title: Ovarian cancer_sample 61

description: 091301 HGU95Av2 SC H1


title: Ovarian cancer_sample 25

status: Public on Jul 11 2010

type: RNA

city: boston

first: panagiotis

last: konstantinopoulos

state: MA

address: 330 brookline av

department: hem/onc

country: USA

institute: bidmc

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: RMA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Ovarian cancer

label_protocol:
RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates

extract_protocol: RNA was isolated using the trizol protocol

tag: overall survival (months)

tag: overall survival (censored)

value: 0 [censored]

tag: dfs

tag: dfs(censored)

tag: histology

value: PS

tag: age

tag: Stage

tag: grade

tag: debulking (1=optimal)


title: Ovarian cancer_sample 26


title: 06-0678A-244k

status: Public on Jul 19 2011

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

hyb_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: Data for both channels were Lowess-normalized using the UNC microarray database, and then the log(2) ratio was taken.

source_name: Human Reference B

extract_protocol: Total RNA isolated by stratagene

tag: sample type

value: reference

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

source_name: cancer-adjacent normal tissue

extract_protocol: Qiagen Rneasy Kit

tag: tissue

value: cancer-adjacent normal tissue


title: Ovarian cancer_sample 60

description: 091301 HGU95Av2 SC G9

value: 1 [event (death)]


title: Ovarian cancer_sample 59

description: 091301 HGU95Av2 SC G7


title: Ovarian cancer_sample 58

description: 091301 HGU95Av2 SC G6

value: E


title: FoldChanges02, MA__2000252324310001, OdT_KK1Ctrl_Cy5_KK1TPA_Cy3_2.4_DS

status: Public on Apr 12 2011

city: Berlin

first: Ulf

middle: Andersson

last: Ørom

address: Ihnestrasse 63-73

department: OWL

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: 02_MA_2000252324310001_OdT_KK1Ctrl_Cy5_KK1TPA_Cy3_2.4.gpr

hyb_protocol: Agilent hybridization protocol.

scan_protocol: Agilent scanner.

data_processing: Extracted raw data were normalized using the limma package (Smyth 2004) developed within the Bioconductor project in the R statistical programming environment. Raw data was background corrected using the normexp method (Ritchie et al. 2007). The two channels were balanced by global lowess normalization, followed by scaling across arrays (Yang et al. 2002). Differential expression analysis was performed using SAM (Significance Analysis of Microarrays, Tusher et al. 2001).

source_name: Primary human keratinocytes isolated from newborn human foreskin, control

label_protocol: Cy3/Cy5 Agilent label protocol.

growth_protocol: Primary human keratinocytes were grown in complete KSFM from Invitrogen.

extract_protocol: Total RNA was extracted with TRIzol according to the manufacturer's recommendations.

treatment_protocol: Cells were left untreated or differentiated with 25 ng/ml TPA.

tag: gender

value: male

value: newborn foreskin

tag: cell type

value: primary keratinocytes

tag: treatment

source_name: Primary human keratinocytes isolated from newborn human foreskin, TPA

value: TPA


title: Ovarian cancer_sample 56

description: 091301 HGU95Av2 SC G4


title: Ovarian cancer_sample 65

description: 091803 HU95AV2 TL 15D7


title: Ovarian cancer_sample 57

description: 091301 HGU95Av2 SC G5


title: Ovarian cancer_sample 20


title: Ovarian cancer_sample 15


title: 06-0121B-244k

label_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

source_name: breast tumor

value: breast tumor


title: UNC04-0115B-244K7ug


title: 07-0158B-244k


title: Ovarian cancer_sample 19


title: Ovarian cancer_sample 14


title: Ovarian cancer_sample 12


title: Ovarian cancer_sample 17


title: Ovarian cancer_sample 21


title: Ovarian cancer_sample 18


title: Ovarian cancer_sample 13


title: UNC98-2049B-244K


title: Ovarian cancer_sample 10


title: Ovarian cancer_sample 27


title: Ovarian cancer_sample 11


title: Ovarian cancer_sample 52

description: 090903 HGU95AV2 TL 14D1


title: Ovarian cancer_sample 50

description: 090903 HGU95AV2 TL 14C8


title: Ovarian cancer_sample 49

description: 090903 HGU95AV2 TL 14C6


title: Ovarian cancer_sample 45

description: 090903 HGU95AV2 TL 14B5


title: 06-1067A-244k


title: Ovarian cancer_sample 8


title: Ovarian cancer_sample 46

description: 090903 HGU95AV2 TL 14B6


title: Ovarian cancer_sample 51

description: 090903 HGU95AV2 TL 14C9


title: Ovarian cancer_sample 6


title: Ovarian cancer_sample 9


title: Ovarian cancer_sample 44

description: 090903 HGU95AV2 TL 14B3


title: UNC04-0550A-244K


title: Ovarian cancer_sample 41

description: 082002 HGU95Av2 DS 7C3


title: Ovarian cancer_sample 5


title: Ovarian cancer_sample 1


title: Ovarian cancer_sample 3


title: Ovarian cancer_sample 54

description: 090903 HGU95AV2 TL 14D5


title: Ovarian cancer_sample 53

description: 090903 HGU95AV2 TL 14D3


title: Ovarian cancer_sample 40

description: 082002 HGU95Av2 DS 7C2


title: Ovarian cancer_sample 48

description: 090903 HGU95AV2 TL 14C3


title: Ovarian cancer_sample 63

description: 091803 HU95AV2 TL 15D4


title: Ovarian cancer_sample 4


title: Ovarian cancer_sample 42

description: 082002 HGU95Av2 DS 7C4


title: Ovarian cancer_sample 43

description: 090903 HGU95AV2 TL 14B2


title: Ovarian cancer_sample 39

description: 082002 HGU95Av2 DS 7B9


title: Ovarian cancer_sample 38

description: 082002 HGU95Av2 DS 7B8


title: Ovarian cancer_sample 47

description: 090903 HGU95AV2 TL 14C2


title: Ovarian cancer_sample 7


title: Ovarian cancer_sample 2


title: Ovarian cancer_sample 29

description: 082002 HGU95Av2 DS 7A3


title: Ovarian cancer_sample 36

description: 082002 HGU95Av2 DS 7B3


title: Ovarian cancer_sample 30

description: 082002 HGU95Av2 DS 7A4


title: Ovarian cancer_sample 31

description: 082002 HGU95Av2 DS 7A5


title: Ovarian cancer_sample 37

description: 082002 HGU95Av2 DS 7B5

value: C


title: Ovarian cancer_sample 32

description: 082002 HGU95Av2 DS 7A6


title: Ovarian cancer_sample 33

description: 082002 HGU95Av2 DS 7A7


title: Ovarian cancer_sample 34

description: 082002 HGU95AV2 DS 7A9


title: Ovarian cancer_sample 35

description: 082002 HGU95Av2 DS 7B2


title: Ovarian cancer_sample 23


title: Ovarian cancer_sample 55

description: 090903 HGU95AV2 TL 14D6


title: Ovarian cancer_sample 16


title: Integrative genomics of ovarian cancer P2205 [GenomeWideSNP_6]

status: Public on Apr 19 2010

type: genomic

city: Melbourne

first: Manasa

last: Ramakrishna

state: Victoria

address: St Andrew's Pl

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: According to Affymetrix protocol using recommended instrumentation

scan_protocol: According to Affymetrix protocol and using GeneChip Operating Software

data_processing: primary data description: Partek's copy number workflow generates copy number ratios relative to matching normal samples or a pooled baseline and then converts and presents these values as whole copy numbers. The file titled SNP6_Normalised-Copy-number.csv contains these values for each sample. In this file, probes on Chromosome Y and the Mitochondrion (MT) have been removed and the probesets are organised first by Chromosome and then by start position. Annotations for this were mapped in Partek using the Affymetrix GenomewideSNP6, CN and SNP annotation files, release number 23. This data was then used for Segmentation using the CBS algorithm in the DNAcopy package in R open-source software.

molecule: genomic DNA

source_name: Ovarian tumours at the time of diagnosis

label_protocol: According to Affymetrix protocol, Biotin labelled

extract_protocol: 10uM slices of tumour were hand-microdissected to obtain regions with >80% epithelial cells and reduce contamination from fibroblasts, blood vessels etc. Following this, for DNA extraction, slides containing sections were stained with Haematoxylin and Eosin and DNA was extracted using the Qiagen DNEasy kit. For RNA, identical slides were stained with Cresyl violet and total RNA was extracted using the Ambion mirVana kit according to manufacturer's instructions.

treatment_protocol: All tumours were fresh-frozen and OCT embedded. Lymphocytic DNA was extracted from stored blood samples.

tag: tissue type (t=tumour; n= normal blood lymphocyte)

value: T

tag: histological subtype

value: serous

tag: stage

tag: scandate(batch)

tag: source


title: Integrative genomics of ovarian cancer P0706 [GenomeWideSNP_6]

value: T&N


title: Integrative genomics of ovarian cancer P1854 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P4075 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P4684 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P4076 [GenomeWideSNP_6]

value: unknown


title: Integrative genomics of ovarian cancer P0933 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P4085 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P7820 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P1348 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC499 [GenomeWideSNP_6]

value: Campbell


title: Integrative genomics of ovarian cancer P1246 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC548 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P4178 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC407 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P4093 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC382 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P4616 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC579 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P1555 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC328 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer IC487 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P2712 [GenomeWideSNP_6]


title: Hepatocellular carcinoma (hcc_120)

status: Public on Sep 08 2009

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description:
na
Surgically resected 118 tumor tissues from patients with hepatocellular carcinoma (HCC)

hyb_protocol: Refer to the Illumina DASL Assay System Manual. Hybridization was performed for 4 DASL assay oligo pool (DAP)s, DAP1~4, including 1536 probes each on 4 separate microarrays.

data_processing: For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were were then normalized using the cubic spline algorithm for each DAP.

label: Cy3 and Cy5

source_name: hepatocellular carcinoma

extract_protocol: Using 10µm sections taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using High Pure Paraffin FFPE kit (Roche).

tag: hepatitis b virus (hbs antigen)

value: positive

tag: hepatitis c virus

value: negative

tag: alcohol (cumulative intake)


title: Integrative genomics of ovarian cancer P1049 [GenomeWideSNP_6]

tag: age


title: Integrative genomics of ovarian cancer P2803 [GenomeWideSNP_6]

tag: grade


title: Integrative genomics of ovarian cancer IC493 [GenomeWideSNP_6]


title: Hepatocellular carcinoma (hcc_115)

scan_protocol: Refer to the Illumina DASL Assay System Manual


title: Integrative genomics of ovarian cancer P1953 [GenomeWideSNP_6]


title: Integrative genomics of ovarian cancer P4219 [GenomeWideSNP_6]


title: Hepatocellular carcinoma (hcc_102)

label_protocol: Refer to the Illumina DASL Assay System Manual


title: Hepatocellular carcinoma (hcc_118)


title: Hepatocellular carcinoma (hcc_110)


title: Hepatocellular carcinoma (hcc_119)


title: Hepatocellular carcinoma (hcc_098)


title: Hepatocellular carcinoma (hcc_095)


title: Hepatocellular carcinoma (hcc_090)


title: Hepatocellular carcinoma (hcc_093)


title: Hepatocellular carcinoma (hcc_088)


title: Hepatocellular carcinoma (hcc_105)


title: Hepatocellular carcinoma (hcc_091)


title: Hepatocellular carcinoma (hcc_089)


title: Hepatocellular carcinoma (hcc_111)


title: Hepatocellular carcinoma (hcc_087)


title: Hepatocellular carcinoma (hcc_081)


title: Hepatocellular carcinoma (hcc_077)


title: Hepatocellular carcinoma (hcc_037)


title: Hepatocellular carcinoma (hcc_122)


title: Hepatocellular carcinoma (hcc_026)


title: Hepatocellular carcinoma (hcc_060)


title: Hepatocellular carcinoma (hcc_085)


title: Hepatocellular carcinoma (hcc_019)


title: Hepatocellular carcinoma (hcc_030)


title: Hepatocellular carcinoma (hcc_034)


title: Hepatocellular carcinoma (hcc_044)


title: Hepatocellular carcinoma (hcc_074)


title: Hepatocellular carcinoma (hcc_050)


title: Hepatocellular carcinoma (hcc_006)


title: Hepatocellular carcinoma (hcc_063)


title: Hepatocellular carcinoma (hcc_013)


title: Hepatocellular carcinoma (hcc_042)


title: Hepatocellular carcinoma (hcc_001)


title: Hepatocellular carcinoma (hcc_018)


title: Hepatocellular carcinoma (hcc_004)


title: Hepatocellular carcinoma (hcc_007)


title: patient193;pretreatment;female;breast tumor

status: Public on Aug 15 2009

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: breast tumor biopsy

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized on U133 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-2v4.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: dChip version2006

source_name: human breast tumor

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

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

value: female

value: pretreatment


title: patient190;pretreatment;female;breast tumor

description: breast tumor biopsy


title: patient195;pretreatment;female;breast tumor

description: breast tumor biopsy


title: Integrative genomics of ovarian cancer IC318 [GenomeWideSNP_6]


title: Hepatocellular carcinoma (hcc_125)

status: Public on Oct 15 2008

tag: used for prognostic prediction

value: No

tag: survival time (days)

tag: survival status (0

value: alive or censored, 1:dead) :1


title: Hepatocellular carcinoma (hcc_114)


title: patient161;pretreatment;female;breast tumor

description: breast tumor biopsy

tag: tissue


title: patient137;pretreatment;female;breast tumor

description: breast tumor biopsy

tag: gender


title: patient109;pretreatment;female;breast tumor

description: breast tumor biopsy


title: patient152;pretreatment;female;breast tumor

description: breast tumor biopsy


title: patient173;pretreatment;female;breast tumor

description: breast tumor biopsy


title: patient136;pretreatment;female;breast tumor

description: breast tumor biopsy


title: patient116;pretreatment;female;breast tumor

description: breast tumor biopsy


title: patient159;pretreatment;female;breast tumor

description: breast tumor biopsy


title: Integrative genomics of ovarian cancer IC315 [GenomeWideSNP_6]


title: Hepatocellular carcinoma (hcc_112)


title: patient133;pretreatment;female;breast tumor

description: breast tumor biopsy


title: patient112;pretreatment;female;breast tumor

description: breast tumor biopsy


title: patient50;pretreatment;female;breast tumor

description: breast tumor biopsy


title: Hepatocellular carcinoma (hcc_078)

value: alive or censored, 1:dead) :0


title: patient40;pretreatment;female;breast tumor

description: breast tumor biopsy


title: patient126;pretreatment;female;breast tumor

description: breast tumor biopsy


title: patient40;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy

value: Letrozole, 2.5mg/day,oral, 3 months


title: Hepatocellular carcinoma (hcc_076)


title: Hepatocellular carcinoma (hcc_099)


title: Integrative genomics of ovarian cancer IC288 [GenomeWideSNP_6]


title: patient117;pretreatment;female;breast tumor

description: breast tumor biopsy


title: Hepatocellular carcinoma (hcc_070)


title: Hepatocellular carcinoma (hcc_054)


title: Hepatocellular carcinoma (hcc_012)


title: Hepatocellular carcinoma (hcc_072)


title: Hepatocellular carcinoma (hcc_008)


title: Hepatitis/cirrhotic liver (bkg_131)

source_name: hepatitis/cirrhotic liver

tag: survival_status (0

value: alive_or_censored, 1:dead): 0

tag: ethnicity

value: Japanese

tag: egf level

value: Low

tag: recurrence status (0

value: no recurrence of censored, 1:recurrence):1

tag: time to hcc recurrence (days)

tag: early recurrence status (0

value: no recurrence of censored, 1:recurrence < 2 years):0

tag: late recurrence status (0

value: no recurrence of censored, 1:recurrence >= 2 years):1


title: Hepatocellular carcinoma (hcc_003)

tag: hepatitis b virus (hbs antigen)


title: Hepatocellular carcinoma (hcc_068)

tag: hepatitis c virus


title: Hepatocellular carcinoma (hcc_009)

tag: alcohol (cumulative intake)


title: Hepatitis/cirrhotic liver (bkg_123)

value: no recurrence of censored, 1:recurrence):0

value: no recurrence of censored, 1:recurrence >= 2 years):0


title: Hepatocellular carcinoma (hcc_010)


title: Hepatocellular carcinoma (hcc_014)


title: Hepatitis/cirrhotic liver (bkg_133)

value: Yes


title: Hepatitis/cirrhotic liver (bkg_130)

value: alive_or_censored, 1:dead): 1

value: no recurrence of censored, 1:recurrence < 2 years):1


title: Hepatitis/cirrhotic liver (bkg_126)


title: Hepatitis/cirrhotic liver (bkg_119)


title: Hepatocellular carcinoma (hcc_011)

value: negative

value: positive


title: Hepatitis/cirrhotic liver (bkg_127)

value: High

value: No


title: Integrative genomics of ovarian cancer IC022 [GenomeWideSNP_6]

tag: tissue type (t=tumour; n= normal blood lymphocyte)

value: T&N

tag: histological subtype

value: serous

tag: stage

tag: age

tag: scandate(batch)

tag: source

value: Campbell


title: Hepatitis/cirrhotic liver (bkg_128)

tag: survival time (days)

value: alive_or_censored, 1:dead): 0

value: Japanese

tag: used for prognostic prediction


title: Hepatitis/cirrhotic liver (bkg_122)

tag: survival_status (0

tag: ethnicity

value: Low

value: no recurrence of censored, 1:recurrence):1


title: Hepatitis/cirrhotic liver (bkg_117)

tag: egf level

tag: recurrence status (0

value: no recurrence of censored, 1:recurrence < 2 years):0


title: Hepatitis/cirrhotic liver (bkg_118)

tag: time to hcc recurrence (days)

tag: early recurrence status (0


title: Integrative genomics of ovarian cancer IC325 [GenomeWideSNP_6]

tag: grade


title: Hepatocellular carcinoma (hcc_061)

tag: survival status (0

value: alive or censored, 1:dead) :1

tag: hepatitis b virus (hbs antigen)

tag: hepatitis c virus


title: patient114;pretreatment;female;breast tumor

description: breast tumor biopsy

tag: gender

value: female

tag: tissue

value: breast tumor

tag: treatment

value: pretreatment


title: Hepatitis/cirrhotic liver (bkg_115)

tag: late recurrence status (0

value: no recurrence of censored, 1:recurrence >= 2 years):1


title: Hepatitis/cirrhotic liver (bkg_090)

value: alive_or_censored, 1:dead): 1

value: no recurrence of censored, 1:recurrence < 2 years):1

value: no recurrence of censored, 1:recurrence >= 2 years):0


title: Hepatitis/cirrhotic liver (bkg_107)

value: Yes


title: Hepatitis/cirrhotic liver (bkg_116)


title: Hepatitis/cirrhotic liver (bkg_109)


title: Hepatitis/cirrhotic liver (bkg_083)

value: no recurrence of censored, 1:recurrence):0


title: Hepatitis/cirrhotic liver (bkg_093)

value: No


title: Hepatitis/cirrhotic liver (bkg_097)


title: Hepatitis/cirrhotic liver (bkg_084)


title: Hepatitis/cirrhotic liver (bkg_106)

value: High


title: Hepatitis/cirrhotic liver (bkg_086)

value: alive_or_censored, 1:dead): 0


title: Hepatitis/cirrhotic liver (bkg_094)

value: Japanese


title: Hepatitis/cirrhotic liver (bkg_080)

value: Low


title: Hepatitis/cirrhotic liver (bkg_101)

value: no recurrence of censored, 1:recurrence):1


title: Hepatitis/cirrhotic liver (bkg_098)

value: no recurrence of censored, 1:recurrence < 2 years):0


title: Hepatitis/cirrhotic liver (bkg_079)


title: Hepatitis/cirrhotic liver (bkg_075)


title: Hepatitis/cirrhotic liver (bkg_113)


title: Hepatitis/cirrhotic liver (bkg_077)


title: Hepatitis/cirrhotic liver (bkg_104)


title: Hepatitis/cirrhotic liver (bkg_134)


title: Hepatitis/cirrhotic liver (bkg_091)


title: Hepatitis/cirrhotic liver (bkg_073)


title: Integrative genomics of ovarian cancer IC026 [GenomeWideSNP_6]

tag: tissue type (t=tumour; n= normal blood lymphocyte)

value: T&N

tag: histological subtype

value: serous

tag: stage

tag: age

tag: scandate(batch)

tag: source

value: Campbell


title: Hepatitis/cirrhotic liver (bkg_067)

tag: survival time (days)

tag: survival_status (0

tag: ethnicity

tag: egf level

tag: used for prognostic prediction

tag: recurrence status (0


title: Hepatitis/cirrhotic liver (bkg_069)

tag: time to hcc recurrence (days)

tag: early recurrence status (0


title: Hepatitis/cirrhotic liver (bkg_050)


title: Hepatitis/cirrhotic liver (bkg_047)


title: Hepatitis/cirrhotic liver (bkg_055)


title: Hepatitis/cirrhotic liver (bkg_056)


title: Hepatitis/cirrhotic liver (bkg_045)


title: Hepatitis/cirrhotic liver (bkg_058)


title: Hepatitis/cirrhotic liver (bkg_059)


title: Hepatitis/cirrhotic liver (bkg_053)


title: Hepatitis/cirrhotic liver (bkg_043)


title: Hepatitis/cirrhotic liver (bkg_049)


title: Hepatitis/cirrhotic liver (bkg_040)


title: Hepatitis/cirrhotic liver (bkg_066)


title: Hepatitis/cirrhotic liver (bkg_062)


title: Hepatitis/cirrhotic liver (bkg_039)


title: Hepatitis/cirrhotic liver (bkg_036)


title: Hepatitis/cirrhotic liver (bkg_048)


title: Hepatitis/cirrhotic liver (bkg_038)


title: Hepatitis/cirrhotic liver (bkg_065)


title: Hepatitis/cirrhotic liver (bkg_064)


title: Hepatitis/cirrhotic liver (bkg_033)


title: Hepatitis/cirrhotic liver (bkg_052)


title: Integrative genomics of ovarian cancer IC201 [GenomeWideSNP_6]

tag: grade


title: Hepatitis/cirrhotic liver (bkg_051)


title: Hepatocellular carcinoma (hcc_132)

tag: survival status (0

value: alive or censored, 1:dead) :0

tag: hepatitis b virus (hbs antigen)

value: negative

tag: hepatitis c virus

value: positive

tag: alcohol (cumulative intake)


title: Hepatitis/cirrhotic liver (bkg_031)

value: alive_or_censored, 1:dead): 1

tag: late recurrence status (0

value: no recurrence of censored, 1:recurrence >= 2 years):1


title: Hepatitis/cirrhotic liver (bkg_041)

value: Yes

value: no recurrence of censored, 1:recurrence >= 2 years):0


title: Hepatitis/cirrhotic liver (bkg_027)

value: no recurrence of censored, 1:recurrence):0


title: Hepatitis/cirrhotic liver (bkg_028)


title: Hepatitis/cirrhotic liver (bkg_029)


title: Hepatitis/cirrhotic liver (bkg_025)


title: Hepatitis/cirrhotic liver (bkg_026)

value: No

value: no recurrence of censored, 1:recurrence < 2 years):1


title: Hepatitis/cirrhotic liver (bkg_035)

value: Japanese


title: Hepatitis/cirrhotic liver (bkg_032)

value: alive_or_censored, 1:dead): 0

value: Low


title: Hepatitis/cirrhotic liver (bkg_021)

value: no recurrence of censored, 1:recurrence):1


title: Hepatitis/cirrhotic liver (bkg_020)


title: Hepatitis/cirrhotic liver (bkg_016)

value: no recurrence of censored, 1:recurrence < 2 years):0


title: Hepatitis/cirrhotic liver (bkg_023)


title: Hepatitis/cirrhotic liver (bkg_022)


title: Hepatitis/cirrhotic liver (bkg_017)


title: Hepatitis/cirrhotic liver (bkg_006)


title: Hepatitis/cirrhotic liver (bkg_002)


title: Hepatitis/cirrhotic liver (bkg_015)


title: Hepatitis/cirrhotic liver (bkg_003)

value: High


title: Hepatitis/cirrhotic liver (bkg_018)


title: PRB9907 (HG-U133B)

status: Public on Mar 15 2006

city: South San Francisco

first: Thomas

middle: D.

last: Wu

state: CA

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 8 ug of total RNA was processed to produce biotynylated cRNA targets

extract_protocol: Qiagen RNeasy Mini Kit

tag: who grade

value: IV with necrosis

tag: age

tag: Sex

value: M

tag: survival (weeks)

tag: censor

value: yes

tag: specimen type

value: primary

tag: matching sample


title: PRB4793 (HG-U133A)

description: high-grade astrocytoma

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

value: III

value: no


title: PRB9907 (HG-U133A)

description: high-grade astrocytoma


title: PRB5070 (HG-U133A)

description: high-grade astrocytoma

value: F


title: PRB5070 (HG-U133B)

description: high-grade astrocytoma


title: PRB4784 (HG-U133A)

description: high-grade astrocytoma


title: PRB5063 (HG-U133A)

description: high-grade astrocytoma


title: PRB4783 (HG-U133A)

description: high-grade astrocytoma


title: PRB9938 (HG-U133B)

description: high-grade astrocytoma

value: IV

value: recurrent


title: PRB9938 (HG-U133A)

description: high-grade astrocytoma


title: PRB4793 (HG-U133B)

description: high-grade astrocytoma


title: PRB5063 (HG-U133B)

description: high-grade astrocytoma


title: Hepatitis/cirrhotic liver (bkg_005)

tag: survival time (days)

tag: survival_status (0

value: alive_or_censored, 1:dead): 1

tag: ethnicity

tag: egf level

tag: used for prognostic prediction

value: Yes

value: no recurrence of censored, 1:recurrence >= 2 years):0


title: PRB4783 (HG-U133B)

description: high-grade astrocytoma


title: PRB4790 (HG-U133B)

description: high-grade astrocytoma


title: PRB4779 (HG-U133B)

description: high-grade astrocytoma


title: PRB4779 (HG-U133A)

description: high-grade astrocytoma


title: PRB4781 (HG-U133A)

description: high-grade astrocytoma


title: PRB4790 (HG-U133A)

description: high-grade astrocytoma


title: PRB4780 (HG-U133A)

description: high-grade astrocytoma


title: PRB4781 (HG-U133B)

description: high-grade astrocytoma


title: PRB4780 (HG-U133B)

description: high-grade astrocytoma


title: PRB4778 (HG-U133B)

description: high-grade astrocytoma


title: PRB4784 (HG-U133B)

description: high-grade astrocytoma


title: PRB4778 (HG-U133A)

description: high-grade astrocytoma


title: Hepatitis/cirrhotic liver (bkg_024)

value: alive_or_censored, 1:dead): 0

value: Japanese

tag: recurrence status (0

tag: time to hcc recurrence (days)

tag: early recurrence status (0

value: no recurrence of censored, 1:recurrence < 2 years):1


title: Hepatitis/cirrhotic liver (bkg_082)

value: no recurrence of censored, 1:recurrence):1


title: Hepatitis/cirrhotic liver (bkg_103)

value: Low

value: no recurrence of censored, 1:recurrence < 2 years):0

value: no recurrence of censored, 1:recurrence >= 2 years):1


title: PRB4770 (HG-U133B)

description: high-grade astrocytoma


title: PRB4773 (HG-U133B)

description: high-grade astrocytoma

value: M


title: PRB4770 (HG-U133A)

description: high-grade astrocytoma

value: primary


title: PRB4765 (HG-U133A)

description: high-grade astrocytoma

value: III


title: PRB4774 (HG-U133B)

description: high-grade astrocytoma

value: no


title: PRB4765 (HG-U133B)

description: high-grade astrocytoma


title: PRB4757 (HG-U133B)

description: high-grade astrocytoma

value: yes


title: PRB4761 (HG-U133B)

description: high-grade astrocytoma

value: IV

value: F


title: PRB4773 (HG-U133A)

description: high-grade astrocytoma

value: recurrent


title: PRB4755 (HG-U133A)

description: high-grade astrocytoma


title: PRB4756 (HG-U133A)

description: high-grade astrocytoma


title: PRB4755 (HG-U133B)

description: high-grade astrocytoma


title: PRB4751 (HG-U133B)

description: high-grade astrocytoma


title: PRB4776 (HG-U133A)

description: high-grade astrocytoma


title: PRB4776 (HG-U133B)

description: high-grade astrocytoma


title: PRB4750 (HG-U133B)

description: high-grade astrocytoma


title: PRB4774 (HG-U133A)

description: high-grade astrocytoma


title: PRB4745 (HG-U133B)

description: high-grade astrocytoma


title: PRB4757 (HG-U133A)

description: high-grade astrocytoma


title: PRB4756 (HG-U133B)

description: high-grade astrocytoma


title: PRB4750 (HG-U133A)

description: high-grade astrocytoma


title: PRB4746 (HG-U133B)

description: high-grade astrocytoma


title: PRB4749 (HG-U133B)

description: high-grade astrocytoma


title: PRB4751 (HG-U133A)

description: high-grade astrocytoma


title: PRB4749 (HG-U133A)

description: high-grade astrocytoma


title: PRB4746 (HG-U133A)

description: high-grade astrocytoma


title: PRB4761 (HG-U133A)

description: high-grade astrocytoma


title: PRB4745 (HG-U133A)

description: high-grade astrocytoma


title: 20C, t=168hr

status: Public on Jan 06 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: temperature acclimation, Cold acclimation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30855.gif

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Austrofundulus limnaeus

source_name: Liver Reference RNA 4/17/02, (pooled, 1 ug poly-A)

source_name: 20-168, adult liver (pooled, 1 ug, poly-A)