title: chinmo_E-0-12h

description:
chinmo_E-0-12h
test: 0-12h_chinmo.CEL
test: chimmo_1_9.CEL
test: chimmo_2_10.CEL
reference: 0-12h_Input.CEL
reference: input_0-12h_16.CEL

value: chinmo


title: dCtBP7667_E-0-12h

status: Public on May 12 2009

type: genomic

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

country: USA

institute: University of Chicago

description:
dCtBP7667_E-0-12h
test: 67.CEL
test: B2_7667.CEL
test: B2_7667_5.CEL
reference: B2_Mock.CEL
reference: B2_Mock_5.CEL
reference: I.CEL

hyb_protocol: Affymetrix Hybridization Protocol - Hybridizations were performed at the Functional Genomics Facility (FGF) at the University of Chicago.

scan_protocol: Affymetrix Protocol - Scans were performed at the Functional Genomics Facility (FGF) at the University of Chicago.

data_processing:
.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks.
.bed and .bar were generated with MAT.

label: biotin

molecule: genomic DNA

organism: Drosophila melanogaster

label_protocol: Affymetrix Labeling Protocol (TdT labeling)

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-12 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 pm and flies are allowed to lay eggs for 12 hours. 3. Embryos are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.

extract_protocol: Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.

treatment_protocol: No Treatment

tag: antibody

tag: tissue

value: Embryos

tag: time point

tag: reference

value: input


title: dll_E-0-12h

description:
dll_E-0-12h
test: dll_1.CEL
test: dll_2.CEL
test: dll_3.CEL
reference: KW_Input_1.CEL
reference: KW_Input_2.CEL
reference: KW_Input_3.CEL

value: dll


title: bks_E-0-12h

description:
bks_E-0-12h
test: bks_1.CEL
test: bks_2.CEL
test: bks_3.CEL
reference: KW_Input_1.CEL
reference: KW_Input_2.CEL
reference: KW_Input_3.CEL

value: bks


title: FTZ-F1_E0-12h

description:
FTZ-F1_E0-12h
test: A1_ftz_f1.CEL
test: B1_ftz_f1.CEL
test: ftz-f1.CEL
reference: A1_Mock_B.CEL
reference: B1_Mock_S.CEL
reference: I.CEL


title: ENserum_E0-12h

description:
ENserum_E0-12h
test: 3_LM-EN.CEL
test: 7_K-EN.CEL
test: A1_EN.CEL
reference: 1_LM-IPUT.CEL
reference: 2_LM-_MOCK.CEL
reference: 5_K-M.CEL
reference: A1_Mock.CEL

value: ENserum


title: INVGFP_E0-12h

description:
INVGFP_E0-12h
test: INV_GFP_R1.CEL
test: INV_GFP_R2.CEL
test: INV_GFP_R3.CEL
reference: INV_GFP_input.CEL

value: INVGFP

source_name: input


title: D_E0-12h

description:
ChIP-chip of D in Drosohila embryos at E0-12h time point.
test: 2-4-09-D.CEL
test: A2__D.CEL
test: B2_D.CEL
test: sD.CEL
reference: 2-4-09-Input_0-12h_3%.CEL
reference: I.CEL
reference: S_A2_Mock.CEL
reference: S_B2_Mock.CEL

value: D


title: CNC_E0-12h

description:
ChIP-chip of CNC in Drosohila embryos at E0-12h time point.
test: A2_CNC.CEL
test: B2_CNC.CEL
test: c_nc.CEL
test: cnc.CEL
reference: I.CEL
reference: input_0-12h_3%.CEL
reference: S_A2_Mock.CEL
reference: S_B2_Mock.CEL

value: CNC


title: bab1_E0-12h

description:
ChIP-chip of bab1 in Drosohila embryos at 0-12 hours of development
test: 0-12h_bab_1_R1.CEL
test: 0-12h_bab_1_R2.CEL
test: bab_I_8.CEL
reference: 0-12h_Input.CEL
reference: Input_1.CEL

data_processing:
MAT_bab1_E0-12h.bed and MAT_bab1_E0-12h.Dm_tiling2_MR_v01_dm3.NR.bpmap_matscore.bar were generated with MAT.
.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks.

source_name: Embryo 0-12 hours

extract_protocol: Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IP'd material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.


title: Stat92E_E0-12h

description:
test: 0-12h_stat_92E.CEL
test: stat_92E_1_7.CEL
test: stat_92E_28.CEL
reference: 0-12h_Input.CEL
reference: input_0-12h_16.CEL
Stat92E_E0-12h


title: SampleNumber: 70

status: Public on Apr 30 2006

type: RNA

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Ave

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

description: Experimental factor value:  Day 1 samples = control, SIRS, or septic shock. Day 3 samples = SIRS, septic shock, or SIRS resolved

hyb_protocol: The protocol and conditions used during hybridization, blocking and washing:  Create a hybridization cocktail for a single probe array that contains 0.05 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm

scan_protocol: The image file was captured on an Affymetrix Gene Chip Scanner 3000

data_processing:
Processed with Microarray suite 5.0 (Affymetrix) to generate .CEL files that were subject to RMA normalization (Irizarry et al 2003) using GeneSpring software.
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.2 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. All the samples were then normalized to the median of the controls

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to manufacturer’s instructions.

extract_protocol:
Total RNA was extracted from whole blood samples using the PaxGene Blood RNA System (PreAnalytiX, Qiagen/Becton Dickson) according the manufacturer’s specifications.
Quality control steps:   RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used

tag: Dx

value: SIRS

tag: survival

value: survivor

tag: day

tag: ptID

tag: DxSurv

tag: PRISM

tag: steroid

value: no

tag: organism

value: Lung

value: Grp A

value: Grp A2


title: mod(mdg4)_replicates 1,2,3

status: Public on May 29 2009

description:
test CEL files: mod_mdg4_A2.CEL mod_mdg4_B2.CEL mod_mdg4_ss7_mdj4.CEL
control CEL files: mod_mdg4_A2_input.CEL mod_mdg4_B2_input_2.CEL mod_mdg4_ss2_input.CEL
mod(mdg4)_replicates 1,2,3

data_processing:
.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files and peak finding
.bar and .bed are generated by MAT. .bar contains log2(IP/Input) fold changes for each probe. .bed files contains the peak calls at 1%fdr from MAT.

extract_protocol: Drosophila embryos are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IP'd material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.

treatment_protocol: No treatment

tag: test

value: Chromatin

value: INPUT


title: SampleNumber: 5

value: Enterococcus

value: Urine

value: Grp B

value: Grp B1


title: SampleNumber: 90

value: Grp B4


title: SampleNumber: 73

value: SepticShock

value: Rickettsia

value: Systemic


title: SampleNumber: 121

value: Herpes simplex

value: Grp A4


title: SampleNumber: 62

value: survivor

value: yes

value: C. diff.

value: Colitis

value: Grp C

value: Grp C2


title: 01-0063A_SIRS_day1_19

status: Public on Dec 12 2008

description: 1) Controls: 2) Septic shock; 3) Sepsis; 4) SIRS; 5) SIRS resolved

hyb_protocol: Create a hybridization cocktail for a single probe array that contains 0.05 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL  files were subjected to RMA  normalization using  the  GeneSpring GX 7.1.
Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
GeneSpring 7.2 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. All the samples were then normalized to the median of the controls.

label_protocol: 120 ng of total RNA from 2 wild type [WT] and 4 beta-catenin knock-out [KO] pancreata at the 14.5 and 16.5 time points was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].

extract_protocol:
Total RNA was extracted from whole blood using the PaxGene protocol.
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].

treatment_protocol: Samples were not manipulated.

tag: Whole blood from normal children and children with SIRS, sepsis, or septic shock.


title: SampleNumber: 45

value: SIRS

value: no

value: Staph Aureus

value: Lung

value: Grp B3


title: SampleNumber: 79

value: Appendicitis

value: Grp B


title: SampleNumber: 4

value: Enterococcus

value: Urine

value: Grp B1


title: SampleNumber: 43


title: SampleNumber: 54

value: Group B Strep

value: Blood and CSF

value: Grp A

value: Grp A2


title: HeLa cells control 1 (Luciferase siRNA transfection)

status: Public on Mar 01 2007

city: Heidelberg

first: Marcelo

last: Viegas

address: IM NEUENHEIMER FELD 156

country: Germany

institute: EMBL-MMPU

description: HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the first control (luciferase siRNA transfection).

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Oligonucleotide arrays were scanned using a confocal laser scanner (GeneArrayTM, Hewlett Packard, Palo Alto, CA).

data_processing: We used the Affymetrix GeneChip Suite 5.0 software (MAS 5.0) to calculate raw expression values for each of the 22,283 probe sets on the U133A oligonucleotide arrays.

molecule: cytoplasmic RNA

source_name: HeLa cells, 72 hs after transfection

label_protocol: Standard Affymetrix protocol

extract_protocol: protocol used in (Gehring et al., Mol.Cell, 2003); PMID: 12718880

tag: subject id

value: Subject 13

tag: gender

value: female

tag: diet enriched in

value: full-fat dairy products

tag: sample type

value: milk fat globule


title: SampleNumber: 61

value: SIRS

value: survivor

value: no

value: Candida albicans

value: Blood


title: SampleNumber: 68

value: Eikenella

value: Retropharyngeal abscess


title: SampleNumber: 44

value: yes

value: Staph Aureus

value: Lung

value: Grp B

value: Grp B3


title: SampleNumber: 77


title: SampleNumber: 71

value: SepticShock

value: Grp A

value: Grp A1


title: SampleNumber: 63

value: E coli

value: Urine


title: SampleNumber: 75

value: Neisseria

value: Grp B2


title: SampleNumber: 72

value: SIRS

value: survivor

value: Rickettsia

value: Systemic


title: SampleNumber: 9

value: Blood

value: Grp C

value: Grp C2


title: SampleNumber: 53

value: no

value: Staph Epi

value: Peritoneal fluid

value: NC


title: SampleNumber: 80

value: Appendicitis

value: Grp B

value: Grp B3


title: SampleNumber: 8

value: Grp B1


title: SampleNumber: 66

value: SepticShock

value: yes

value: Staph Aureus

value: Toxic shock syndrome

value: Grp B4


title: SampleNumber: 69

value: SIRS

value: survivor

value: Lung

value: Grp A

value: Grp A2


title: SampleNumber: 111

value: SirsReslv

value: Pseudomonas

value: Grp A3


title: SampleNumber: 36

value: no

value: Enterobacter

value: Grp C

value: Grp C3


title: SampleNumber: 34

value: Neisseria

value: Blood and CSF


title: SampleNumber: 23

value: yes

value: Staph Aureus

value: Cellulitis

value: Grp B

value: Grp B1


title: SampleNumber: 24

value: SepticShock

value: survivor

value: mult  gram neg

value: Blood


title: SampleNumber: 102

value: SIRS

value: H. flu

value: Lung

value: Grp B4


title: SampleNumber: 33

value: no

value: Grp A

value: Grp A3


title: SampleNumber: 117

value: SirsReslv


title: SampleNumber: 81

value: Varicella

value: Systemic


title: SampleNumber: 115

value: Strep viridans

value: Grp A1


title: SampleNumber: 98

value: yes

value: Grp B

value: Grp B3


title: SampleNumber: 91

value: survivor

value: mult  gram neg

value: Grp C

value: Grp C2


title: SampleNumber: 22

value: Staph Aureus

value: Cellulitis

value: Grp B1


title: SampleNumber: 88

value: SepticShock

value: no


title: SampleNumber: 112

value: SIRS

value: Pseudomonas

value: Lung

value: Grp A

value: Grp A3


title: SampleNumber: 96

value: SirsReslv

value: yes

value: Enterococcus

value: Blood

value: Grp A1


title: SampleNumber: 67

value: survivor

value: Eikenella

value: Retropharyngeal abscess


title: SampleNumber: 120

value: Herpes simplex

value: Systemic

value: Grp A4


title: SampleNumber: 26

value: nonsurvivor

value: no

value: Grp A2


title: SampleNumber: 32

value: SIRS

value: Lung


title: SampleNumber: 101

value: SepticShock

value: Strep Pneumo

value: Blood, CSF, and Lung

value: Grp C

value: Grp C3


title: SampleNumber: 42

value: SirsReslv

value: Grp B

value: Grp B3


title: SampleNumber: 28

value: survivor

value: Grp A

value: Grp A3


title: SampleNumber: 113

value: Grp A1


title: SampleNumber: 84

value: yes


title: SampleNumber: 94

value: no

value: Strep Viridans

value: Peritoneal fluid


title: SampleNumber: 10

value: Staph Aureus

value: Blood

value: Grp C2


title: SampleNumber: 55

value: Rotavirus

value: Colitis


title: SampleNumber: 107


title: SampleNumber: 27

value: SIRS

value: nonsurvivor

value: NC


title: SampleNumber: 86

value: SepticShock

value: Group B Strep

value: Blood and CSF


title: SampleNumber: 83

value: survivor

value: Neisseria

value: CSF

value: Grp A

value: Grp A4


title: SampleNumber: 29

value: no

value: Grp A3


title: SampleNumber: 97

value: yes

value: Enterococcus

value: Blood

value: Grp C

value: Grp C3


title: SampleNumber: 95

value: Strep Viridans

value: Peritoneal fluid

value: Grp B

value: Grp B2


title: SampleNumber: 99

value: SepticShock

value: Grp C2


title: SampleNumber: 14

value: survivor


title: SampleNumber: 87

value: Group B Strep

value: Blood and CSF

value: Grp A2


title: SampleNumber: 2

value: Group A Strep

value: Grp B1


title: SampleNumber: 85

value: yes

value: Lung

value: Grp A


title: SampleNumber: 122

value: no

value: Influenza

value: Systemic

value: Grp A4


title: SampleNumber: 17

value: Grp B

value: Grp B4


title: SampleNumber: 65

value: SepticShock


title: SampleNumber: 106

value: E coli

value: Blood

value: Grp C

value: Grp C2


title: SampleNumber: 82

value: survivor

value: Varicella

value: Grp B2


title: SampleNumber: 11

value: Grp B1


title: SampleNumber: 76

value: yes

value: Neisseria

value: Grp C3


title: SampleNumber: 109

value: Candida albicans

value: Grp A


title: SampleNumber: 92

value: mult  gram neg


title: SampleNumber: 64

value: no

value: Urine

value: Grp B

value: Grp B3


title: SampleNumber: 6

value: SepticShock

value: Staph Epi

value: Blood


title: SampleNumber: 78

value: survivor


title: SampleNumber: 3

value: Group A Strep


title: SampleNumber: 50

value: Grp A1


title: SampleNumber: 30

value: Grp B2


title: SampleNumber: 15

value: Grp C


title: SampleNumber: 74

value: Grp B1


title: SampleNumber: 35

value: SirsReslv

value: Lung

value: Grp C3


title: SampleNumber: 108

value: yes

value: Grp A

value: Grp A2


title: SampleNumber: 123

value: no

value: Candida albicans

value: Grp B


title: SampleNumber: 110

value: SepticShock

value: Grp A4


title: SampleNumber: 12

value: nonsurvivor

value: Blood


title: SampleNumber: 56

value: survivor

value: Rotavirus

value: Colitis


title: SampleNumber: 116

value: Strep viridans


title: SampleNumber: 1

value: Strep Pneumo

value: Grp B1


title: SampleNumber: 58

value: Influenza

value: Systemic


title: SampleNumber: 59

value: CMV

value: Grp B3


title: SampleNumber: 89

value: no


title: SampleNumber: 40

value: yes

value: Grp C

value: Grp C1


title: SampleNumber: 18

value: SepticShock

value: Lung

value: Grp B

value: Grp B4


title: SampleNumber: 13

value: nonsurvivor

value: Group A Strep

value: Blood

value: Grp B2


title: SampleNumber: 114

value: survivor

value: Grp A

value: Grp A1


title: SampleNumber: 41


title: SampleNumber: 93

value: Group B Strep

value: blood

value: Grp C3


title: SampleNumber: 51

value: Control

value: Ctrl

value: no


title: SampleNumber: 105

value: SepticShock

value: Influenza


title: SampleNumber: 49


title: SampleNumber: 48


title: SampleNumber: 103

value: yes

value: Grp B

value: Grp B3


title: SampleNumber: 104

value: nonsurvivor

value: Lung


title: SampleNumber: 52


title: SampleNumber: 57

value: Systemic

value: Grp A4


title: SampleNumber: 124

value: Grp C

value: Grp C1


title: SampleNumber: 60

value: CMV

value: Blood


title: SampleNumber: 7

value: Neisseria


title: SampleNumber: 118

value: survivor

value: Staph Aureus

value: Grp A

value: Grp A3


title: SampleNumber: 46

value: Control

value: Ctrl

value: no


title: SampleNumber: 39


title: SampleNumber: 47


title: SampleNumber: 38


title: SampleNumber: 37


title: SampleNumber: 21


title: SampleNumber: 119

value: SepticShock

value: Grp B

value: Grp B3


title: SampleNumber: 31


status: Public on Jun 07 2004

city: Carlsbad

first: Xiao-Jun

last: Ma

state: CA

address: 2715 Loker Ave. W.

institute: AviaraDx, Inc.

description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1507;Tumor.type=D;Size=3.7;Grade=3;Nodes=0/40;ER=Pos;PR=Pos;HER2=Neg ;Age=70;DFS=70;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1507 labeled with Cy5

source_name: human universal reference RNA (Stratagene) labeled with Cy3


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1363;Tumor.type=D;Size=2.1;Grade=2;Nodes=0/15;ER=Pos;PR=Pos;HER2=Neg ;Age=56;DFS=114;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1363 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1206;Tumor.type=D;Size=4.1;Grade=3;Nodes=0/15;ER=Pos;PR=Neg;HER2=Neg;Age=84;DFS=56;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1206 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1093;Tumor.type=D;Size=1;Grade=3;Nodes=1/14;ER=Pos;PR=Pos;HER2=Neg ;Age=66;DFS=85;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1093 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1260;Tumor.type=D;Size=3.5;Grade=2;Nodes=0/14;ER=Pos;PR=Pos;HER2=Neg;Age=58;DFS=79;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1260 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1343;Tumor.type=D;Size=2.5;Grade=3;Nodes=ND;ER=Pos;PR=Pos;HER2=Neg;Age=79;DFS=21;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1343 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1389;Tumor.type=D;Size=1.7;Grade=2;Nodes=0/1;ER=Pos;PR=Pos;HER2=Neg;Age=80;DFS=94;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1389 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1218;Tumor.type=D;Size=4.5;Grade=1;Nodes=3/16;ER=Pos;PR=Pos;HER2=Neg;Age=62;DFS=10;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1218 labeled with Cy5


title: SampleNumber: 19


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1370;Tumor.type=D;Size=2;Grade=2;Nodes=ND;ER=Pos;PR=Pos;HER2=Neg;Age=73;DFS=61;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1370 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1304;Tumor.type=D;Size=2;Grade=3;Nodes=0/14;ER=Pos;PR=Pos;HER2=Neg;Age=57;DFS=20;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1304 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1279;Tumor.type=D;Size=2;Grade=2;Nodes=0/12;ER=Pos;PR=Pos;HER2=Neg;Age=68;DFS=102;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1279 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1405;Tumor.type=D;Size=1;Grade=3;Nodes=ND;ER=Pos (<10%);PR=Pos;HER2=Neg;Age=81;DFS=95;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1405 labeled with Cy5


title: SampleNumber: 20


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1368;Tumor.type=D;Size=2.6;Grade=2;Nodes=ND;ER=Pos;PR=Pos;HER2=Neg ;Age=82;DFS=63;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1368 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1125;Tumor.type=D;Size=2.6;Grade=2;Nodes=0/18;ER=Pos;PR=Neg;HER2=Neg;Age=54;DFS=123;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1125 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1047;Tumor.type=D/L;Size=2.6;Grade=2;Nodes=0/18;ER=Pos;PR=Neg;HER2=Neg;Age=70;DFS=128;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1047 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1085;Tumor.type=D;Size=4.7;Grade=2;Nodes=0/8;ER=Pos;PR=Pos;HER2=Neg;Age=48;DFS=101;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1085 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=868;Tumor.type=D;Size=3;Grade=3;Nodes=0/13;ER=Pos;PR=Pos;HER2=Neg;Age=65;DFS=130;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 868 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1205;Tumor.type=D;Size=2.7;Grade=2;Nodes=1/19;ER=Pos;PR=Pos;HER2=Neg ;Age=71;DFS=88;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1205 labeled with Cy5

source_name: human universal reference RNA (Stratagene) labeled with Cy3


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=849;Tumor.type=D;Size=2;Grade=1;Nodes=0/26;ER=Pos;PR=Pos;HER2=Neg;Age=75;DFS=23;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 849 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=878;Tumor.type=D/L;Size=1.6;Grade=2;Nodes=0/9;ER=Pos;PR=Neg;HER2=Neg;Age=76;DFS=138;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 878 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1037;Tumor.type=D/L;Size=1.5;Grade=2;Nodes=0/4;ER=Pos;PR=Pos;HER2=Neg ;Age=85;DFS=83;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1037 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1045;Tumor.type=D;Size=2.5;Grade=3;Nodes=1/12;ER=Pos;PR=Neg;HER2=Pos;Age=73;DFS=121;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1045 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=648;Tumor.type=D;Size=1.1;Grade=2;Nodes=0/15;ER=Pos;PR=Pos;HER2=Neg;Age=62;DFS=160;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 648 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=687;Tumor.type=D;Size=3.5;Grade=3;Nodes=3/16;ER=Pos;PR=Pos;HER2=Neg;Age=73;DFS=142;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 687 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=843;Tumor.type=D;Size=3.4;Grade=2;Nodes=11/20;ER=Pos;PR=Neg;HER2=Neg;Age=76;DFS=122;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 843 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=763;Tumor.type=D;Size=1.8;Grade=2;Nodes=0/14;ER=Pos;PR=Pos;HER2=ND;Age=63;DFS=118;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 763 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=651;Tumor.type=D;Size=4.7;Grade=3;Nodes=10/13;ER=Pos;PR=Pos;HER2=Neg;Age=48;DFS=137;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 651 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=638;Tumor.type=D;Size=2;Grade=2;Nodes=1/24;ER=Pos;PR=Pos;HER2=Neg;Age=67;DFS=148;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 638 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=633;Tumor.type=D;Size=2.7;Grade=3;Nodes=0/11;ER=Pos;PR=Pos;HER2=Neg;Age=61;DFS=20;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 633 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=871;Tumor.type=D;Size=4;Grade=3;Nodes=0/16;ER=Pos;PR=Pos;HER2=Neg;Age=61;DFS=6;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 871 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=772;Tumor.type=D;Size=2.5;Grade=2;Nodes=0/18;ER=Pos;PR=Pos;HER2=Neg;Age=68;DFS=69;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 772 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=829;Tumor.type=D;Size=1.2;Grade=2;Nodes=0/9;ER=Pos;PR=Pos;HER2=Neg ;Age=69;DFS=136;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 829 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=856;Tumor.type=D;Size=1.6;Grade=2;Nodes=0/16;ER=Pos;PR=Pos;HER2=ND;Age=73;DFS=88;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 856 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=605;Tumor.type=D;Size=2.2;Grade=2;Nodes=6/18;ER=Pos;PR=Pos;HER2=Neg;Age=70;DFS=110;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 605 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=547;Tumor.type=D/L;Size=1.5;Grade=2;Nodes=ND;ER=Pos;PR=Pos;HER2=Neg;Age=74;DFS=129;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 547 labeled with Cy5

source_name: human universal reference RNA (Stratagene) labeled with Cy3


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1419;Tumor.type=D;Size=2.5;Grade=2;Nodes=1/8;ER=Pos;PR=Pos;HER2=Neg;Age=59;DFS=86;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1419 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=469;Tumor.type=D;Size=1;Grade=1;Nodes=0/19;ER=Pos;PR=Pos;HER2=Neg ;Age=66;DFS=161;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 469 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=823;Tumor.type=D;Size=2;Grade=2;Nodes=0/6;ER=Pos;PR=Pos;HER2=Neg;Age=51;DFS=69;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 823 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=607;Tumor.type=D;Size=1.2;Grade=2;Nodes=5/14;ER=Pos;PR=Pos;HER2=Neg;Age=76;DFS=114;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 607 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=518;Tumor.type=L;Size=5.5;Grade=2;Nodes=3/20;ER=Pos;PR=Pos;HER2=Neg;Age=68;DFS=156;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 518 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=655;Tumor.type=D;Size=2;Grade=3;Nodes=ND;ER=Pos;PR=Pos;HER2=ND;Age=73;DFS=143;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 655 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=356;Tumor.type=D;Size=1;Grade=2;Nodes=2/20;ER=Pos (<10%);PR=Neg;HER2=Pos;Age=58;DFS=24;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 356 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=749;Tumor.type=D;Size=1.8;Grade=2;Nodes=2/9;ER=Pos;PR=Neg;HER2=Neg;Age=61;DFS=137;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 749 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=420;Tumor.type=D/L;Size=2;Grade=3;Nodes=ND;ER=Pos;PR=Pos;HER2=Neg;Age=72;DFS=58;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 420 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=317;Tumor.type=D;Size=1.2;Grade=3;Nodes=1/10;ER=Pos;PR=Neg;HER2=Neg;Age=71;DFS=5;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 317 labeled with Cy5


title: SampleNumber: 25

description: Experimental factor value:  Day 1 samples = control, SIRS, or septic shock. Day 3 samples = SIRS, septic shock, or SIRS resolved

source_name: whole blood


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=1437;Tumor.type=D;Size=1.7;Grade=2;Nodes=2/22;ER=Pos;PR=Pos;HER2=Neg;Age=67;DFS=89;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 1437 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=319;Tumor.type=D;Size=4;Grade=2;Nodes=1/13;ER=Pos;PR=Pos;HER2=Neg;Age=67;DFS=44;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 319 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=297;Tumor.type=D;Size=0.8;Grade=2;Nodes=1/16;ER=Pos;PR=Pos;HER2=ND;Age=66;DFS=169;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 297 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=260;Tumor.type=D/L;Size=0.9;Grade=2;Nodes=1/13;ER=Pos;PR=Pos;HER2=Neg;Age=73;DFS=42;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 260 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=280;Tumor.type=D;Size=2.2;Grade=3;Nodes=0/12;ER=Pos;PR=Pos;HER2=Neg;Age=66;DFS=44;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 280 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=662;Tumor.type=D;Size=1;Grade=3;Nodes=6/11;ER=Pos;PR=Pos;HER2=Neg;Age=79;DFS=27;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 662 labeled with Cy5

source_name: human universal reference RNA (Stratagene) labeled with Cy3


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=289;Tumor.type=D;Size=3;Grade=2;Nodes=0/15;ER=Pos;PR=Pos;HER2=Neg;Age=75;DFS=63;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 289 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=374;Tumor.type=D;Size=1;Grade=3;Nodes=0/15;ER=Pos (<10%);PR=Pos;HER2=Pos;Age=57;DFS=47;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 374 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=295;Tumor.type=D;Size=3.5;Grade=2;Nodes=3/21;ER=Pos;PR=Pos;HER2=Neg;Age=52;DFS=118;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 295 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=140;Tumor.type=L;Size=>2.0;Grade=2;Nodes=18/28;ER=Pos;PR=Pos;HER2=Neg;Age=63;DFS=43;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 140 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=59;Tumor.type=L;Size=3;Grade=2;Nodes=33/38;ER=Pos;PR=Pos;HER2=ID (+2);Age=70;DFS=21;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 59 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=180;Tumor.type=D;Size=1.6;Grade=2;Nodes=2/19;ER=Pos;PR=Pos;HER2=Neg ;Age=69;DFS=169;Status=non-recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 180 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=342;Tumor.type=D;Size=3;Grade=2;Nodes=9/21;ER=Pos;PR=Neg;HER2=Neg;Age=62;DFS=102;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 342 labeled with Cy5


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=68;Tumor.type=D;Size=3;Grade=2;Nodes=0/17;ER=Pos;PR=Pos;HER2=Neg;Age=53;DFS=38;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 68 labeled with Cy5


title: SampleNumber: 16


description:
Highly enriched breast cancer cells procured by LCM.
Clinical information: Sample.ID=25;Tumor.type=D;Size=3.5;Grade=2;Nodes=0/9;ER=Neg;PR=Pos;HER2=Neg;Age=62;DFS=75;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

source_name: RNA from microdissected breast cancer cells from case 25 labeled with Cy5