title: c_D_1123

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C12_609904


title: c_D_1114

status: Public on Sep 12 2012

type: genomic

city: Boston

first: Björn

last: Chapuy

state: MA

address: 450 Brookline Ave.

department: Medical Onology

country: USA

institute: Dana-Farber Cancer Institute

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C04_609816

hyb_protocol: Following fragmentation, biotinylated PCR fragments were hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix)

data_processing: The raw cel files were converted into probeset-specific expression values using Affymetrix MAS5 summarization method as implemented in the BioConductor package simpleaffy (Gentleman et al., 2004). All samples were scaled to have a mean expression level of 100. Copy number values were inferred from raw CEL files with a GenePattern pipeline which runs the following modules: SNPFileCreator, CopyNumberInference, RemoveCopyNumberOutliers, DivideByNormals and Quality Control.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: fresh frozen tumor sample

label_protocol: PCR products were labeled with a single biotin according to the Affymetrix protocol.

extract_protocol: For total RNA, frozen tissue sections were homogenized in Trizol and RNA was extracted according to standard protocols. For high molecular weight genomic DNA,  frozen tissue sections were homogenized in 1 ml of G2-buffer supplemented with 2 ml RNase (Qiagen). Subsequently, DNA was extracted  using the genomic buffer kit with 20/G genomic-tips (Qiagen) following the manufacturer's recommendations.

treatment_protocol: 10-20 x 20mm sections from frozen tumor specimens from newly diagnosed previously untreated diffuse large B-cell lymphomas and peripheral blood lymphocytes from normal donors were directly transferred to extraction buffers.

tag: type

value: primary DLBCL


title: c_D_1121

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C10_609892


title: ozone/Pam3Cys 4 hours O3/PC3/4h rep4

status: Public on Aug 01 2012

type: RNA

city: Aurora

first: David

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

hyb_protocol: standard Agilent hyb protocol

scan_protocol: standard protocol on the Agilent scanner

data_processing:
Agi4x44PreProcess
RMA by Partek

molecule: total RNA

organism: Mus musculus

source_name: lung tissue

label_protocol: 0.5-1.0 microgram of Total RNA was used as a template for synthesis of cDNA utilizing the One Color Low input Agilent Quick Amp Labeling Kit.

extract_protocol: Total RNA including small RNA species was isolated from approximately 100 mg of snap-frozen lung tissue using the mirVana kit (AB/Ambion, Austin TX).

treatment_protocol: Mice were exposed to either 2ppm ozone or filtered air (FA) for 3 hours.  24 hours following ozone exposure, mice from either the ozone or FA group were treated intratracheally with either 100ug of Pam3CYS in saline or saline alone. Animals were euthanized 4 or 24 hours post-Pam3CYS exposure.

tag: treatment

tag: time

value: 4 hours

tag: strain

tag: tissue

value: lung


title: c_D_1119

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C08_609852


title: c_D_1144

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E07_609794


title: ozone/Pam3Cys 4 hours O3/PC3/4h rep1


title: free air/Pam3Cys 4 hours FA/P3C/4h rep4

value: free air/Pam3Cys


title: O3/saline 4 hours O3/sal/4h rep3


title: free air/Pam3Cys 4 hours FA/P3C/4h rep3


title: free air/Pam3Cys 4 hours FA/P3C/4h rep2


title: O3/saline 4 hours O3/sal/4h rep2


title: ozone/Pam3Cys 4 hours O3/PC3/4h rep3


title: free air/saline 4 hours FA/sal/4h rep3

value: free air/saline


title: O3/saline 4 hours O3/sal/4h rep1


title: free air/saline 24 hours FA/sal/24h rep1

value: 24 hours


title: free air/saline 4 hours FA/sal/4h rep2


title: ozone/Pam3Cys 4 hours O3/PC3/4h rep2


title: free air/saline 4 hours FA/sal/4h rep4


title: free air/saline 4 hours FA/sal/4h rep1


title: c_D_1113

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C03_609894


title: c_D_1110

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B12_609886


title: c_D_1107

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B09_609728


title: E2F1_20hrLPS_5

status: Public on Jul 01 2012

data_processing: The data was analyzed using the Agi4x44k preprocess in R (Lopez-Romero, 2010). The analysis ran using the default parameters provided with the package documentation.

source_name: liver_LPS_knockout_20 hrs

treatment_protocol: Mice were treated systemically with LPS or saline and liver tissue was collected 6 or 20 hours post-treatment.

tag: e2f1 genotype

value: liver

value: LPS

value: 20 hr


title: E2F1_20hrLPS_6


title: O3/saline 4 hours O3/sal/4h rep4


title: E2F1_20hrLPS_3


title: free air/Pam3Cys 4 hours FA/P3C/4h rep1


title: E2F1_20hrLPS_4


title: E2F1_20hrLPS_1


title: c_D_1105

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B07_609760


title: c_D_1104

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B06_609770


title: c_D_1026

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B02_609748


title: E2F1_saline_1

source_name: liver_saline_knockout_20 hrs

value: saline


title: E2F1_6hrLPS_4

source_name: liver_LPS_knockout_6 hrs

value: 6 hr


title: B6129_saline_2

source_name: liver_saline_wild type_20 hrs


title: B6129_20hrLPS_1

source_name: liver_LPS_wild type_20 hrs


title: B6129_20hrLPS_3


title: B6129_20hrLPS_5


title: B6129_20hrLPS_2


title: E2F1_saline_4


title: B6129_saline_3


title: B6129_saline_6


title: E2F1_6hrLPS_2


title: B6129_saline_1


title: E2F1_saline_6


title: E2F1_6hrLPS_3


title: B6129_6hrLPS_2

source_name: liver_LPS_wild type_6 hrs


title: E2F1_saline_5


title: B6129_saline_5


title: B6129_20hrLPS_6


title: B6129_6hrLPS_3


title: E2F1_saline_2


title: B6129_6hrLPS_1


title: B6129_20hrLPS_4


title: E2F1_saline_3


title: B6129_6hrLPS_4


title: E2F1_6hrLPS_1


title: B6129_saline_4


title: c_D_1111

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C01_609884


title: c_D_1045

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B01_609828


title: c_D_1044

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_A06_609810


title: E2F1_20hrLPS_2


title: IPF_PBB_NJ-5085

description:
Gene expression IPF
IPF_PBB_NJ-5085_9416_1_4/2

source_name: idiopathic pulmonary fibrosis (IPF)_PBB

extract_protocol: RNA extraction was performed manually utilizing the PAXgene Blood RNA kit (PreAnalytiX 762164 according to the manufacturer's protocol. Qualtiy of the RNA was assessed with a RNA 6000 NanoChip (Agilent) on the 2100 Bioanalyzer (Agilent) by the ratio comparison of the 18S and 28S rRNA bands.

treatment_protocol: Peripheral blood drawn into PAxRNA tubes, fasting morning blood samples

tag: gender

value: female

tag: age

value: peripheral blood

tag: dlco

tag: fvp


title: IPF_PBB_DS-282-212

description:
Gene expression IPF
IPF_PBB_DS-282-212_9363_1_4/2

value: male


title: N_PBB_IC-9999-89

description:
Gene expression IPF
N_PBB_IC-9999-89_9363_1_1/1

source_name: healthy control (N)_PBB


title: N_PBB_IC-9999-90

description:
Gene expression IPF
N_PBB_IC-9999-90_9413_1_2/1


title: IPF_PBB_NJ-6042

description:
Gene expression IPF
IPF_PBB_NJ-6042_9413_1_1/2


title: IPF_PBB_NJ-55-310

description:
Gene expression IPF
IPF_PBB_NJ-55-310_9414_1_1/2


title: IPF_PBB_NJ-6026

description:
Gene expression IPF
IPF_PBB_NJ-6026_9414_1_2/2


title: IPF_PBB_NJ-4914

description:
Gene expression IPF
IPF_PBB_NJ-4914_9361_1_1/2


title: IPF_PBB_DS-412-203

description:
Gene expression IPF
IPF_PBB_DS-412-203_9362_1_2/2


title: IPF_PBB_NJ-5520

description:
Gene expression IPF
IPF_PBB_NJ-5520_9415_1_3/2


title: IPF_PBB_NJ-6088

description:
Gene expression IPF
IPF_PBB_NJ-6088_9362_1_3/2


title: N_PBB_DS-1-305

description:
Gene expression IPF
N_PBB_DS-1-305_9361_1_4/1


title: IPF_PBB_NJ-97-205

description:
Gene expression IPF
IPF_PBB_NJ-97-205_9415_1_4/2


title: IPF_PBB_NJ-95-305

description:
Gene expression IPF
IPF_PBB_NJ-95-305_9361_1_2/2


title: IPF_PBB_DS-83-302

description:
Gene expression IPF
IPF_PBB_DS-83-302_9415_1_2/2


title: IPF_PBB_NJ-5879

description:
Gene expression IPF
IPF_PBB_NJ-5879_9414_1_3/2


title: IPF_PBB_DS-5-209

description:
Gene expression IPF
IPF_PBB_DS-5-209_9416_1_1/2


title: IPF_PBB_NJ-6019

description:
Gene expression IPF
IPF_PBB_NJ-6019_9415_1_1/2


title: N_PBB_VF-13-311

description:
Gene expression IPF
N_PBB_VF-13-311_9416_1_3/1


title: N_PBB_DS-451-202

description:
Gene expression IPF
N_PBB_DS-451-202_9414_1_4/1


title: IPF_PBB_NJ-5718

description:
Gene expression IPF
IPF_PBB_NJ-5718_9362_1_1/2


title: IPF_PBB_DS-378-203

description:
Gene expression IPF
IPF_PBB_DS-378-203_9363_1_2/2


title: IPF_PBB_DS-366-301

description:
Gene expression IPF
IPF_PBB_DS-366-301_9361_1_3/2


title: IPF_PBB_NJ-5606

description:
Gene expression IPF
IPF_PBB_NJ-5606_9360_1_3/2


title: IPF_PBB_NJ-5900

description:
Gene expression IPF
IPF_PBB_NJ-5900_9413_1_3/2


title: IPF_PBB_NJ-5867

description:
Gene expression IPF
IPF_PBB_NJ-5867_9416_1_2/2


title: N_PBB_VF-101-310

description:
Gene expression IPF
N_PBB_VF-101-310_9363_1_3/1


title: IPF_PBB_IC-158-101

description:
Gene expression IPF
IPF_PBB_IC-158-101_9362_1_4/2


title: N_PBB_DS-425-301

description:
Gene expression IPF
N_PBB_DS-425-301_9413_1_4/1


title: IPF_PBB_DS-466-207

description:
Gene expression IPF
IPF_PBB_DS-466-207_9360_1_1/2


title: IPF_PBB_NJ-56-305

description:
Gene expression IPF
IPF_PBB_NJ-56-305_9359_1_2/2


title: N_PBB_DS-453-301

description:
Gene expression IPF
N_PBB_DS-453-301_9360_1_4/1


title: IPF_PBB_NJ-5991

description:
Gene expression IPF
IPF_PBB_NJ-5991_9292_1_1/2


title: IPF_PBB_NJ-81-204

description:
Gene expression IPF
IPF_PBB_NJ-81-204_9292_1_2/2


title: IPF_PBB_NJ-5632

description:
Gene expression IPF
IPF_PBB_NJ-5632_9292_1_3/2


title: N_PBB_NJ-69-401

description:
Gene expression IPF
N_PBB_NJ-69-401_9289_1_1/1


title: N_PBB_NJ-100-305

description:
Gene expression IPF
N_PBB_NJ-100-305_9289_1_2/1


title: N_PBB_DS-354-311

description:
Gene expression IPF
N_PBB_DS-354-311_9289_1_3/1


title: N_PBB_DS-446-202

description:
Gene expression IPF
N_PBB_DS-446-202_9359_1_4/1


title: IPF_PBB_NJ-5073

description:
Gene expression IPF
IPF_PBB_NJ-5073_9359_1_1/2


title: IPF_PBB_NJ-6035

description:
Gene expression IPF
IPF_PBB_NJ-6035_9291_1_3/2


title: IPF_PBB_DS-386-202

description:
Gene expression IPF
IPF_PBB_DS-386-202_9135_1_3/2


title: N_PBB_NJ-105-301

description:
Gene expression IPF
N_PBB_NJ-105-301_9289_1_4/1


title: IPF_PBB_DS-363-306

description:
Gene expression IPF
IPF_PBB_DS-363-306_9135_1_1/2


title: N_PBB_NJ-47-306

description:
Gene expression IPF
N_PBB_NJ-47-306_9291_1_4/1


title: N_PBB_NJ-92-204

description:
Gene expression IPF
N_PBB_NJ-92-204_9292_1_4/1


title: IPF_PBB_DS-442-202

description:
Gene expression IPF
IPF_PBB_DS-442-202_9135_1_4/2


title: IPF_PBB_DS-211-204

description:
Gene expression IPF
IPF_PBB_DS-211-204_9290_1_2/2


title: IPF_PBB_NJ-26-201

description:
Gene expression IPF
IPF_PBB_NJ-26-201_9288_1_2/2


title: IPF_PBB_DS-71-201

description:
Gene expression IPF
IPF_PBB_DS-71-201_9290_1_3/2


title: IPF_PBB_NJ-100-206

description:
Gene expression IPF
IPF_PBB_NJ-100-206_9288_1_1/2


title: IPF_PBB_NJ-6005

description:
Gene expression IPF
IPF_PBB_NJ-6005_9291_1_2/2


title: IPF_PBB_DS-184-208

description:
Gene expression IPF
IPF_PBB_DS-184-208_9291_1_1/2


title: N_PBB_NJ-110-205

description:
Gene expression IPF
N_PBB_NJ-110-205_9290_1_4/1


title: IPF_PBB_NJ-4921

description:
Gene expression IPF
IPF_PBB_NJ-4921_9288_1_4/2


title: IPF_PBB_DS-118-201

description:
Gene expression IPF
IPF_PBB_DS-118-201_9290_1_1/2


title: N_PBB_DS-445-302

description:
Gene expression IPF
N_PBB_DS-445-302_9288_1_3/1


title: IPF_PBB_NJ-99-201

description:
Gene expression IPF
IPF_PBB_NJ-99-201_9134_1_2/2


title: IPF_PBB_NJ-121-206

description:
Gene expression IPF
IPF_PBB_NJ-121-206_9135_1_2/2


title: IPF_PBB_NJ-5711

description:
Gene expression IPF
IPF_PBB_NJ-5711_9360_1_2/2


title: IPF_PBB_NJ-5258

description:
Gene expression IPF
IPF_PBB_NJ-5258_9134_1_3/2


title: N_PBB_NJ-103-202

description:
Gene expression IPF
N_PBB_NJ-103-202_9134_1_4/1


title: IPF_PBB_VF-139-306

description:
Gene expression IPF
IPF_PBB_VF-139-306_9134_1_1/2


title: N_PBB_NJ-101-203

description:
Gene expression IPF
N_PBB_NJ-101-203_9133_1_4/1


title: IPF_PBB_NJ-5612

description:
Gene expression IPF
IPF_PBB_NJ-5612_9132_1_2/2


title: IPF_PBB_NJ-5674

description:
Gene expression IPF
IPF_PBB_NJ-5674_9132_1_3/2


title: IPF_PBB_NJ-4908

description:
Gene expression IPF
IPF_PBB_NJ-4908_9133_1_2/2


title: IPF_PBB_NJ-5596

description:
Gene expression IPF
IPF_PBB_NJ-5596_0448_1_3/2


title: IPF_PBB_DS-316-305

description:
Gene expression IPF
IPF_PBB_DS-316-305_0448_1_2/2


title: IPF_PBB_NJ-5347

description:
Gene expression IPF
IPF_PBB_NJ-5347_9131_1_1/2


title: N_PBB_NJ-78-303

description:
Gene expression IPF
N_PBB_NJ-78-303_0447_1_4/1


title: IPF_PBB_NJ-5397

description:
Gene expression IPF
IPF_PBB_NJ-5397_3499_1_1/2


title: IPF_PBB_NJ-25-320

description:
Gene expression IPF
IPF_PBB_NJ-25-320_3612_1_1/2


title: N_PBB_DS-335-201

description:
Gene expression IPF
N_PBB_DS-335-201_0447_1_3/1


title: IPF_PBB_NJ-93-201

description:
Gene expression IPF
IPF_PBB_NJ-93-201_9131_1_2/2


title: IPF_PBB_DS-34-302

description:
Gene expression IPF
IPF_PBB_DS-34-302_3612_1_2/2


title: IPF_PBB_NJ-5779

description:
Gene expression IPF
IPF_PBB_NJ-5779_3498_1_2/2


title: IPF_PBB_IC-160-101

description:
Gene expression IPF
IPF_PBB_IC-160-101_9131_1_4/2


title: IPF_PBB_NJ-5369

description:
Gene expression IPF
IPF_PBB_NJ-5369_3499_1_3/2


title: IPF_PBB_NJ-5824

description:
Gene expression IPF
IPF_PBB_NJ-5824_9131_1_3/2


title: IPF_PBB_NJ-5640

description:
Gene expression IPF
IPF_PBB_NJ-5640_9132_1_1/2


title: IPF_PBB_DS-388-301

description:
Gene expression IPF
IPF_PBB_DS-388-301_3612_1_3/2


title: IPF_PBB_NJ-108-206

description:
Gene expression IPF
IPF_PBB_NJ-108-206_3498_1_3/2


title: IPF_PBB_NJ-80-205

description:
Gene expression IPF
IPF_PBB_NJ-80-205_3499_1_2/2


title: IPF_PBB_NJ-5972

description:
Gene expression IPF
IPF_PBB_NJ-5972_0448_1_4/2


title: IPF_PBB_NJ-2967

description:
Gene expression IPF
IPF_PBB_NJ-2967_3498_1_1/2


title: N_PBB_DS-236-301

description:
Gene expression IPF
N_PBB_DS-236-301_0447_1_1/1


title: N_PBB_NJ-111-301

description:
Gene expression IPF
N_PBB_NJ-111-301_3499_1_4/1


title: IPF_PBB_NJ-4609

description:
Gene expression IPF
IPF_PBB_NJ-4609_0447_1_2/2


title: IPF_PBB_VF-164-205

description:
Gene expression IPF
IPF_PBB_VF-164-205_0448_1_1/2


title: IPF_PBB_NJ-5835

description:
Gene expression IPF
IPF_PBB_NJ-5835_0446_1_4/2


title: N_PBB_DS-83-303

description:
Gene expression IPF
N_PBB_DS-83-303_0445_1_2/1


title: IPF_PBB_NJ-5859

description:
Gene expression IPF
IPF_PBB_NJ-5859_0446_1_1/2


title: IPF_PBB_IC-50-101

description:
Gene expression IPF
IPF_PBB_IC-50-101_0445_1_3/2


title: IPF_PBB_NJ-102-202

description:
Gene expression IPF
IPF_PBB_NJ-102-202_0446_1_2/2


title: N_PBB_IC-9999-93

description:
Gene expression IPF
N_PBB_IC-9999-93_0445_1_4/1


title: IPF_PBB_NJ-5393-0445

description:
Gene expression IPF
IPF_PBB_NJ-5393_0445_1_1/2


title: IPF_PBB_DS-406-202

description:
Gene expression IPF
IPF_PBB_DS-406-202_0444_1_2/2


title: IPF_PBB_NJ-5870-0439

description:
Gene expression IPF
IPF_PBB_NJ-5870_0439_1_1/2


title: N_PBB_NJ-36-203

description:
Gene expression IPF
N_PBB_NJ-36-203_0444_1_3/1


title: IPF_PBB_NJ-5848

description:
Gene expression IPF
IPF_PBB_NJ-5848_0432_1_1/2


title: IPF_PBB_NJ-5623

description:
Gene expression IPF
IPF_PBB_NJ-5623_0432_1_3/2


title: IPF_PBB_NJ-5393-0438

description:
Gene expression IPF
IPF_PBB_NJ-5393_0438_1_2/2


title: IPF_PBB_DS-444-302

description:
Gene expression IPF
IPF_PBB_DS-444-302_0438_1_3/2


title: IPF_PBB_NJ-4769

description:
Gene expression IPF
IPF_PBB_NJ-4769_0444_1_1/2


title: IPF_PBB_NJ-88-203

description:
Gene expression IPF
IPF_PBB_NJ-88-203_0444_1_4/2


title: IPF_PBB_NJ-5870-0438

description:
Gene expression IPF
IPF_PBB_NJ-5870_0438_1_1/2


title: IPF_PBB_DS-156-207

description:
Gene expression IPF
IPF_PBB_DS-156-207_0431_1_3/2


title: E2F1_20hrLPS_6

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Intensity data were log2-transformed, quantile normalized using RMA, and expression levels were summarized on a miRNA level using the median-polished value of all probesets mapping to each miRNA. Non-mouse miRNA probesets were removed.

label_protocol: miRNA microarray target labeling was conducted using 1000 ng of total RNA and the FlashTag kit (Genisphere, Hatfield, PA)


title: E2F1_20hrLPS_4


title: IPF_PBB_NJ-5200

description:
Gene expression IPF
IPF_PBB_NJ-5200_0431_1_1/2


title: N_PBB_NJ-25-321

description:
Gene expression IPF
N_PBB_NJ-25-321_0438_1_4/1


title: IPF_PBB_NJ-5310

description:
Gene expression IPF
IPF_PBB_NJ-5310_0431_1_2/2


title: E2F1_20hrLPS_5


title: E2F1_20hrLPS_3


title: IPF_PBB_NJ-5608

description:
Gene expression IPF
IPF_PBB_NJ-5608_0430_1_3/2


title: IPF_PBB_NJ-2642

description:
Gene expression IPF
IPF_PBB_NJ-2642_0430_1_1/2


title: IPF_PBB_NJ-5475

description:
Gene expression IPF
IPF_PBB_NJ-5475_0429_1_3/2


title: IPF_PBB_VF-125-301

description:
Gene expression IPF
IPF_PBB_VF-125-301_0430_1_2/2


title: IPF_PBB_NJ-120-101

description:
Gene expression IPF
IPF_PBB_NJ-120-101_0429_1_1/2


title: E2F1_20hrLPS_2


title: E2F1_20hrLPS_1


title: N_PBB_NJ-116-301

description:
Gene expression IPF
N_PBB_NJ-116-301_0432_1_4/1


title: IPF_PBB_NJ-5573

description:
Gene expression IPF
IPF_PBB_NJ-5573_0428_1_4/2


title: B6129_20hrLPS_5


title: B6129_20hrLPS_1


title: B6129_20hrLPS_2


title: B6129_20hrLPS_6


title: B6129_20hrLPS_4


title: B6129_20hrLPS_3


title: E2F1_6hrLPS_4


title: IPF_PBB_NJ-5238

description:
Gene expression IPF
IPF_PBB_NJ-5238_0432_1_2/2


title: IPF_PBB_NJ-119-201

description:
Gene expression IPF
IPF_PBB_NJ-119-201_0428_1_1/2


title: N_PBB_IC-9999-98

description:
Gene expression IPF
N_PBB_IC-9999-98_0431_1_4/1


title: N_PBB_DS-439-310

description:
Gene expression IPF
N_PBB_DS-439-310_0429_1_4/1


title: IPF_PBB_NJ-72-206

description:
Gene expression IPF
IPF_PBB_NJ-72-206_0428_1_3/2


title: B6129_6hrLPS_3


title: E2F1_6hrLPS_3


title: B6129_6hrLPS_4


title: B6129_6hrLPS_2


title: E2F1_6hrLPS_2


title: B6129_6hrLPS_1


title: E2F1_6hrLPS_1


title: E2F1_saline_5


title: B6129_saline_3


title: E2F1_saline_6


title: E2F1_saline_4


title: E2F1_saline_1


title: B6129_saline_1


title: B6129_saline_5


title: E2F1_saline_3


title: E2F1_saline_2


title: B6129_saline_6


title: B6129_saline_4


title: B6129_saline_2


title: medulloblastoma blood BL-2016

status: Public on Jan 20 2012

city: Toronto

middle: J. H.

last: Shih

state: ON

address: 686 Bay St

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

hyb_protocol: As per instructions from manufacturer (Affymetrix).

data_processing:
CRMAv2 normalization using aroma.affymetrix. Probe signals were cablirated for crosstalk between allele probe pairs, normalized for nucleotide-position probe sequence effects, and summarized using the RmaCnPlm method (for the Mapping250K_Nsp platform) or the AvgCnPlm method for (the GenomeWideSNP_6 platform). Probe signals were then normalized for PCR fragment-length effects. Subsequently, raw copy-numbers were calcuated based on either the a pool of reference samples or pair-matched normals.
DNA copy-number values exported from aroma.affymetrix.

source_name: blood

extract_protocol: High molecular weight genomic DNA was extracted from primary tissue and cell lines using either the standard SDS/Proteinase K method or Qiagen DNEasy Blood and Tissue Kits.

tag: sample id

value: M

tag: disease state

value: medulloblastoma

value: blood


title: medulloblastoma blood BL-2035

scan_protocol: As per instructions from manufacturer (Affymetrix).

value: F


title: medulloblastoma blood BL-2005

label_protocol: As per instructions from manufacturer (Affymetrix).


title: medulloblastoma blood BL-2038


title: medulloblastoma blood BL-2018


title: medulloblastoma blood BL-2039


title: medulloblastoma blood BL-2050


title: medulloblastoma blood BL-2034


title: medulloblastoma blood BL-2037


title: medulloblastoma blood BL-2040


title: medulloblastoma blood BL-2031


title: medulloblastoma blood BL-2024


title: medulloblastoma blood BL-2017


title: medulloblastoma blood BL-2046


title: medulloblastoma blood BL-2012


title: medulloblastoma blood BL-2004


title: medulloblastoma blood BL-2020


title: medulloblastoma blood BL-2019


title: medulloblastoma blood BL-2002


title: medulloblastoma tumor MB-518

source_name: tumour sample

value: medulloblastoma tumor


title: medulloblastoma tumor MB-496


title: medulloblastoma tumor MB-361


title: medulloblastoma tumor MB-471


title: medulloblastoma tumor MB-387


title: medulloblastoma tumor MB-460


title: medulloblastoma tumor MB-486


title: medulloblastoma tumor MB-383


title: medulloblastoma tumor MB-463


title: medulloblastoma tumor MB-391


title: medulloblastoma tumor MB-462


title: serotype 13 reference strain

status: Public on Mar 31 2010

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

country: China

institute: Huazhong Agricultural University

description: cultured in TSB medium to middle exponential phase

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit (Agilent). 1μg of cRNA were mixed with blocking agent, fragmentation buffer and incubated at 60°C for 30 min for fragmentation. GEx Hybridization Buffer were added and 100 μl mixture were hybridized at 65°C for 17 hours with 10 rpm rotation. The arrays were washed two times using wash buffer 1 and 2 from Gene Expression Wash Buffer Kit (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5).  The values of signal intensity were normalized and transformed into log base 2.

organism: Actinobacillus pleuropneumoniae

source_name: serotype 13 strain N-273

label_protocol: cDNA were transcribed into cRNA using T7 RNA Polymerase and aaUTP (Ambion). cRNA were purified using QIAGEN RNeasy Mini kit (QIAGEN). 4μg cRNA were stirred with DMSO and 0.3M NaHCO3 and then Cy3 NHS ester (GE healthcare) were added. The mixture were incubated at 25°C for 1 hour. 4M Hydroxylamine were added and incubated at 25°C for 15min. The labeled cRNA were purified using QIAGEN RNeasy Mini kit (QIAGEN).

growth_protocol: A. pleuropneumoniae strains were cultured in TSB medium supplemented with 10 μg/ml of nicotinamide adenine dinucleotide (NAD) and 10% (v/v) filtered cattle serum at 37°C. The samples were collected from mid-log phase and the total RNA were extracted using Trizol reagent according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from cells using Trizol reagent (Invitrogen) according to the manufacturer’s protocol and the RNA concentration was measured on a NanoDrop ND-1000 UV spectrometry. The treated RNA was purified with a QIAGEN RNeasy Mini Kit (QIAGEN).


title: serotype 12 reference strain

source_name: serotype 12 strain 1096


title: RIKEN_Cage_GM12878_cytosol_longNonPolyA

status: Public on Dec 16 2011

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

library_source: transcriptomic

molecule: cytoplasmic RNA

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage

tag: datatype

value: Cage

tag: datatype description

value: CAGE 5' RNA Tags

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: rnaextract

value: longNonPolyA

tag: rnaextract description

value: Poly(A)- RNA longer than 200 nt

tag: biorep

tag: labexpid

tag: labversion

value: bedtools v2.7.1,IDR

tag: cell lineage

value: mesoderm

tag: cell sex

tag: localization

value: cytosol

tag: localization description

value: The fluid between the cells outer membrane and the nucleus

value: Delve version 0.9


title: serotype 11 reference strain

source_name: serotype 11 strain 56153

tag: strain


title: serotype 8 reference strain

source_name: serotype 8 strain 405


title: serotype 7 reference strain

source_name: serotype 7 strain WF83


title: serotype 9 reference strain

source_name: serotype 9 strain CVJ13261


title: serotype 6 reference strain

source_name: serotype 6 strain Femφ

value: Femφ


title: serotype 5b reference strain

source_name: serotype 5b strain L20


title: serotype 5a reference strain

source_name: serotype 5a strain K17


title: serotype 10 reference strain

source_name: serotype 10 strain D13039


title: serotype 4 reference strain

source_name: serotype 4 strain M62


title: serotype 3 reference strain

source_name: serotype 3 strain S1421


title: serotype 2 reference strain

source_name: serotype 2 strain 4226


title: field strain JL03

source_name: serotype 3 strain JL03


title: PRB4791 (HG-U133B)

status: Public on Mar 15 2006

city: South San Francisco

first: Thomas

middle: D.

last: Wu

address: 1 DNA Way

institute: Genentech, Inc.

description: high-grade astrocytoma

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: Brain tumor

label_protocol: Approximately 1-5 ug of total RNA was processed to produce biotynylated cRNA targets

extract_protocol: Qiagen RNeasy Mini Kit

tag: who grade

value: IV

tag: age

tag: Sex

tag: survival (weeks)

tag: censor

tag: specimen type

value: recurrent

tag: matching sample


title: serotype 1 reference strain

source_name: serotype 1 strain 4074


title: PRB4788 (HG-U133A)

description: high-grade astrocytoma

value: IV without necrosis

value: M

value: no

value: primary


title: PRB4788 (HG-U133B)

description: high-grade astrocytoma


title: PRB4785 (HG-U133B)

description: high-grade astrocytoma


title: PRB4782 (HG-U133B)

description: high-grade astrocytoma

value: F


title: PRB4782 (HG-U133A)

description: high-grade astrocytoma


title: PRB4787 (HG-U133A)

description: high-grade astrocytoma


title: PRB4791 (HG-U133A)

description: high-grade astrocytoma


title: PRB4771 (HG-U133A)

description: high-grade astrocytoma


title: PRB4777 (HG-U133A)

description: high-grade astrocytoma


title: PRB4787 (HG-U133B)

description: high-grade astrocytoma


title: PRB4777 (HG-U133B)

description: high-grade astrocytoma


title: PRB4767 (HG-U133B)

description: high-grade astrocytoma

value: III


title: medulloblastoma tumor MB-2017

source_name: blood

tag: sample id

tag: gender

tag: disease state

value: medulloblastoma

tag: tissue

value: medulloblastoma tumor


title: PRB4785 (HG-U133A)

description: high-grade astrocytoma


title: medulloblastoma tumor MB-2020


title: PRB4753 (HG-U133B)

description: high-grade astrocytoma

value: yes


title: PRB4759 (HG-U133A)

description: high-grade astrocytoma


title: PRB4759 (HG-U133B)

description: high-grade astrocytoma


title: PRB4754 (HG-U133A)

description: high-grade astrocytoma


title: medulloblastoma tumor MB-2016


title: medulloblastoma tumor MB-2050


title: medulloblastoma tumor MB-2031


title: medulloblastoma tumor MB-2034


title: PRB4753 (HG-U133A)

description: high-grade astrocytoma


title: PRB4767 (HG-U133A)

description: high-grade astrocytoma


title: PRB4754 (HG-U133B)

description: high-grade astrocytoma


title: PRB4129 (HG-U133B)

description: high-grade astrocytoma

value: IV with necrosis


title: PRB4747 (HG-U133B)

description: high-grade astrocytoma


title: medulloblastoma tumor MB-2002


title: medulloblastoma tumor MB-2035


title: medulloblastoma tumor MB-2004


title: medulloblastoma tumor MB-2039


title: PRB4128 (HG-U133A)

description: high-grade astrocytoma


title: PRB4129 (HG-U133A)

description: high-grade astrocytoma


title: PRB4747 (HG-U133A)

description: high-grade astrocytoma


title: medulloblastoma tumor MB-2012


title: PRB4127 (HG-U133B)

description: high-grade astrocytoma


title: medulloblastoma tumor MB-2005


title: PRB4128 (HG-U133B)

description: high-grade astrocytoma


title: PRB4771 (HG-U133B)

description: high-grade astrocytoma


title: medulloblastoma tumor MB-2038


title: PRB4126 (HG-U133B)

description: high-grade astrocytoma


title: medulloblastoma tumor MB-2037


title: PRB4125 (HG-U133B)

description: high-grade astrocytoma


title: PRB4126 (HG-U133A)

description: high-grade astrocytoma


title: PRB4127 (HG-U133A)

description: high-grade astrocytoma


title: medulloblastoma tumor MB-2019


title: medulloblastoma tumor MB-2040


title: medulloblastoma tumor MB-2018


title: PRB4124 (HG-U133A)

description: high-grade astrocytoma


title: PRB4124 (HG-U133B)

description: high-grade astrocytoma


title: PRB4123 (HG-U133A)

description: high-grade astrocytoma


title: PRB4123 (HG-U133B)

description: high-grade astrocytoma


title: PRB4122 (HG-U133B)

description: high-grade astrocytoma


title: PRB4102 (HG-U133A)

description: high-grade astrocytoma


title: PRB4125 (HG-U133A)

description: high-grade astrocytoma


title: PRB4097 (HG-U133B)

description: high-grade astrocytoma


title: PRB4103 (HG-U133A)

description: high-grade astrocytoma


title: PRB4103 (HG-U133B)

description: high-grade astrocytoma


title: PRB4097 (HG-U133A)

description: high-grade astrocytoma


title: PRB4098 (HG-U133A)

description: high-grade astrocytoma


title: PRB4098 (HG-U133B)

description: high-grade astrocytoma


title: PRB4122 (HG-U133A)

description: high-grade astrocytoma


title: PRB4102 (HG-U133B)

description: high-grade astrocytoma


title: medulloblastoma tumor MB-2024


title: medulloblastoma tumor MB-2046


title: PRB4096 (HG-U133B)

description: high-grade astrocytoma


title: PRB4094 (HG-U133B)

description: high-grade astrocytoma


title: PRB4094 (HG-U133A)

description: high-grade astrocytoma


title: PRB4095 (HG-U133A)

description: high-grade astrocytoma


title: PRB4096 (HG-U133A)

description: high-grade astrocytoma


title: PRB4095 (HG-U133B)

description: high-grade astrocytoma


title: PRB3910 (HG-U133A)

description: high-grade astrocytoma


title: PRB3910 (HG-U133B)

description: high-grade astrocytoma


title: PRB3906 (HG-U133B)

description: high-grade astrocytoma


title: PRB3907 (HG-U133A)

description: high-grade astrocytoma


title: PRB3899 (HG-U133A)

description: high-grade astrocytoma


title: PRB3906 (HG-U133A)

description: high-grade astrocytoma


title: PRB3901 (HG-U133B)

description: high-grade astrocytoma


title: PRB3903 (HG-U133A)

description: high-grade astrocytoma


title: PRB3905 (HG-U133B)

description: high-grade astrocytoma


title: PRB3840 (HG-U133A)

description: high-grade astrocytoma


title: PRB3905 (HG-U133A)

description: high-grade astrocytoma


title: PRB3895 (HG-U133B)

description: high-grade astrocytoma


title: PRB3840 (HG-U133B)

description: high-grade astrocytoma


title: PRB3839 (HG-U133B)

description: high-grade astrocytoma


title: PRB3897 (HG-U133B)

description: high-grade astrocytoma


title: PRB3907 (HG-U133B)

description: high-grade astrocytoma


title: PRB3900 (HG-U133B)

description: high-grade astrocytoma


title: PRB3901 (HG-U133A)

description: high-grade astrocytoma


title: PRB3839 (HG-U133A)

description: high-grade astrocytoma


title: PRB3900 (HG-U133A)

description: high-grade astrocytoma


title: PRB3903 (HG-U133B)

description: high-grade astrocytoma


title: PRB3899 (HG-U133B)

description: high-grade astrocytoma


title: PRB3832 (HG-U133B)

description: high-grade astrocytoma


title: PRB3897 (HG-U133A)

description: high-grade astrocytoma


title: PRB3895 (HG-U133A)

description: high-grade astrocytoma


title: PRB3830 (HG-U133B)

description: high-grade astrocytoma


title: PRB3836 (HG-U133A)

description: high-grade astrocytoma


title: PRB3833 (HG-U133B)

description: high-grade astrocytoma


title: PRB3825 (HG-U133B)

description: high-grade astrocytoma


title: PRB3836 (HG-U133B)

description: high-grade astrocytoma


title: PRB3834 (HG-U133B)

description: high-grade astrocytoma


title: PRB3833 (HG-U133A)

description: high-grade astrocytoma


title: PRB3832 (HG-U133A)

description: high-grade astrocytoma


title: PRB3825 (HG-U133A)

description: high-grade astrocytoma


title: PRB3830 (HG-U133A)

description: high-grade astrocytoma


title: PRB3827 (HG-U133A)

description: high-grade astrocytoma


title: PRB3786 (HG-U133B)

description: high-grade astrocytoma


title: PRB3784 (HG-U133B)

description: high-grade astrocytoma


title: PRB3827 (HG-U133B)

description: high-grade astrocytoma


title: PRB3826 (HG-U133A)

description: high-grade astrocytoma


title: PRB3781 (HG-U133A)

description: high-grade astrocytoma


title: PRB3782 (HG-U133B)

description: high-grade astrocytoma


title: PRB3826 (HG-U133B)

description: high-grade astrocytoma


title: PRB3780 (HG-U133B)

description: high-grade astrocytoma


title: PRB3834 (HG-U133A)

description: high-grade astrocytoma


title: PRB3786 (HG-U133A)

description: high-grade astrocytoma


title: PRB3782 (HG-U133A)

description: high-grade astrocytoma


title: PRB3781 (HG-U133B)

description: high-grade astrocytoma


title: PRB3779 (HG-U133A)

description: high-grade astrocytoma


title: PRB3778 (HG-U133B)

description: high-grade astrocytoma


title: PRB3777 (HG-U133B)

description: high-grade astrocytoma


title: PRB3779 (HG-U133B)

description: high-grade astrocytoma


title: PRB3784 (HG-U133A)

description: high-grade astrocytoma


title: PRB3785 (HG-U133A)

description: high-grade astrocytoma


title: PRB3780 (HG-U133A)

description: high-grade astrocytoma


title: PRB3778 (HG-U133A)

description: high-grade astrocytoma


title: PRB3776 (HG-U133B)

description: high-grade astrocytoma


title: PRB3775 (HG-U133B)

description: high-grade astrocytoma


title: PRB3776 (HG-U133A)

description: high-grade astrocytoma


title: PRB3758 (HG-U133B)

description: high-grade astrocytoma


title: PRB3777 (HG-U133A)

description: high-grade astrocytoma


title: PRB3775 (HG-U133A)

description: high-grade astrocytoma


title: PRB3774 (HG-U133B)

description: high-grade astrocytoma


title: PRB3774 (HG-U133A)

description: high-grade astrocytoma


title: PRB3756 (HG-U133B)

description: high-grade astrocytoma


title: PRB3757 (HG-U133B)

description: high-grade astrocytoma


title: PRB3751 (HG-U133B)

description: high-grade astrocytoma


title: PRB3755 (HG-U133B)

description: high-grade astrocytoma


title: PRB3758 (HG-U133A)

description: high-grade astrocytoma


title: PRB3759 (HG-U133B)

description: high-grade astrocytoma


title: PRB3756 (HG-U133A)

description: high-grade astrocytoma


title: PRB3754 (HG-U133B)

description: high-grade astrocytoma


title: PRB3759 (HG-U133A)

description: high-grade astrocytoma


title: PRB3749 (HG-U133B)

description: high-grade astrocytoma


title: PRB3752 (HG-U133A)

description: high-grade astrocytoma


title: PRB3753 (HG-U133A)

description: high-grade astrocytoma


title: PRB3752 (HG-U133B)

description: high-grade astrocytoma


title: PRB3754 (HG-U133A)

description: high-grade astrocytoma


title: PRB3753 (HG-U133B)

description: high-grade astrocytoma


title: PRB3785 (HG-U133B)

description: high-grade astrocytoma


title: PRB3748 (HG-U133B)

description: high-grade astrocytoma


title: PRB3751 (HG-U133A)

description: high-grade astrocytoma


title: PRB3757 (HG-U133A)

description: high-grade astrocytoma


title: PRB3749 (HG-U133A)

description: high-grade astrocytoma


title: PRB3748 (HG-U133A)

description: high-grade astrocytoma


title: PRB3755 (HG-U133A)

description: high-grade astrocytoma


title: PRB3746 (HG-U133B)

description: high-grade astrocytoma


title: PRB3746 (HG-U133A)

description: high-grade astrocytoma


title: PRB3744 (HG-U133A)

description: high-grade astrocytoma


title: PRB3745 (HG-U133B)

description: high-grade astrocytoma


title: PRB3745 (HG-U133A)

description: high-grade astrocytoma


title: PRB3744 (HG-U133B)

description: high-grade astrocytoma


title: PRB3747 (HG-U133B)

description: high-grade astrocytoma


title: PRB3747 (HG-U133A)

description: high-grade astrocytoma


title: brain, Left Temporal Lobe: Extract47_le1

status: Public on Mar 08 2006

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description:
GBM
Treatment, type=remove

hyb_protocol: Standard Affymetrix protocols were used.

source_name: brain, Left Temporal Lobe

label_protocol: Probes were prepared using standard Affymetrix protocols and hybridized to Affymetrix HG-U133A and HG-U133B arrays (Affymetrix, Santa Clara, CA).

extract_protocol: RNA extraction was performed as described previously (Mischel PS, Shai R, Shi T, et al Identification of molecular subtypes of glioblastoma by gene expression profiling. Oncogene, 2003;22:2361-73) and analyzed on both a spectrophotometer and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: brain, Left Temporal Lobe

tag: histology

value: GBM

tag: tumor number (as appears in figure 3)

value: FEMALE

tag: grade

tag: living

value: ALIVE

tag: survival time

tag: survival cluster

tag: array


title: brain, Left Temporal Lobe: Extract45_le1

description:
GBM
Treatment, type=remove

scan_protocol: Standard Affymetrix protocols were used.

tag: age

value: DECEASED


title: brain, Left Temporal Lobe: Extract49_le2

description:
GBM
Treatment, type=remove

value: MALE


title: brain, Thalamus: Extract51_le2

description:
GBM
Treatment, type=remove

source_name: brain, Thalamus

value: brain, Thalamus


title: brain, Left Temporal Parietal: Extract50_le1

description:
GBM
Treatment, type=remove

source_name: brain, Left Temporal Parietal

value: brain, Left Temporal Parietal


title: brain, Left Parietal Occipital: Extract43_le1

description:
GBM
Treatment, type=remove

source_name: brain, Left Parietal Occipital

value: brain, Left Parietal Occipital


title: brain, Left Temporal Lobe: Extract48_le1

description:
GBM
Treatment, type=remove


title: brain, Left Temporal Lobe: Extract47_le2

description:
GBM
Treatment, type=remove


title: brain, Right Anterior Temporal: Extract52_le2

description:
GBM
Treatment, type=remove

source_name: brain, Right Anterior Temporal

value: brain, Right Anterior Temporal


title: brain, Left Temporal Lobe: Extract46_le2

description:
GBM
Treatment, type=remove


title: brain, Right Anterior Temporal: Extract52_le1

description:
GBM
Treatment, type=remove


title: brain, Left Temporal Lobe: Extract45_le2

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract38_le1

description:
GBM
Treatment, type=remove

source_name: brain, left frontal temporal lobe

value: brain, left frontal temporal lobe


title: brain, left frontal temporal lobe: Extract37_le2

description:
GBM
Treatment, type=remove


title: brain, Thalamus: Extract51_le1

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract36_le1

description:
GBM
Treatment, type=remove


title: brain, Left Temporal Lobe: Extract46_le1

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract38_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract35_le2

description:
GBM
Treatment, type=remove

source_name: brain, Left frontal Lobe

value: brain, Left frontal Lobe


title: brain, Left Temporal Parietal: Extract50_le2

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract37_le1

description:
GBM
Treatment, type=remove


title: brain, Left Temporal Lobe: Extract49_le1

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract36_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract33_le2

description:
GBM
Treatment, type=remove


title: brain, Left Temporal Lobe: Extract48_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract30_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract34_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract31_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract32_le1

description:
GBM
Treatment, type=remove


title: brain, Left Parietal Occipital: Extract43_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract31_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract32_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract29_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract29_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract30_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract34_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract35_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract28_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract27_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract28_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract33_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract24_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract27_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract25_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract25_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract22_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract26_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract23_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract26_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract23_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract21_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract24_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract21_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract20_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract19_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract19_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract22_le2

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Parietal: Extract85_le1

description:
GBM
Treatment, type=remove

source_name: brain, Right Temporal Parietal

value: brain, Right Temporal Parietal


title: brain, Right Temporal Parietal: Extract83_le1

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract20_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract18_le1

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Parietal: Extract84_le1

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract2_le2

description:
GBM
Treatment, type=remove


title: brain, Left frontal Lobe: Extract18_le2

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract82_le1

description:
GBM
Treatment, type=remove

source_name: brain, Right Temporal Lobe

value: brain, Right Temporal Lobe


title: brain, left frontal temporal lobe: Extract3_le1

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract81_le1

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract82_le2

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract80_le2

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract81_le2

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Parietal: Extract83_le2

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract1_le2

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract1_le1

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract78_le1

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract79_le2

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Parietal: Extract85_le2

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract42_le2

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract42_le1

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract80_le1

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract79_le1

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Parietal: Extract84_le2

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract2_le1

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract78_le2

description:
GBM
Treatment, type=remove


title: brain, left frontal temporal lobe: Extract3_le2

description:
GBM
Treatment, type=remove


title: brain, Right Parietal Lobe: Extract74_le1

description:
GBM
Treatment, type=remove

source_name: brain, Right Parietal Lobe

value: brain, Right Parietal Lobe


title: brain, Right Parietal Lobe: Extract74_le2

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract77_le2

description:
GBM
Treatment, type=remove


title: brain, Right Temporal Lobe: Extract77_le1

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Temporal: Extract69_le2

description:
GBM
Treatment, type=remove

source_name: brain, Right Frontal Temporal

value: brain, Right Frontal Temporal


title: brain, Right Parietal Lobe: Extract73_le2

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Temporal: Extract70_le1

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Parietal: Extract66_le1

description:
GBM
Treatment, type=remove

source_name: brain, Right Frontal Parietal

value: brain, Right Frontal Parietal


title: brain, Right Parietal Lobe: Extract73_le1

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Temporal: Extract68_le1

description:
GBM
Treatment, type=remove


title: brain, Right Parietal Occipital: Extract75_le2

description:
GBM
Treatment, type=remove

source_name: brain, Right Parietal Occipital

value: brain, Right Parietal Occipital


title: brain, Right Frontal Temporal: Extract70_le2

description:
GBM
Treatment, type=remove

value: GBM


title: brain, Right Frontal Temporal: Extract69_le1

description:
GBM
Treatment, type=remove

value: FEMALE


title: brain, Right Frontal Parietal: Extract66_le2

description:
GBM
Treatment, type=remove

value: ALIVE


title: brain, Right Frontal Lobe: Extract63_le2

description:
GBM
Treatment, type=remove

source_name: brain, Right Frontal Lobe

value: brain, Right Frontal Lobe

value: DECEASED


title: brain, Right Frontal Temporal: Extract68_le2

description:
GBM
Treatment, type=remove

value: MALE


title: brain, Right Frontal Parietal: Extract65_le1

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Temporal: Extract67_le1

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract63_le1

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Temporal: Extract67_le2

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract61_le1

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract62_le2

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract64_le1

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract60_le1

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract64_le2

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract62_le1

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Parietal: Extract65_le2

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract59_le2

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract59_le1

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract60_le2

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract61_le2

description:
GBM
Treatment, type=remove


title: brain, Right Frontal Lobe: Extract58_le2

description:
GBM
Treatment, type=remove

hyb_protocol: Standard Affymetrix protocols were used. Standard Affymetrix protocols were used.

label_protocol:
Probes were prepared using standard Affymetrix protocols and hybridized to Affymetrix HG-U133A and HG-U133B arrays (Affymetrix, Santa Clara, CA).
Probes were prepared using standard Affymetrix protocols and hybridized to Affymetrix HG-U133A and HG-U133B arrays (Affymetrix, Santa Clara, CA).

extract_protocol:
RNA extraction was performed as described previously (Mischel PS, Shai R, Shi T, et al Identification of molecular subtypes of glioblastoma by gene expression profiling. Oncogene, 2003;22:2361-73) and analyzed on both a spectrophotometer and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
RNA extraction was performed as described previously (Mischel PS, Shai R, Shi T, et al Identification of molecular subtypes of glioblastoma by gene expression profiling. Oncogene, 2003;22:2361-73) and analyzed on both a spectrophotometer and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).


title: brain, Right Frontal Lobe: Extract58_le1

description:
GBM
Treatment, type=remove


title: brain, Right Parietal Occipital: Extract75_le1

description:
GBM
Treatment, type=remove