description: Gene expression profiling data from human multiple myeloma patient MM-004

source_name: Human multiple myeloma patient MM-004


title: MM-139_5

description: Gene expression profiling data from human multiple myeloma patient MM-139

source_name: Human multiple myeloma patient MM-139


title: MM-208_5

description: Gene expression profiling data from human multiple myeloma patient MM-208

source_name: Human multiple myeloma patient MM-208


title: MM-224_5

description: Gene expression profiling data from human multiple myeloma patient MM-224

source_name: Human multiple myeloma patient MM-224


title: MM-154_5

description: Gene expression profiling data from human multiple myeloma patient MM-154

source_name: Human multiple myeloma patient MM-154


title: MM-206_5

description: Gene expression profiling data from human multiple myeloma patient MM-206

source_name: Human multiple myeloma patient MM-206


title: MM-025_5

description: Gene expression profiling data from human multiple myeloma patient MM-025

source_name: Human multiple myeloma patient MM-025


title: MM-233_5

description: Gene expression profiling data from human multiple myeloma patient MM-233

source_name: Human multiple myeloma patient MM-233


title: MM-195_5

description: Gene expression profiling data from human multiple myeloma patient MM-195

source_name: Human multiple myeloma patient MM-195


title: MM-158_5

description: Gene expression profiling data from human multiple myeloma patient MM-158

source_name: Human multiple myeloma patient MM-158


title: MM-185_5

description: Gene expression profiling data from human multiple myeloma patient MM-185

source_name: Human multiple myeloma patient MM-185


title: MM-173_5

description: Gene expression profiling data from human multiple myeloma patient MM-173

source_name: Human multiple myeloma patient MM-173


title: MM-205_5

description: Gene expression profiling data from human multiple myeloma patient MM-205

source_name: Human multiple myeloma patient MM-205


title: MM-133_5

description: Gene expression profiling data from human multiple myeloma patient MM-133

source_name: Human multiple myeloma patient MM-133


title: MM-138_5

description: Gene expression profiling data from human multiple myeloma patient MM-138

source_name: Human multiple myeloma patient MM-138


title: MM-123_5

description: Gene expression profiling data from human multiple myeloma patient MM-123

source_name: Human multiple myeloma patient MM-123


title: MM-113_5

description: Gene expression profiling data from human multiple myeloma patient MM-113

source_name: Human multiple myeloma patient MM-113


title: MM-087_5

description: Gene expression profiling data from human multiple myeloma patient MM-087

source_name: Human multiple myeloma patient MM-087


title: MM-083_5

description: Gene expression profiling data from human multiple myeloma patient MM-083

source_name: Human multiple myeloma patient MM-083


title: MM-109_5

description: Gene expression profiling data from human multiple myeloma patient MM-109

source_name: Human multiple myeloma patient MM-109


title: MM-104_5

description: Gene expression profiling data from human multiple myeloma patient MM-104

source_name: Human multiple myeloma patient MM-104


title: MM-089_5

description: Gene expression profiling data from human multiple myeloma patient MM-089

source_name: Human multiple myeloma patient MM-089


title: MM-074_5

description: Gene expression profiling data from human multiple myeloma patient MM-074

source_name: Human multiple myeloma patient MM-074


title: MM-066_5

description: Gene expression profiling data from human multiple myeloma patient MM-066

source_name: Human multiple myeloma patient MM-066


title: MM-063_5

description: Gene expression profiling data from human multiple myeloma patient MM-063

source_name: Human multiple myeloma patient MM-063


title: MM-021_5

description: Gene expression profiling data from human multiple myeloma patient MM-021

source_name: Human multiple myeloma patient MM-021


title: MM-042_5

description: Gene expression profiling data from human multiple myeloma patient MM-042

source_name: Human multiple myeloma patient MM-042


title: MM-049_GWP

status: Public on May 16 2009

type: genomic

description:
Legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005)
Gene-wide profiling data from human multiple myeloma patient MM-049

hyb_protocol: Following fragmentation, 40 micrograms of biotin-labeled DNA were hybridized for 16 hr at 48°C on GeneChip Human Mapping 50K XbaI Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Human Mapping 50K XbaI arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data. FBN procedure was finally applied to infer exact local copy number as described in the mentioned Reference.

molecule: genomic DNA

source_name: Human multiple myeloma patient MM-049

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 nanograms of genomic DNA.

extract_protocol: Genomic DNA extraction was performed using Wizard® Genomic DNA Purification kit according to the manufacturer's instructions (Promega).

tag: tc classification


title: MM-067_5

description: Gene expression profiling data from human multiple myeloma patient MM-067

source_name: Human multiple myeloma patient MM-067


title: MM-257_5

description: Gene expression profiling data from human multiple myeloma patient MM-257

source_name: Human multiple myeloma patient MM-257


title: MM-209_5

description: Gene expression profiling data from human multiple myeloma patient MM-209

source_name: Human multiple myeloma patient MM-209


title: MM-250_5

description: Gene expression profiling data from human multiple myeloma patient MM-250

source_name: Human multiple myeloma patient MM-250


title: MM-238_5

description: Gene expression profiling data from human multiple myeloma patient MM-238

source_name: Human multiple myeloma patient MM-238


title: MM-219_5

description: Gene expression profiling data from human multiple myeloma patient MM-219

source_name: Human multiple myeloma patient MM-219


title: MM-229_5

description: Gene expression profiling data from human multiple myeloma patient MM-229

source_name: Human multiple myeloma patient MM-229


title: MM-227_5

description: Gene expression profiling data from human multiple myeloma patient MM-227

source_name: Human multiple myeloma patient MM-227


title: MM-253_5

description: Gene expression profiling data from human multiple myeloma patient MM-253

source_name: Human multiple myeloma patient MM-253


title: MM-200_5

description: Gene expression profiling data from human multiple myeloma patient MM-200

source_name: Human multiple myeloma patient MM-200


title: MM-228_5

description: Gene expression profiling data from human multiple myeloma patient MM-228

source_name: Human multiple myeloma patient MM-228


title: MM-033_5

description: Gene expression profiling data from human multiple myeloma patient MM-033

source_name: Human multiple myeloma patient MM-033


title: MM-197_5

description: Gene expression profiling data from human multiple myeloma patient MM-197

source_name: Human multiple myeloma patient MM-197


title: MM-239_5

description: Gene expression profiling data from human multiple myeloma patient MM-239

source_name: Human multiple myeloma patient MM-239


title: MM-210_5

description: Gene expression profiling data from human multiple myeloma patient MM-210

source_name: Human multiple myeloma patient MM-210


title: MM-177_5

description: Gene expression profiling data from human multiple myeloma patient MM-177

source_name: Human multiple myeloma patient MM-177


title: MM-184_5

description: Gene expression profiling data from human multiple myeloma patient MM-184

source_name: Human multiple myeloma patient MM-184


title: MM-202_5

description: Gene expression profiling data from human multiple myeloma patient MM-202

source_name: Human multiple myeloma patient MM-202


title: MM-129_5

description: Gene expression profiling data from human multiple myeloma patient MM-129

source_name: Human multiple myeloma patient MM-129


title: MM-160_5

description: Gene expression profiling data from human multiple myeloma patient MM-160

source_name: Human multiple myeloma patient MM-160


title: MM-161_5

description: Gene expression profiling data from human multiple myeloma patient MM-161

source_name: Human multiple myeloma patient MM-161


title: MM-149_5

description: Gene expression profiling data from human multiple myeloma patient MM-149

source_name: Human multiple myeloma patient MM-149


title: MM-167_5

description: Gene expression profiling data from human multiple myeloma patient MM-167

source_name: Human multiple myeloma patient MM-167


title: MM-155_5

description: Gene expression profiling data from human multiple myeloma patient MM-155

source_name: Human multiple myeloma patient MM-155


title: MM-191_5

description: Gene expression profiling data from human multiple myeloma patient MM-191

source_name: Human multiple myeloma patient MM-191


title: MM-150_5

description: Gene expression profiling data from human multiple myeloma patient MM-150

source_name: Human multiple myeloma patient MM-150


title: MM-174_5

description: Gene expression profiling data from human multiple myeloma patient MM-174

source_name: Human multiple myeloma patient MM-174


title: MM-114_5

description: Gene expression profiling data from human multiple myeloma patient MM-114

source_name: Human multiple myeloma patient MM-114


title: MM-152_5

description: Gene expression profiling data from human multiple myeloma patient MM-152

source_name: Human multiple myeloma patient MM-152


title: MM-107_5

description: Gene expression profiling data from human multiple myeloma patient MM-107

source_name: Human multiple myeloma patient MM-107


title: MM-106_5

description: Gene expression profiling data from human multiple myeloma patient MM-106

source_name: Human multiple myeloma patient MM-106


title: MM-101_5

description: Gene expression profiling data from human multiple myeloma patient MM-101

source_name: Human multiple myeloma patient MM-101


title: MM-094_5

description: Gene expression profiling data from human multiple myeloma patient MM-094

source_name: Human multiple myeloma patient MM-094


title: MM-117_5

description: Gene expression profiling data from human multiple myeloma patient MM-117

source_name: Human multiple myeloma patient MM-117


title: MM-148_5

description: Gene expression profiling data from human multiple myeloma patient MM-148

source_name: Human multiple myeloma patient MM-148


title: MM-103_5

description: Gene expression profiling data from human multiple myeloma patient MM-103

source_name: Human multiple myeloma patient MM-103


title: MM-153_5

description: Gene expression profiling data from human multiple myeloma patient MM-153

source_name: Human multiple myeloma patient MM-153


title: MM-082_5

description: Gene expression profiling data from human multiple myeloma patient MM-082

source_name: Human multiple myeloma patient MM-082


title: MM-068_5

description: Gene expression profiling data from human multiple myeloma patient MM-068

source_name: Human multiple myeloma patient MM-068


title: MM-081_5

description: Gene expression profiling data from human multiple myeloma patient MM-081

source_name: Human multiple myeloma patient MM-081


title: MM-072_5

description: Gene expression profiling data from human multiple myeloma patient MM-072

source_name: Human multiple myeloma patient MM-072


title: MM-047_5

description: Gene expression profiling data from human multiple myeloma patient MM-047

source_name: Human multiple myeloma patient MM-047


title: MM-040_5

description: Gene expression profiling data from human multiple myeloma patient MM-040

source_name: Human multiple myeloma patient MM-040


title: MM-050_5

description: Gene expression profiling data from human multiple myeloma patient MM-050

source_name: Human multiple myeloma patient MM-050


title: MM-048_5

description: Gene expression profiling data from human multiple myeloma patient MM-048

source_name: Human multiple myeloma patient MM-048


title: MM-092_5

description: Gene expression profiling data from human multiple myeloma patient MM-092

source_name: Human multiple myeloma patient MM-092


title: MM-045_5

description: Gene expression profiling data from human multiple myeloma patient MM-045

source_name: Human multiple myeloma patient MM-045


title: MM-078_5

description: Gene expression profiling data from human multiple myeloma patient MM-078

source_name: Human multiple myeloma patient MM-078


title: MM-027_5

description: Gene expression profiling data from human multiple myeloma patient MM-027

source_name: Human multiple myeloma patient MM-027


title: MM-016_5

description: Gene expression profiling data from human multiple myeloma patient MM-016

source_name: Human multiple myeloma patient MM-016


title: MM-240_5

description: Gene expression profiling data from human multiple myeloma patient MM-240

source_name: Human multiple myeloma patient MM-240


title: MM-190_5

description: Gene expression profiling data from human multiple myeloma patient MM-190

source_name: Human multiple myeloma patient MM-190


title: MM-203_5

description: Gene expression profiling data from human multiple myeloma patient MM-203

source_name: Human multiple myeloma patient MM-203


title: MM-036_5

description: Gene expression profiling data from human multiple myeloma patient MM-036

source_name: Human multiple myeloma patient MM-036


title: MM-194_5

description: Gene expression profiling data from human multiple myeloma patient MM-194

source_name: Human multiple myeloma patient MM-194


title: MM-146_5

description: Gene expression profiling data from human multiple myeloma patient MM-146

source_name: Human multiple myeloma patient MM-146


title: MM-178_5

description: Gene expression profiling data from human multiple myeloma patient MM-178

source_name: Human multiple myeloma patient MM-178


title: MM-151_5

description: Gene expression profiling data from human multiple myeloma patient MM-151

source_name: Human multiple myeloma patient MM-151


title: MM-183_5

description: Gene expression profiling data from human multiple myeloma patient MM-183

source_name: Human multiple myeloma patient MM-183


title: MM-143_5

description: Gene expression profiling data from human multiple myeloma patient MM-143

source_name: Human multiple myeloma patient MM-143


title: MM-131_5

description: Gene expression profiling data from human multiple myeloma patient MM-131

source_name: Human multiple myeloma patient MM-131


title: MM-118_5

description: Gene expression profiling data from human multiple myeloma patient MM-118

source_name: Human multiple myeloma patient MM-118


title: MM-121_5

description: Gene expression profiling data from human multiple myeloma patient MM-121

source_name: Human multiple myeloma patient MM-121


title: MM-077_5

description: Gene expression profiling data from human multiple myeloma patient MM-077

source_name: Human multiple myeloma patient MM-077


title: MM-079_5

description: Gene expression profiling data from human multiple myeloma patient MM-079

source_name: Human multiple myeloma patient MM-079


title: MM-116_5

description: Gene expression profiling data from human multiple myeloma patient MM-116

source_name: Human multiple myeloma patient MM-116


title: MM-243_5

description: Gene expression profiling data from human multiple myeloma patient MM-243

source_name: Human multiple myeloma patient MM-243


title: MM-043_5

description: Gene expression profiling data from human multiple myeloma patient MM-043

source_name: Human multiple myeloma patient MM-043


title: MM-049_5

description: Gene expression profiling data from human multiple myeloma patient MM-049

source_name: Human multiple myeloma patient MM-049


title: MM-039_5

description: Gene expression profiling data from human multiple myeloma patient MM-039

source_name: Human multiple myeloma patient MM-039


title: MM-034_5

description: Gene expression profiling data from human multiple myeloma patient MM-034

source_name: Human multiple myeloma patient MM-034


title: MM-213_5

description: Gene expression profiling data from human multiple myeloma patient MM-213

source_name: Human multiple myeloma patient MM-213


title: MM-225_5

description: Gene expression profiling data from human multiple myeloma patient MM-225

source_name: Human multiple myeloma patient MM-225


title: MM-030_5

description: Gene expression profiling data from human multiple myeloma patient MM-030

source_name: Human multiple myeloma patient MM-030


title: MM-056_5

description: Gene expression profiling data from human multiple myeloma patient MM-056

source_name: Human multiple myeloma patient MM-056


title: MM-014_5

description: Gene expression profiling data from human multiple myeloma patient MM-014

source_name: Human multiple myeloma patient MM-014


title: MM-180_5

description: Gene expression profiling data from human multiple myeloma patient MM-180

source_name: Human multiple myeloma patient MM-180


title: MM-035_5

description: Gene expression profiling data from human multiple myeloma patient MM-035

source_name: Human multiple myeloma patient MM-035


title: MM-246_5

description: Gene expression profiling data from human multiple myeloma patient MM-246

source_name: Human multiple myeloma patient MM-246


title: MM-128_5

description: Gene expression profiling data from human multiple myeloma patient MM-128

source_name: Human multiple myeloma patient MM-128


title: MM-207_5

description: Gene expression profiling data from human multiple myeloma patient MM-207

source_name: Human multiple myeloma patient MM-207


title: MM-212_5

description: Gene expression profiling data from human multiple myeloma patient MM-212

source_name: Human multiple myeloma patient MM-212


title: MM-140_5

description: Gene expression profiling data from human multiple myeloma patient MM-140

source_name: Human multiple myeloma patient MM-140


title: MM-179_5

description: Gene expression profiling data from human multiple myeloma patient MM-179

source_name: Human multiple myeloma patient MM-179


title: MM-186_5

description: Gene expression profiling data from human multiple myeloma patient MM-186

source_name: Human multiple myeloma patient MM-186


title: MM-100_5

description: Gene expression profiling data from human multiple myeloma patient MM-100

source_name: Human multiple myeloma patient MM-100


title: MM-221_5

description: Gene expression profiling data from human multiple myeloma patient MM-221

source_name: Human multiple myeloma patient MM-221


title: MM-237_5

description: Gene expression profiling data from human multiple myeloma patient MM-237

source_name: Human multiple myeloma patient MM-237


title: MM-064_5

description: Gene expression profiling data from human multiple myeloma patient MM-064

source_name: Human multiple myeloma patient MM-064


title: MM-111_5

description: Gene expression profiling data from human multiple myeloma patient MM-111

source_name: Human multiple myeloma patient MM-111


title: MM-038_5

description: Gene expression profiling data from human multiple myeloma patient MM-038

source_name: Human multiple myeloma patient MM-038


title: MM-159_5

description: Gene expression profiling data from human multiple myeloma patient MM-159

source_name: Human multiple myeloma patient MM-159


title: MM-119_5

description: Gene expression profiling data from human multiple myeloma patient MM-119

source_name: Human multiple myeloma patient MM-119


title: MM-070_5

description: Gene expression profiling data from human multiple myeloma patient MM-070

source_name: Human multiple myeloma patient MM-070


title: MM-055_5

description: Gene expression profiling data from human multiple myeloma patient MM-055

source_name: Human multiple myeloma patient MM-055


title: MM-115_5

description: Gene expression profiling data from human multiple myeloma patient MM-115

source_name: Human multiple myeloma patient MM-115


title: MM-054_5

description: Gene expression profiling data from human multiple myeloma patient MM-054

source_name: Human multiple myeloma patient MM-054


title: MM-126_5

description: Gene expression profiling data from human multiple myeloma patient MM-126

source_name: Human multiple myeloma patient MM-126


title: MM-052_5

description: Gene expression profiling data from human multiple myeloma patient MM-052

source_name: Human multiple myeloma patient MM-052


title: MM-037_5

description: Gene expression profiling data from human multiple myeloma patient MM-037

source_name: Human multiple myeloma patient MM-037


title: MGUS-031_5

description: Gene expression profiling data from human monoclonal gammopathy of undetermined significance patient MGUS-031

source_name: Human monoclonal gammopathy of undetermined significance patient MGUS-031

value: MGUS


title: MM-032_5

description: Gene expression profiling data from human multiple myeloma patient MM-032

source_name: Human multiple myeloma patient MM-032


title: MM-015_5

description: Gene expression profiling data from human multiple myeloma patient MM-015

source_name: Human multiple myeloma patient MM-015


title: N-002_5

description: Gene expression profiling data from human normal donor N-002

source_name: Human normal donor N-002

value: N


title: MM-019_5

description: Gene expression profiling data from human multiple myeloma patient MM-019

source_name: Human multiple myeloma patient MM-019


title: MGUS-005_5

description: Gene expression profiling data from human monoclonal gammopathy of undetermined significance patient MGUS-005

source_name: Human monoclonal gammopathy of undetermined significance patient MGUS-005


title: MM-026_5

description: Gene expression profiling data from human multiple myeloma patient MM-026

source_name: Human multiple myeloma patient MM-026


title: N-005_5

description: Gene expression profiling data from human normal donor N-005

source_name: Human normal donor N-005


title: MGUS-018_5

description: Gene expression profiling data from human monoclonal gammopathy of undetermined significance patient MGUS-018

source_name: Human monoclonal gammopathy of undetermined significance patient MGUS-018


title: MGUS-015_5

description: Gene expression profiling data from human monoclonal gammopathy of undetermined significance patient MGUS-015

source_name: Human monoclonal gammopathy of undetermined significance patient MGUS-015


title: MGUS-008_5

description: Gene expression profiling data from human monoclonal gammopathy of undetermined significance patient MGUS-008

source_name: Human monoclonal gammopathy of undetermined significance patient MGUS-008


title: MGUS-026_5

description: Gene expression profiling data from human monoclonal gammopathy of undetermined significance patient MGUS-026

source_name: Human monoclonal gammopathy of undetermined significance patient MGUS-026


title: MGUS-012_5

description: Gene expression profiling data from human monoclonal gammopathy of undetermined significance patient MGUS-012

source_name: Human monoclonal gammopathy of undetermined significance patient MGUS-012


title: MM-031_5

description: Gene expression profiling data from human multiple myeloma patient MM-031

source_name: Human multiple myeloma patient MM-031


title: C-20460-FLT3/ITD(4HSTI571-3)_U74C

status: Public on Jul 12 2008

city: Boston

first: Winnie

middle: F

last: Tam

state: MA

address: 1 Blackfan Circle

department: Hematology

country: USA

institute: Brigham and Women's Hospital, Harvard Medical School

description: Gene expression data

hyb_protocol: After cleaning up with Rneasy Mini Kit, labeled cRNA was fragmented by incubation at 95 oC for 35 minutes in fragmentation buffer (40mM Tris-acetate, pH8.1, 100mM KOAc and 30mM MgOAc).  The fragmented cRNA was hybridized against Affymetrix Murine Genome U74v2 set oligonucleotide arrays.

scan_protocol: GeneChips were scanned using GeneArray Scanner with Affymetrix Microarray Suite version 5

data_processing:
The arrays were analyzed using GeneCluster 2.0 software (Whitehead/MIT Center for Genome Research, Cambridge, MA).
Data was preprocessed so that the absolute values were between 20 and 16000.  A variation filter was applied to the data so that the ratio of maximum value to minimum value was greater than 3.0, and the difference between maximum value and minimum value was greater than 100 in the same row.  The filtered datasets were then analyzed by neighborhood analysis to identify genes of interest.

organism: Mus musculus

source_name: FLT3/ITD(4h, inhibitor STI571-3)

label_protocol: The cDNA was used for in vitro transcription with the BioArray Highyield RNA Transcript Labeling Kit (ENZO, NY).

growth_protocol: Cells were maintained in RPMI 1640 with 10% FBS and 1mg/ml G418

extract_protocol: Total RNA was extracted from cells using RNAeasy Mini Kit (Qiagen, CA).  Total RNA was reverse transcribed with Superscript Choice System cDNA synthesis kit (Invitrogen, CA) in the presence of an oligo dT-T7 primer (GENSET, CA).  After phenol/chloroform extraction and ethanol precipitation, the cDNA pellet was air dried briefly and resuspended in 12 ul of RNAase-free water.

treatment_protocol: To completely inhibit kinase activity in a short period of time (4 hours), a concentration of inhibitor that was at least 10 times higher than IC50 for its respective activated tyrosine kinase was used (5 uM for imatinib, 0.5 uM for MLN518


title: C-20377-T/A(untreated)_U74C

description: Gene expression data

source_name: TEL-ABL(untreated)


title: C-20462-FLT3/ITD(4HMLN518-3)_U74C

description: Gene expression data

source_name: FLT3/ITD(4h, inhibitor MLN518-3)


title: MGUS-019_5

description: Gene expression profiling data from human monoclonal gammopathy of undetermined significance patient MGUS-019

source_name: Human monoclonal gammopathy of undetermined significance patient MGUS-019


title: C-20459-FLT3/ITD(4HSTI571-2)_U74C

description: Gene expression data

source_name: FLT3/ITD(4h, inhibitor STI571-2)


title: MGUS-020_5

description: Gene expression profiling data from human monoclonal gammopathy of undetermined significance patient MGUS-020

source_name: Human monoclonal gammopathy of undetermined significance patient MGUS-020


title: C-20313-T/P(untreated)_U74C

description: Gene expression data

source_name: TEL-PDGF-betaR(untreated)


title: MGUS-034_5

description: Gene expression profiling data from human monoclonal gammopathy of undetermined significance patient MGUS-034

source_name: Human monoclonal gammopathy of undetermined significance patient MGUS-034


title: N-001_5

description: Gene expression profiling data from human normal donor N-001

source_name: Human normal donor N-001


title: C-20314-T/P(4hSTI571)_U74C

description: Gene expression data

source_name: TEL-PDGF-betaR(4h, inhibitor STI571)


title: C-20312-TA(4hSTI571)_U74C

description: Gene expression data

source_name: TEL-ABL(4h, inhibitor STI571)


title: MGUS-017_5

description: Gene expression profiling data from human monoclonal gammopathy of undetermined significance patient MGUS-017

source_name: Human monoclonal gammopathy of undetermined significance patient MGUS-017


title: N-004_5

description: Gene expression profiling data from human normal donor N-004

source_name: Human normal donor N-004


title: C-20317-FLT3/ITD(4HMLN518-1)_U74C

description: Gene expression data

source_name: FLT3/ITD(4h, inhibitor MLN518-1)


title: C-20316-FLT3/ITD(4HSTI571-1)_U74C

description: Gene expression data

source_name: FLT3/ITD(4h, inhibitor STI571-1)


title: C-20458-FLT3/ITD(untreated3)_U74C

description: Gene expression data


title: C-20457-Flt3/ITD(untreated2)_U74C

description: Gene expression data


title: C-20461-FLT3/ITD(4HMLN518-2)_U74C

description: Gene expression data

source_name: FLT3/ITD(4h, inhibitor MLN518-2)


title: C-20309-B/A(4hSTI571-1)_U74C

description: Gene expression data

source_name: BCR-ABL(4h, inhibitor STI571-1)


title: C-20315-Flt3/ITD(untreated1)_U74C

description: Gene expression data


title: C-20451-B/A(untreated2)_U74C

description: Gene expression data


title: C-20455-B/A(4hMLN518-2)_U74C

description: Gene expression data

source_name: BCR-ABL(4h, inhibitor MLN518-2)


title: C-20310-B/A(4hMLN518-1)_U74C

description: Gene expression data

source_name: BCR-ABL(4h, inhibitor MLN518-1)


title: C-20376-B/A(untreated1)_U74C

description: Gene expression data


title: C-20454-B/A(4hSTI571-3)_U74C

description: Gene expression data

source_name: BCR-ABL(4h, inhibitor STI571-3)


title: C-20456-BA(4hMLN518-3)_U74C

description: Gene expression data

source_name: BCR-ABL(4h, inhibitor MLN518-3)


title: C-20453-B/A(4hSTI571-2)_U74C

description: Gene expression data

source_name: BCR-ABL(4h, inhibitor STI571-2)


title: C-20314-T/P(4hSTI571)_U74B

description: Gene expression data


title: C-20313-T/P(untreated)_U74B

description: Gene expression data


title: C-20312-TA(4hSTI571)_U74B

description: Gene expression data


title: C-20377-T/A(untreated)_U74B

description: Gene expression data

source_name: TEL-ABL(untreated)


title: C-20458-FLT3/ITD(untreated3)_U74B

description: Gene expression data


title: C-20316-FLT3/ITD(4HSTI571-1)_U74B

description: Gene expression data


title: C-20317-FLT3/ITD(4HMLN518-1)_U74B

description: Gene expression data


title: C-20462-FLT3/ITD(4HMLN518-3)_U74B

description: Gene expression data

source_name: FLT3/ITD(4h, inhibitor MLN518-3)


title: C-20457-Flt3/ITD(untreated2)_U74B

description: Gene expression data


title: C-20309-B/A(4hSTI571-1)_U74B

description: Gene expression data


title: C-20453-B/A(4hSTI571-2)_U74B

description: Gene expression data


title: C-20452-B/A(untreated3)_U74C

description: Gene expression data


title: C-20461-FLT3/ITD(4HMLN518-2)_U74B

description: Gene expression data


title: C-20315-Flt3/ITD(untreated1)_U74B

description: Gene expression data


title: C-20456-BA(4hMLN518-3)_U74B

description: Gene expression data


title: C-20460-FLT3/ITD(4HSTI571-3)_U74B

description: Gene expression data

source_name: FLT3/ITD(4h, inhibitor STI571-3)


title: C-20451-B/A(untreated2)_U74B

description: Gene expression data


title: C-20454-B/A(4hSTI571-3)_U74B

description: Gene expression data


title: C-20455-B/A(4hMLN518-2)_U74B

description: Gene expression data


title: C-20452-B/A(untreated3)_U74B

description: Gene expression data


title: C-20313-T/P(untreated)_U74A

description: Gene expression data

source_name: TEL-PDGF-betaR(untreated)


title: C-20376-B/A(untreated1)_U74B

description: Gene expression data


title: C-20317-FLT3/ITD(4HMLN518-1)_U74A

description: Gene expression data


title: C-20310-B/A(4hMLN518-1)_U74B

description: Gene expression data


title: C-20459-FLT3/ITD(4HSTI571-2)_U74B

description: Gene expression data

source_name: FLT3/ITD(4h, inhibitor STI571-2)


title: C-20314-T/P(4hSTI571)_U74A

description: Gene expression data

source_name: TEL-PDGF-betaR(4h, inhibitor STI571)


title: C-20460-FLT3/ITD(4HSTI571-3)_U74A

description: Gene expression data


title: C-20312-TA(4hSTI571)_U74A

description: Gene expression data

source_name: TEL-ABL(4h, inhibitor STI571)


title: C-20377-T/A(untreated)_U74A

description: Gene expression data


title: C-20459-FLT3/ITD(4HSTI571-2)_U74A

description: Gene expression data


title: C-20462-FLT3/ITD(4HMLN518-3)_U74A

description: Gene expression data


title: C-20461-FLT3/ITD(4HMLN518-2)_U74A

description: Gene expression data


title: C-20456-BA(4hMLN518-3)_U74A

description: Gene expression data


title: C-20315-Flt3/ITD(untreated1)_U74A

description: Gene expression data


title: C-20458-FLT3/ITD(untreated3)_U74A

description: Gene expression data


title: C-20309-B/A(4hSTI571-1)_U74A

description: Gene expression data


title: C-20454-B/A(4hSTI571-3)_U74A

description: Gene expression data


title: C-20310-B/A(4hMLN518-1)_U74A

description: Gene expression data


title: C-20453-B/A(4hSTI571-2)_U74A

description: Gene expression data


title: C-20455-B/A(4hMLN518-2)_U74A

description: Gene expression data


title: C-20452-B/A(untreated3)_U74A

description: Gene expression data


title: C-20376-B/A(untreated1)_U74A

description: Gene expression data


title: C-20457-Flt3/ITD(untreated2)_U74A

description: Gene expression data


title: C-20451-B/A(untreated2)_U74A

description: Gene expression data


title: C-20316-FLT3/ITD(4HSTI571-1)_U74A

description: Gene expression data


title: C99313

status: Public on Feb 12 2008

city: St Louis

first: Jacqueline

last: Payton

state: MO

address: 4320 Forest Park Avenue, Suite 211

institute: Washington University School of Medicine

description: A study that used high-throughput re-sequencing of the kinase domains of 26 Tyrosine kinase genes that are expressed in most acute myeloid leukemia patients. Used genomic DNA from bone marrow (tumor).

hyb_protocol: Chips hybridized according to Manufacturer's protocol

data_processing: Data scaled to array mean of 1500

source_name: Bone marrow specimen from Tumor cells

label_protocol: Chips labeled with biotin according to Manufacturer's protocol

growth_protocol: Bone marrow specimen from Tumor cells

extract_protocol: Trizol reagent standard protocol

tag: fab

tag: Sex

value: F

tag: race

value: C

tag: age on study

tag: cytogenetic change

value: Normal

tag: flt3 d835

tag: flt3 itd

tag: npm1 ins


title: C97398

value: M

value: H


title: C00969


title: C011658


title: germ cell tumors (GCT) and normal controls 192A 1

status: Public on Nov 10 2005

city: New York

first: James

last: Korkola

state: NY

address: 1275 York Ave

department: Cell Biology

institute: Memorial Sloan-Kettering

description: Adult Male Germ Cell Tumor

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA (robust multi-array)

source_name: germ cell tumor

label_protocol: Approximately 12 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Frozen tissue from a germ cell tumor was minced and homogenized in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: pure GCT (Seminoma)