title: siPBX1 treated with DMSO rep1

city: Lebanon

first: luca

last: magnani

state: NH

address: NCCC one medical drive

department: Genetics

institute: Dartmouth College

description:
PBX1_V1
replicate 1

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: MCF7 breast cancer cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Cells were grown in stripped media (DMEM w/o phenol, CDT treated serum 10%, glutamine and penicillin/streptomycin).

extract_protocol: RNA was extracted with  with QIAGEN RNeasy  kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. Efficient knock down was validated with RT-qPCR.

treatment_protocol: 72h post transfection with the appropriate siRNA, cells were stimulated with 10nM E2 or DMSO for 3h prior RNA extraction

value: MCF7 breast cancer cells

tag: era status

value: positive

tag: genotype/variation

value: PBX1 knock down

tag: agent

value: DMSO


title: MOYO-R; 3 hr, replication 1

status: Public on Sep 30 2011

type: RNA

city: NOTRE DAME

first: David

middle: W

last: Severson

state: IN

address: Galvin Life Science

department: Dept. of Biological Sciences

country: USA

institute: University of Notre Dame

description:
Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points. These consisted of four DENV2 infected samples (Moyo-S-3hr, Moyo-R-3hr, Moyo-S-18hr and Moyo-R-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Thus, a total of 15 independent samples were used for array hybridizations.

The Aedes aegypti strain MOYO-R was used. These mosquitoes show 19.54% susceptibility to dengue serotype-2. Early interactions between host and virus is important. So, we profiled the gene expression changes in dengue-2 infected MOYO-R females at 3 hr post infection. The control was prepared in parallel to the test. The control mosquitoes were mock transfected by normal blood meal without dengue.

hyb_protocol: The array hybridization and washing was performed by NimbleGen as per protocol described at http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf

scan_protocol: Scanning was also performed by NimbleGen as described in http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf

data_processing: The raw data from array expressions were normalized using quintile normalization method and the Robust Multichip Average (RMA) algorithm by NimbleGen. The Statistical Analysis of Microarray (SAM) program was employed, using the Microsoft Excel addin v1.21, to determine differential expression between test and control samples. The control and infected samples were compared as two-class unpaired response types. The significant gene list was further subjected to filter for the genes that showed either positive (up-regulation) or negative (down-regulation) in both the Moyo-S and Moyo-R strains for both the post-infection time points. This step was performed because each of the test samples were compared to a common uninfected control (prepared by pooling equal amount of the individual control for these samples). This approach was adopted to ensure the identification of genes showing differential expression in response to DENV but not due to genetic differences between the two strains or developmental associated changes between the two observation time points.

molecule: total RNA

organism: Aedes aegypti

source_name: MOYO-R; 3 hr

label_protocol: The cDNA labeling was performed by NimbelGene. The manufacturer protocol for labeling is as follows. First, the RNA samples are tested for quality control so that they are free of contamination and intact (not degraded). The RNA is then used to prepare first and second strand cDNA. The cDNA is cleaned up and checked for quality control. Then cy3 dye was used to label the cDNA as described in http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf.

growth_protocol: Fully engorged females were isolated and maintained at 26 °C with 84% humidity and in a 16-h light/8-h dark cycle. At 3 hr and 18 hr post blood feeding, DENV2 infected and control females were sampled for each strain. Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points.

extract_protocol: At the appropriate time point, RNA was extracted from 20 females per sample (the blood meal was removed from each female using a micro syringe needle prior to RNA extractions) using a Qiagen RNAeasy Kit as per manufacturer’s instructions. The RNA quality was assessed by a Bioanalyzer and quantified by a Nanodrop spectrophotometer.

treatment_protocol: The starved females were provided with an artificial infectious blood meal, freshly prepared using defibrinated sheep blood (Colorado Serum Co., CS1122) mixed with (equal volume) a dengue viral suspension. DENV2 strain JAM1409 was cultured using C6/36 mosquito cells until 80-90% confluence in MEM-EBSS media (HyClone SH3002401) supplemented with 25 mM Hepes buffer, 1 mM sodium pyruvate, 0.025 mg/ml Gentamycin, 1x (0.01 mM) non-essential amino acids and 10% fetal bovine serum (heat inactivated). A 0.1 MOI (multiplicity of infection) was used for infecting the mosquito cells. The multiplicity of infection refers to the average number of viral particles that infect a single cell, which for our purpose, is equal to plaque-forming units (pfu) per cell. The flasks were incubated at 28°C for 7 days after which the viral supernatant was obtained by centrifugation at 1500 rpm for 5 min at 4ºC. All DENV infection work was performed in a BSL3 facility.

tag: strain

value: MOYO-R


title: siControl treated with DMSO rep2

description:
Control_V2
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

label: biotin

organism: Homo sapiens

tag: cell line

value: control


title: siControl treated with E2 rep2

description:
Control_E2
replicate 2

value: estradiol (E2)


title: MOYO-S; 3 hr, replication 3

description:
Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points. These consisted of four DENV2 infected samples (Moyo-S-3hr, Moyo-R-3hr, Moyo-S-18hr and Moyo-R-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Thus, a total of 15 independent samples were used for array hybridizations.

The Aedes aegypti strain MOYO-S was used. These mosquitoes show 56.60% susceptibility to dengue serotype-2. Early interactions between host and virus is important. So, we profiled the gene expression changes in dengue-2 infected MOYO-S females at 3 hr post infection. The control was prepared in parallel to the test. The control mosquitoes were mock transfected by normal blood meal without dengue.

source_name: MOYO-S; 3 hr

value: MOYO-S


title: MOYO-S; 18 hr, replication 3

source_name: MOYO-S; 18 hr


title: siPBX1 treated with E2 rep1

description:
PBX1_E1
replicate 1


title: C5_control

city: Lisbon

first: Sofia

middle: A

last: Oliveira

state: Portugal

address: Av. Prof Egas Moniz

department: Edificio Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

description: Image analysis was carried out using the ImaGene 7.0 software (BioDiscovery, Inc., USA) and the resulting ImaGene output files were analyzed using the Limma package  (Smyth GK Stat Appl Genet Mol Biol. 2004; 3:Article3) implemented using R freeware (http://cran.r-project.org/).

hyb_protocol: RNA samples were sent to Exiqon (Vedbaek, Denmark) for miRNA profiling. Briefly, the Hy3-labeled sample and the Hy5-labeled common reference pool were co-hybridized to the miRCURYTM locked nucleic acid (LNA) array (version 10.0) using a Tecan (Austria) HS4800 hybridization station.

scan_protocol: Arrays were scanned with an Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and stored in an ozone-free environment in order to prevent potential bleaching of the fluorescent dyes.

data_processing: Background correction was performed using the normexp method (with offset=10). Intensities of good quality spots were then subjected to within-array (loess method) normalization. Intensities lower than 1.5 times the median signal intensity of the respective slide and label were discarded. The calling of a miRNA on a particular array fails if two or more of the four replicated capture probes for this miRNA are flagged as bad quality spots by the image analysis software. Differential expression between controls and PD patients was assessed using linear regression analysis and empirical Bayes methods implemented in the Limma package.

source_name: Control C5

label_protocol: RNA sample was sent to Exiqon (Vedbaek, Denmark) for miRNA profiling. 1µg of total RNA was labeled with the miRCURY Hy3 power labeling kit.

extract_protocol: Approximately 16 ml of whole blood was collected by venipuncture into two BD Vacutainer CPT glass tubes (Becton-Dickinson, Franklin Lakes, USA). Whithin two hours of blood collection, peripheral blood mononuclear cells (PBMCs) were isolated from the CPT tubes by centrifugation (30 min, 2800 rpm, room temperature) and washed twice with PBS (15 min, 1300 rpm, 4ºC). Total RNA containing small RNAs was extracted from PBMCs using the miRNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, aliquoted and stored at -80ºC. All samples passed extensive quality controls (e.g. OD260/OD280 between 1.8 and 2.1 in the Nanodrop ND1000 and RIN (RNA Integrity Number) > 7 in the Agilent 2100 Bioanalyser).

tag: disease state

value: unaffected with parkinson´s disease

tag: sex

value: Male

tag: age

value: 73 yrs

tag: tissue

value: PBMCs

source_name: Common reference pool

label_protocol: RNA samples were sent to Exiqon (Vedbaek, Denmark) for miRNA profiling. 1µg of total RNA from each of the 39 samples was pooled and labeled with the miRCURY Hy5 power labeling kit.

extract_protocol: Same protocol as channel 1

tag: sample

value: Pool composed of 39 samples (the 32 samples under study and 7 additional samples which were later excluded from differential expression analysis due to array quality control problems).


title: siPBX1 treated with E2 rep2

description:
PBX1_E2
replicate 2


title: C2_control

source_name: Control C2

value: 64 yrs


title: MOYO-S; 3 hr, replication 2

description:
Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points. These consisted of four DENV2 infected samples (Moyo-S-3hr, Moyo-R-3hr, Moyo-S-18hr and Moyo-R-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Thus, a total of 15 independent samples were used for array hybridizations.

The Aedes aegypti strain MOYO-S was used. These mosquitoes show 56.60% susceptibility to dengue serotype-2. Early interactions between host and virus is important. So, we profiled the gene expression changes in dengue-2 infected MOYO-S females at 3 hr post infection. The control was prepraed in parallel to the test. The control mosquitoes were mock transfected by normal blood meal without dengue.


title: C3_control

source_name: Control C3

value: 66 yrs


title: C1_control

source_name: Control C1

value: 63 yrs


title: siPBX1 treated with DMSO rep2

description:
PBX1_V2
replicate 2


title: siControl treated with E2 rep1

description:
Control_E1
replicate 1


title: C4_control

source_name: Control C4

value: 71 yrs


title: MOYO-S; 3 hr, replication 1

description:
Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points. These consisted of four DENV2 infected samples (Moyo-S-3hr, Moyo-R-3hr, Moyo-S-18hr and Moyo-R-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Thus, a total of 15 independent samples were used for array hybridizations.

The Aedes aegypti strain MOYO-S was used. These mosquitoes show 56.60% susceptibility to dengue serotype-2. Early interactions between host mosquito and dengue virus is important. Thus, we profiled gene expression of the infected females along with uninfected control at 3 hr post-infection period. The control sample was prepared in parallel to test sample where the mosquitoes were mock-transected with normal blood (no dengue was added).


title: siControl treated with DMSO rep1

description:
Control_V1
replicate 1

value: MCF7 breast cancer cells


title: muscle_f2_f_2886

status: Public on Sep 29 2011

city: Berne

first: Martin

middle: H

last: Braunschweig

state: Berne

address: Bremgartenstrasse 109A

department: Vetsuisse Faculty

country: Switzerland

institute: University of Bern

description: control_diet 8

hyb_protocol: RNA was hybridized to the porcine gene expression microarray from Agilent Technologies according to standard protocol used at the Functional Genomic Center Zürich.

scan_protocol: Spot Intensities were extracted from the TIFF images using Agilent Feature Extraction Software 9.5.

data_processing: From the generated TXT files the gMedianSignal of the spots was used as raw expression value and further analyzed using R/Bioconductor. Expression values were normalized using quantile normalization and differential expression was computed using a t-test on the log2-transformed signals.

organism: Sus scrofa

source_name: F2 skeletal muscle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 600 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Quich Amp Labeling) with Tecan HS Pro Hybridization according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hombrechtikon, Switzerland).  Dye incorporation and cRNA yield were inspected with a NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Trizol followed by Qiagen RNeasy cleanup and DNase treatment

treatment_protocol: F0 boars received either a standard diet or a standard diet supplemented with methylating micronutrients from one to ten months of age. The supplemented diet contained additional methionine, choline, betaine, vitamin B6, B12 and Folate.

tag: gender

value: female

tag: diet

value: standard diet


title: muscle_f2_m_2878

description: control_diet 6

value: male


title: muscle_f2_f_2969

description: control_diet 4


title: muscle_f2_m_2943

description: suppl_diet 5

value: standard diet supplemented with methylating micronutrients


title: muscle_f2_f_2949

description: suppl_diet 2


title: muscle_f2_f_2968

description: control_diet 3


title: muscle_f2_f_2897

description: suppl_diet 8


title: muscle_f2_m_2891

description: suppl_diet 7


title: muscle_f2_f_2950

description: suppl_diet 3


title: muscle_f2_f_2899

description: suppl_diet 4


title: muscle_f2_m_2944

description: suppl_diet 1


title: muscle_f2_m_2890

description: suppl_diet 6


title: muscle_f2_m_2875

description: control_diet 5


title: muscle_f2_m_2962

description: control_diet 2


title: muscle_f2_f_2884

description: control_diet 7


title: muscle_f2_m_2961

description: control_diet 1


title: kidney_f2_m_2890

description: suppl_diet 7

source_name: F2 kidney


title: kidney_f2_m_2943

description: suppl_diet 8


title: kidney_f2_m_2875

description: control_diet 5


title: kidney_f2_f_2899

description: suppl_diet 6


title: kidney_f2_f_2884

description: control_diet 7


title: kidney_f2_f_2969

description: control_diet 4


title: kidney_f2_f_2886

description: control_diet 8


title: kidney_f2_m_2878

description: control_diet 6


title: kidney_f2_m_2891

description: suppl_diet 4


title: kidney_f2_f_2897

description: suppl_diet 5


title: kidney_f2_f_2968

description: control_diet 3


title: kidney_f2_m_2944

description: suppl_diet 1


title: kidney_f2_f_2949

description: suppl_diet 2


title: kidney_f2_m_2961

description: control_diet 1


title: liver_f2_m_2878

description: control_diet 6

source_name: F2 liver


title: liver_f2_f_2949

description: suppl_diet 2


title: liver_f2_m_2961

description: control_diet 1


title: kidney_f2_f_2950

description: suppl_diet 3


title: liver_f2_f_2969

description: control_diet 4


title: liver_f2_m_2943

description: suppl_diet 4


title: liver_f2_f_2884

description: control_diet 7


title: liver_f2_f_2968

description: control_diet 3


title: liver_f2_m_2891

description: suppl_diet 6


title: liver_f2_f_2897

description: suppl_diet 7


title: liver_f2_f_2950

description: suppl_diet 3


title: liver_f2_m_2944

description: suppl_diet 1


title: liver_f2_m_2962

description: control_diet 2


title: liver_f2_m_2875

description: control_diet 5


title: liver_f2_f_2899

description: suppl_diet 8


title: liver_f2_f_2886

description: control_diet 8


title: kidney_f2_m_2962

description: control_diet 2


title: liver_f2_m_2890

description: suppl_diet 5


title: ME:M14 [118220hp133a11]

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

description: Melanotic melanoma

hyb_protocol: Done by Genelogic according to manufacturer's recommendations

scan_protocol: Affymetrix MicroArraySuite

data_processing: Probes were normalized using RMA in Partek Genomics Suite version 6.2

source_name: Melanotic melanoma

growth_protocol: Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0,5 x 10-6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 370C. Spin down suspended cells, and resuspend in ~3ml growth media. Count cells. Pass 1x10-6 cells into new T162’s w 30 ml media.  Repeat growth cycle until desired amount of cells are available. Cells are not grown past passage 20.

extract_protocol: Growth schedule prior to harvest: Grow cells to ~80 confluencey. Re-feed cells the day prior to harvest. Draw off media from attached cells, or spin down suspended cells. Rinse cells with ~10 ml 1x PBS. Purify using Quiagen Midi Kit (Cat # 75144) per instructions.  In brief, lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml) per 4 T162s. Scrape (attached) cells. Pipet into a 50 ml tube.  Repeat with the next set of 4 flasks.  When done, vortex 10 sec.. Draw lysate thru a 20 guage needle 12x’s. Freeze lysate at -80 deg C. Use a maximum of 100 x 10-6 cells per column.

treatment_protocol: No treatment

tag: tissue of origin

value: Melanoma

tag: epithelial

value: no

tag: ploidy

tag: p53 mutation

value: MT

tag: doubling time

tag: contributing institute

tag: contributing person

value: D.H. Kern, John Wayne Cancer Clinic, UCLA School of Medicine

tag: reference


title: ME:MALME_3M [118221hp133a11]

description: Malignant melanotic melanoma

source_name: Malignant melanotic melanoma

label_protocol: Done by Genelogic according to manufacturer's recommendations

tag: Sex

value: M

tag: prior treatment

tag: source

value: Metastasis

value: WT

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh


title: ME:SK_MEL_5 [118224hp133a11]

description: Malignant melanotic melanoma

tag: cell line

value: F

value: 4n+, Hypertetraploid (93-103)

value: T. Takahashi


title: ME:SK_MEL_2 [118222hp133a11]

description: Malignant melanotic melanoma

tag: age

value: 4n-, Hypotetraploid (81-91)

value: G. Trempe; L.J. Old

value: Human Tumor Cells in vitro, pp 115-159, 1975


title: BR:T47D [118227hp133a11]

description: infiltrating ductal carcinoma

source_name: infiltrating ductal carcinoma

value: Breast

value: yes

value: 2n+, Hyperdiploid (47-57)

value: I. Keydar


title: ME:UACC_257 [118225hp133a11]

description: Melanotic melanoma

value: Melanoma

value: no

value: 3n+, Hypertriploid (70-80)

value: University of Arizona

value: A. Leibovitz, UACC


title: ME:UACC_62 [118226hp133a11]

description: Melanotic melanoma

value: WT


title: PR:PC_3 [118218hp133a11]

description: Adenocarcinoma-prostate; metastatic site: bone;

value: Prostate

value: M

value: 4n, Tetraploid (92)

value: MT

value: Pasadena Center for Medical Research

value: M.E. Kaighn


title: ME:LOXIMVI [118219hp133a11]

description: Malignant amelanotic melanoma

source_name: Malignant amelanotic melanoma

value: LOXIMVI

value: Norsk Hydro's Institut, Norway


title: OV:OVCAR_5 [118214hp133a11]

description: Adenocarcinoma-well differentiated

source_name: Adenocarcinoma

value: Ovarian

value: F

value: yes

value: National Cancer Institute, NIH

value: R. Ozols


title: OV:IGROV1 [118211hp133a11]

description: Cystoadenocarcinoma-poor differentiation

source_name: Cystoadenocarcinoma

value: Rad

value: Institute Gustave Roussy, France


title: OV:SK_OV_3 [118216hp133a11]

description: Adenocarcinoma-very poorly differentiated

value: Thiotepa

value: Ascites

value: Memorial Sloan Kettering Cancer Center

value: Human Tumor Cells in vitro, pp. 115-159, 1975


title: OV:OVCAR_4 [118213hp133a11]

description: Adenocarcinoma-moderate differentiation

value: CyPh/CsPt/Adr

value: WT

value: T.C. Hamilton


title: OV:OVCAR_8 [118215hp133a11]

description: Carcinoma-undifferentiated

source_name: Carcinoma

value: Ctx/Adr/CsPt/CyPh

value: 2n+, Hyperdiploid (47-57)

value: MT


title: PR:DU_145(DTP) [118217hp133a11]

description: Derived from metastatic site: brain (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)

source_name: Adenocarcinoma-prostate; metastatic site: brain; carcinoma

value: Prostate

value: M

value: Androgen independent and unresponsive to hormone therapy

value: Metastasis

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone


title: LC:NCI_H522 [118210hp133a11]

value: Non-Small Cell Lung

value: yes

value: National Cancer Institute, NIH


title: LC:NCI_H460 [118209hp133a11]

description: Large Cell Carcinoma-undifferentiated

source_name: Large Cell Carcinoma

value: Pleural effusion

value: J.D. Minna; A.F. Gazdar


title: LC:A549 [118202hp133a11]

description: Adenocarcinoma-poor to moderate differentiation

value: Giard DJ


title: LC:HOP_62 [118204hp133a11]

description: adenocarcinoma-undifferentiated

source_name: adenocarcinoma

value: F

value: 4n+, Hypertetraploid (93-103)

value: Johns Hopkins University


title: LC:NCI_H322M [118208hp133a11]

description: Small cell Bronchioalveolar Carcinoma

source_name: Small cell Bronchioalveolar Carcinoma


title: RE:UO_31 [118201hp133a11]

description: Renal cell carcinoma-very poorly differentiated

source_name: Renal cell carcinoma

value: Renal

value: WT


title: Ovarian cancer ascitic effusion PEO4

type: genomic

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description: Genomic DNA extracted from PEO4 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

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

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

data_processing: Data was processed in BeadStudio using the standard Illumina protocol. Log R Ratio and B Allele Frequency values were produced by tQN (Staaf et al 2008)

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Ovarian cancer ascitic effusion PEO4

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from cell pellet was performed using DNeasy blood and tissue kiit according to manufacturer's instruction.

tag: patient number

tag: disease stage

value: Relapse


title: RE:TK_10 [118200hp133a11]

description: Renal Spindle cell carcinoma

source_name: Renal Spindle cell carcinoma

value: M

value: 4n, Tetraploid (92)

value: MT

value: R.V.Clayman, Washington Univ.School of Medicine


title: LC:HOP_92 [118205hp133a11]

description: Large cell-undifferentiated

source_name: Large cell


title: LC:EKVX [118203hp133a11]

description: Adenocarcinoma-moderate differentiation

value: EKVX

value: Norsk Hydro's Institut, Norway


title: OV:OVCAR_3 [118212hp133a11]

description: Adenocarcinoma-moderate differentiation

value: Ovarian

value: CyPh/CsPt/Adr

value: yes

value: Ascites

value: T.C. Hamilton


title: RE:SN12C [118199hp133a11]

description: Renal cell carcinoma-poor differentiation

value: 3n, Triploid (69)

value: MD Anderson Hospital and Tumor Institute


title: RE:ACHN [118196hp133a11]

description: Renal cell carcinoma-poor to moderate differentiation

value: ACHN

value: Rad/VB/CCNU/Mto/Pred

value: Southern Research Inst. (T.F. Hogan, Middleton memorial VA hospital)


title: RE:RXF_393 [118198hp133a11]

description: hypernephroma-poor differentiation

source_name: hypernephroma

value: Renal

value: NCI/DCT/DTP

value: Contrib oncol 42, 1992


title: CO:SW_620 [118193hp133a11]

description: Carcinoma-undifferentiated

value: Colon

value: M

value: MT

value: Scott White Clinic

value: A. Leibovitz


title: CO:HT29 [118191hp133a11]

description: Adenocarcinoma-moderate differentiation

value: F

value: Primary

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor Cells in vitro:115-159, 1975


title: RE:786_0 [118194hp133a11]

description: Adenocarcinoma

value: yes

value: R.D.Williams, Univ. of Iowa


title: CO:HCT_116 [118189hp133a11]

description: carcinoma-very poorly differentiated

source_name: carcinoma

value: 2n-, Hypodiploid (35-45)

value: Baylor College


title: RE:A498 [118195hp133a11]

description: Adenocarcinoma

value: Renal

value: 3n, Triploid (69)

value: WT

value: National Cancer Institute, NIH


title: CO:KM12 [118192hp133a11]

description: Adenocarcinome-poor differentiation

source_name: Adenocarcinome

value: Colon

value: MD Anderson Hospital and Tumor Institute

value: I.J. Fidler, Univ of Texas M.D. Anderson Hospital and Tumor Institute


title: CNS:U251 [118186hp133a11]

description: Glioblastoma-undifferentiated

source_name: Glioblastoma

value: CNS

value: M

value: no

value: 2n+, Hyperdiploid (47-57)

value: MT

value: University of Uppsala, Sweden

value: J Neuropathol Exp Neurol 40:410-427, 1981


title: CO:HCT_15 [118190hp133a11]

value: yes

value: ATCC

value: ATCC (D.L. Dexter, Roger Williams General Hospital)


title: CO:COLO205 [118187hp133a11]

description: Adenocarcinoma

value: Ascites

value: Denver Medical Hospital

value: G.E. Moore


title: CNS:SNB_19 [118184hp133a11]

description: Glioblastoma-undifferentiated

value: NINCDS

value: P.L. Kornblith


title: CNS:SF_539 [118183hp133a11]

description: Glial cell neoplasm

source_name: Glial cell neoplasm

value: F

value: WT

value: University of California

value: M.L. Rosenblum

value: J Neuropathol Exp Neurol 40:201-229, 1981


title: Ovarian cancer ascitic effusion PEA1

description: Genomic DNA extracted from PEA1 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

source_name: Ovarian cancer ascitic effusion PEA1

value: Pre-treatment


title: CNS:SNB_75 [118185hp133a11]

description: Astrocytoma

source_name: Astrocytoma

value: CNS

value: no

value: 2n+, Hyperdiploid (47-57)

value: MT


title: CO:HCC_2998 [118188hp133a11]

description: carcinoma

value: Colon

value: yes

value: MD Anderson Hospital and Tumor Institute


title: Ovarian cancer ascitic effusion PEO14

description: Genomic DNA extracted from PEO14 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

source_name: Ovarian cancer ascitic effusion PEO14


title: Ovarian cancer ascitic effusion PEA2

description: Genomic DNA extracted from PEA2 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

source_name: Ovarian cancer ascitic effusion PEA2

value: Relapse


title: LC:NCI_H23 [118207hp133a11]

description: Adenocarcinoma-undifferentiated

source_name: Adenocarcinoma

value: Non-Small Cell Lung

value: M

value: National Cancer Institute, NIH

value: J.D. Minna; A.F. Gazdar


title: BR:HS578T [118176hp133a11]

description: Carcinosarcoma-mammary gland; breast

source_name: Carcinosarcoma-mammary gland; breast

value: Breast

value: F

value: Primary

value: Naval Bioscience Laboratory

value: A.J. Hackett


title: CNS:SF_295 [118182hp133a11]

description: Glioblastoma-undifferentiated

value: CNS

value: Rad

value: University of California

value: M.L. Rosenblum

value: Acta Neuropathol 75:92-103, 1988


title: ME:MDA_MB_435 [118180hp133a11]

description: Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;

value: Melanoma

value: no

value: Pleural effusion

value: 2n+, Hyperdiploid (47-57)

value: MT

value: R. Cailleau


title: BR:MCF7 [118177hp133a11]

description: Adenocarcinoma-mammary gland; breast; metastatic site: pleural effusion;

value: yes

value: 3n-, Hypotriploid (58-68)

value: WT

value: Michigan Cancer Foundtion

value: C.M. McGrath


title: LE:K_562 [118174hp133a11]

description: CML

source_name: CML

value: Leukemia

value: F

value: Bisulfan/PiBr

value: University of Tennesse

value: H.T. Holden


title: LE:CCRF_CEM [118169hp133a11]

description: ALL

source_name: ALL

value: Rad/Mtx/Cyx

value: Children's Cancer research Foudation

value: G.E. Foley


title: OV:NCI_ADR_RES [118178hp133a11]

description: Adenocarcinoma

value: Ovarian

value: National Cancer Institute, NIH

value: K.Cowan, NCI


title: LE:HL_60 [118170hp133a11]

description: Pro myelocytic leukemia

source_name: Pro myelocytic leukemia

value: M

value: no

value: PBL

value: MT

value: R.C. Gallo


title: BR:T47D [113500hp133a11]

description: infiltrating ductal carcinoma

source_name: infiltrating ductal carcinoma

value: Breast

value: yes

value: 2n+, Hyperdiploid (47-57)

value: I. Keydar


title: BR:MDA_MB_231 [118179hp133a11]

description: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site: pleural effusion;

value: F

value: Pleural effusion

value: MD Anderson Hospital and Tumor Institute

value: R. Cailleau


title: LE:SR [118173hp133a11]

description: Lymphoma

source_name: Lymphoma

value: Leukemia

value: SR

value: Y

value: Program Resources, Inc.

value: W.J. Urba, Program Resources, Inc.


title: CNS:SF_268 [118181hp133a11]

description: Glioblastoma-undifferentiated

value: CNS

value: Rad

value: no

value: Acta Neuropathol 75:92-103, 1987


title: BR:BT_549 [118175hp133a11]

description: Papillary infiltrating ductal carcinoma-mammary gland; breast

value: Breast

value: Metastasis

value: W. Coutinho; E.Y. Lasfargues


title: ME:SK_MEL_2 [113495hp133a11]

description: Malignant melanotic melanoma

source_name: Malignant melanotic melanoma

value: Melanoma

value: M

value: 4n-, Hypotetraploid (81-91)

value: WT

value: Memorial Sloan Kettering Cancer Center

value: G. Trempe; L.J. Old

value: Human Tumor Cells in vitro, pp 115-159, 1975


title: LE:MOLT_4 [118171hp133a11]

description: ALL (cells were taken when patient was in relapse)

value: Leukemia

value: PB

value: 4n, Tetraploid (92)

value: Roswell Park Memorial Institute

value: J. Minowada


title: ME:M14 [113493hp133a11]

description: Melanotic melanoma

source_name: Melanotic melanoma

value: no

value: MT

value: D.H. Kern, John Wayne Cancer Clinic, UCLA School of Medicine


title: ME:SK_MEL_28 [113496hp133a11]

description: Malignant melanotic melanoma

value: T. Takahashi


title: OV:SK_OV_3 [116402hp133a11]

value: Ovarian

value: F

value: Thiotepa

value: yes

value: Ascites

value: Human Tumor Cells in vitro, pp. 115-159, 1975


title: PR:DU_145(DTP) [113490hp133a11]

source_name: Adenocarcinoma-prostate; metastatic site: brain; carcinoma

value: Prostate

value: M

value: Androgen independent and unresponsive to hormone therapy

value: Metastasis

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone


title: ME:SK_MEL_5 [113497hp133a11]

description: Malignant melanotic melanoma

value: Melanoma

value: 4n+, Hypertetraploid (93-103)

value: WT

value: Memorial Sloan Kettering Cancer Center


title: ME:UACC_257 [113498hp133a11]

description: Melanotic melanoma

value: no

value: 3n+, Hypertriploid (70-80)

value: University of Arizona

value: A. Leibovitz, UACC


title: ME:LOXIMVI [113492hp133a11]

description: Malignant amelanotic melanoma

source_name: Malignant amelanotic melanoma

value: LOXIMVI

value: Norsk Hydro's Institut, Norway


title: OV:OVCAR_5 [113488hp133a11]

description: Adenocarcinoma-well differentiated

value: Ovarian

value: F

value: yes

value: 2n+, Hyperdiploid (47-57)

value: MT

value: National Cancer Institute, NIH

value: R. Ozols


title: LC:NCI_H460 [113483hp133a11]

description: Large Cell Carcinoma-undifferentiated

source_name: Large Cell Carcinoma

value: Non-Small Cell Lung

value: M

value: Pleural effusion

value: J.D. Minna; A.F. Gazdar


title: PR:PC_3 [113491hp133a11]

description: Adenocarcinoma-prostate; metastatic site: bone;

value: Prostate

value: 4n, Tetraploid (92)

value: Pasadena Center for Medical Research

value: M.E. Kaighn


title: OV:OVCAR_4 [113487hp133a11]

description: Adenocarcinoma-moderate differentiation

value: CyPh/CsPt/Adr

value: WT

value: T.C. Hamilton


title: OV:IGROV1 [113485hp133a11]

description: Cystoadenocarcinoma-poor differentiation

source_name: Cystoadenocarcinoma

value: Ovarian

value: F

value: Rad

value: Institute Gustave Roussy, France


title: LC:NCI_H23 [113481hp133a11]

description: Adenocarcinoma-undifferentiated

value: yes

value: 2n+, Hyperdiploid (47-57)

value: MT

value: National Cancer Institute, NIH


title: ME:MALME_3M [113494hp133a11]

description: Malignant melanotic melanoma

value: Melanoma

value: M

value: no

value: Metastasis

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh


title: OV:OVCAR_8 [113489hp133a11]

description: Carcinoma-undifferentiated

source_name: Carcinoma

value: Ctx/Adr/CsPt/CyPh


title: LC:HOP_62 [113478hp133a11]

description: adenocarcinoma-undifferentiated

source_name: adenocarcinoma

value: Non-Small Cell Lung

value: 4n+, Hypertetraploid (93-103)

value: Johns Hopkins University


title: LE:RPMI_8226 [118172hp133a11]

description: Myeloma

source_name: Myeloma

value: Leukemia

value: PB

value: 3n-, Hypotriploid (58-68)

value: WT

value: G.E. Moore


title: OV:OVCAR_3 [113486hp133a11]

description: Adenocarcinoma-moderate differentiation

value: Ovarian

value: F

value: CyPh/CsPt/Adr

value: yes

value: Ascites

value: MT

value: T.C. Hamilton


title: RE:UO_31 [113475hp133a11]

source_name: Renal cell carcinoma

value: Renal

value: National Cancer Institute, NIH


title: LC:NCI_H226 [113480hp133a11]

description: Squamous cell carcinoma-very poorly differentiated

source_name: Squamous cell carcinoma

value: Non-Small Cell Lung

value: M

value: None (non smoker)

value: 3n, Triploid (69)

value: J.D. Minna; A.F. Gazdar


title: RE:CAKI_1 [113471hp133a11]

description: Clear cell carcinoma

source_name: Clear cell carcinoma

value: Metastasis

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor cells in vitro, pp 115-159, 1975


title: LC:NCI_H322M [113482hp133a11]

description: Small cell Bronchioalveolar Carcinoma

source_name: Small cell Bronchioalveolar Carcinoma


title: RE:786_0 [113468hp133a11]

description: Adenocarcinoma

source_name: Adenocarcinoma

value: R.D.Williams, Univ. of Iowa


title: RE:TK_10 [113474hp133a11]

description: Renal Spindle cell carcinoma

source_name: Renal Spindle cell carcinoma

value: 4n, Tetraploid (92)

value: R.V.Clayman, Washington Univ.School of Medicine


title: LC:A549 [113476hp133a11]

value: yes

value: WT

value: Giard DJ


title: LC:HOP_92 [113479hp133a11]

description: Large cell-undifferentiated

source_name: Large cell

value: MT

value: Johns Hopkins University


title: LC:NCI_H522 [113484hp133a11]

description: Adenocarcinoma-very poorly differentiated

value: Non-Small Cell Lung

value: National Cancer Institute, NIH


title: LC:EKVX [113477hp133a11]

description: Adenocarcinoma-moderate differentiation

value: EKVX

value: M

value: Norsk Hydro's Institut, Norway


title: RE:ACHN [113470hp133a11]

value: Renal

value: ACHN

value: Rad/VB/CCNU/Mto/Pred

value: Southern Research Inst. (T.F. Hogan, Middleton memorial VA hospital)


title: RE:A498 [113469hp133a11]

description: Adenocarcinoma

value: F

value: 3n, Triploid (69)


title: RE:RXF_393 [113472hp133a11]

description: hypernephroma-poor differentiation

source_name: hypernephroma

value: MD Anderson Hospital and Tumor Institute

value: NCI/DCT/DTP

value: Contrib oncol 42, 1992


title: CO:HT29 [113465hp133a11]

description: Adenocarcinoma-moderate differentiation

value: Colon

value: yes

value: Primary

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor Cells in vitro:115-159, 1975


title: CO:KM12 [113466hp133a11]

description: Adenocarcinome-poor differentiation

source_name: Adenocarcinome

value: MT

value: I.J. Fidler, Univ of Texas M.D. Anderson Hospital and Tumor Institute


title: CNS:U251 [113460hp133a11]

description: Glioblastoma-undifferentiated

source_name: Glioblastoma

value: CNS

value: M

value: no

value: 2n+, Hyperdiploid (47-57)

value: University of Uppsala, Sweden

value: J Neuropathol Exp Neurol 40:410-427, 1981


title: RE:SN12C [113473hp133a11]

value: Renal

value: 3n, Triploid (69)

value: MD Anderson Hospital and Tumor Institute


title: CO:HCT_116 [113463hp133a11]

description: carcinoma-very poorly differentiated

source_name: carcinoma

value: Colon

value: 2n-, Hypodiploid (35-45)

value: Baylor College


title: ME:MDA_MB_435 [113454hp133a11]

source_name: Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;

value: Melanoma

value: F

value: Pleural effusion

value: R. Cailleau


title: CNS:SF_268 [113455hp133a11]

description: Glioblastoma-undifferentiated

value: Rad

value: MT

value: Acta Neuropathol 75:92-103, 1987


title: CNS:SF_539 [113457hp133a21]

description: Glial cell neoplasm

source_name: Glial cell neoplasm

value: CNS

value: no

value: WT

value: University of California

value: M.L. Rosenblum

value: J Neuropathol Exp Neurol 40:201-229, 1981


title: BR:MDA_MB_231 [113453hp133a11]

source_name: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site: pleural effusion;

value: Breast

value: yes

value: 2n+, Hyperdiploid (47-57)

value: MD Anderson Hospital and Tumor Institute


title: CO:HCC_2998 [113462hp133a11]

description: carcinoma

value: Colon


title: OV:NCI_ADR_RES [113452hp133a11]

description: Adenocarcinoma

value: Ovarian

value: F

value: National Cancer Institute, NIH

value: K.Cowan, NCI


title: CO:SW_620 [113467hp133a11]

description: Carcinoma-undifferentiated

source_name: Carcinoma

value: M

value: MT

value: Scott White Clinic

value: A. Leibovitz


title: CNS:SNB_19 [113458hp133a11]

description: Glioblastoma-undifferentiated

value: CNS

value: no

value: NINCDS

value: P.L. Kornblith


title: CNS:SF_295 [113456hp133a11]

description: Glioblastoma-undifferentiated

value: Rad

value: University of California

value: M.L. Rosenblum

value: Acta Neuropathol 75:92-103, 1988


title: CO:COLO205 [113461hp133a11]

description: Adenocarcinoma

value: Colon

value: yes

value: Ascites

value: 3n, Triploid (69)

value: Denver Medical Hospital

value: G.E. Moore


title: CO:HCT_15 [113464hp133a11]

description: Adenocarcinoma-poor to moderate differentiation

value: ATCC

value: ATCC (D.L. Dexter, Roger Williams General Hospital)


title: BR:BT_549 [113449hp133a11]

source_name: Papillary infiltrating ductal carcinoma-mammary gland; breast

value: Breast

value: F

value: Metastasis

value: W. Coutinho; E.Y. Lasfargues


title: LE:CCRF_CEM [113443hp133a11]

description: ALL

source_name: ALL

value: Leukemia

value: Rad/Mtx/Cyx

value: no

value: MT

value: Children's Cancer research Foudation

value: G.E. Foley


title: BR:MCF7 [113451hp133a11]

source_name: Adenocarcinoma-mammary gland; breast; metastatic site: pleural effusion;

value: yes

value: Pleural effusion

value: 3n-, Hypotriploid (58-68)

value: WT

value: Michigan Cancer Foundtion

value: C.M. McGrath


title: LE:HL_60 [113444hp133a11]

description: Pro myelocytic leukemia

source_name: Pro myelocytic leukemia

value: M

value: PBL

value: National Cancer Institute, NIH

value: R.C. Gallo


title: BR:HS578T [113450hp133a11]

description: Carcinosarcoma-mammary gland; breast

source_name: Carcinosarcoma-mammary gland; breast

value: Breast

value: F

value: Primary

value: 2n+, Hyperdiploid (47-57)

value: Naval Bioscience Laboratory

value: A.J. Hackett


title: CNS:SNB_75 [113459hp133a11]

description: Astrocytoma

source_name: Astrocytoma

value: CNS

value: no

value: MT

value: NINCDS

value: P.L. Kornblith


title: LE:K_562 [113448hp133a11]

description: CML

source_name: CML

value: Leukemia

value: Bisulfan/PiBr

value: Pleural effusion

value: 3n-, Hypotriploid (58-68)

value: University of Tennesse

value: H.T. Holden


title: LE:MOLT_4 [113445hp133a11]

value: M

value: PB

value: 4n, Tetraploid (92)

value: WT

value: Roswell Park Memorial Institute

value: J. Minowada


title: LE:SR [113447hp133a11]

description: Lymphoma

source_name: Lymphoma

value: SR

value: Y

value: Program Resources, Inc.

value: W.J. Urba, Program Resources, Inc.


title: BR:T47D [113442hp133a11]

description: infiltrating ductal carcinoma

source_name: infiltrating ductal carcinoma

value: Breast

value: F

value: yes

value: 2n+, Hyperdiploid (47-57)

value: MT

value: I. Keydar


title: ME:SK_MEL_5 [113439hp133a11]

description: Malignant melanotic melanoma

source_name: Malignant melanotic melanoma

value: Melanoma

value: no

value: Metastasis

value: 4n+, Hypertetraploid (93-103)

value: Memorial Sloan Kettering Cancer Center

value: T. Takahashi


title: ME:UACC_257 [113440hp133a11]

description: Melanotic melanoma

source_name: Melanotic melanoma

value: 3n+, Hypertriploid (70-80)

value: WT

value: University of Arizona

value: A. Leibovitz, UACC


title: ME:M14 [113435hp133a11]

description: Melanotic melanoma

value: D.H. Kern, John Wayne Cancer Clinic, UCLA School of Medicine


title: ME:UACC_62 [113441hp133a11]

description: Melanotic melanoma


title: ME:SK_MEL_2 [113437hp133a11]

description: Malignant melanotic melanoma

value: M

value: 4n-, Hypotetraploid (81-91)

value: G. Trempe; L.J. Old

value: Human Tumor Cells in vitro, pp 115-159, 1975


title: ME:MALME_3M [113436hp133a11]

description: Malignant melanotic melanoma

value: J. Fogh


title: ME:LOXIMVI [113434hp133a11]

description: Malignant amelanotic melanoma

source_name: Malignant amelanotic melanoma

value: LOXIMVI

value: Norsk Hydro's Institut, Norway


title: ME:SK_MEL_28 [113438hp133a11]

description: Malignant melanotic melanoma

value: Melanoma

value: no

value: MT


title: PR:PC_3 [113433hp133a11]

source_name: Adenocarcinoma-prostate; metastatic site: bone;

value: Prostate

value: yes

value: 4n, Tetraploid (92)

value: Pasadena Center for Medical Research

value: M.E. Kaighn


title: OV:SK_OV_3 [113431hp133a11]

source_name: Adenocarcinoma

value: Ovarian

value: F

value: Thiotepa

value: Ascites

value: Memorial Sloan Kettering Cancer Center

value: Human Tumor Cells in vitro, pp. 115-159, 1975


title: LE:RPMI_8226 [113446hp133a11]

description: Myeloma

source_name: Myeloma

value: Leukemia

value: M

value: PB

value: 3n-, Hypotriploid (58-68)

value: WT

value: G.E. Moore


title: OV:OVCAR_5 [113429hp133a11]

description: Adenocarcinoma-well differentiated

value: 2n+, Hyperdiploid (47-57)

value: MT

value: National Cancer Institute, NIH

value: R. Ozols


title: LC:NCI_H522 [113425hp133a11]

value: Non-Small Cell Lung

value: yes


title: OV:IGROV1 [113426hp133a11]

source_name: Cystoadenocarcinoma

value: Ovarian

value: F

value: Rad

value: Institute Gustave Roussy, France


title: OV:OVCAR_3 [113427hp133a21]

description: Adenocarcinoma-moderate differentiation

value: CyPh/CsPt/Adr

value: Ascites

value: T.C. Hamilton


title: OV:OVCAR_8 [113430hp133a11]

description: Carcinoma-undifferentiated

source_name: Carcinoma

value: Ctx/Adr/CsPt/CyPh


title: OV:OVCAR_4 [113428hp133a11]

description: Adenocarcinoma-moderate differentiation


title: PR:DU_145(DTP) [113432hp133a11]

description: Derived from metastatic site: brain (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)

source_name: Adenocarcinoma-prostate; metastatic site: brain; carcinoma

value: Prostate

value: M

value: Androgen independent and unresponsive to hormone therapy

value: Metastasis

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone


title: LC:HOP_62 [113419hp133a11]

description: adenocarcinoma-undifferentiated

source_name: adenocarcinoma

value: 4n+, Hypertetraploid (93-103)

value: MT

value: Johns Hopkins University


title: LC:HOP_92 [113420hp133a11]

description: Large cell-undifferentiated

source_name: Large cell

value: Non-Small Cell Lung

value: yes


title: LC:NCI_H226 [113421hp133a11]

source_name: Squamous cell carcinoma

value: None (non smoker)

value: 3n, Triploid (69)

value: National Cancer Institute, NIH

value: J.D. Minna; A.F. Gazdar


title: LC:NCI_H460 [113424hp133a11]

description: Large Cell Carcinoma-undifferentiated

source_name: Large Cell Carcinoma

value: Pleural effusion

value: WT


title: RE:UO_31 [113416hp133a11]

description: Renal cell carcinoma-very poorly differentiated

source_name: Renal cell carcinoma

value: Renal

value: F


title: LC:NCI_H23 [113422hp133a11]

description: Adenocarcinoma-undifferentiated

value: M

value: 2n+, Hyperdiploid (47-57)


title: LC:NCI_H322M [113423hp133a11]

description: Small cell Bronchioalveolar Carcinoma

source_name: Small cell Bronchioalveolar Carcinoma


title: LC:EKVX [113418hp133a21]

description: Adenocarcinoma-moderate differentiation

value: EKVX

value: Norsk Hydro's Institut, Norway


title: LC:A549 [113417hp133a11]

value: Giard DJ


title: RE:CAKI_1 [113412hp133a11]

description: Clear cell carcinoma

source_name: Clear cell carcinoma

value: Metastasis

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor cells in vitro, pp 115-159, 1975


title: RE:RXF_393 [113413hp133a11]

description: hypernephroma-poor differentiation

source_name: hypernephroma

value: yes

value: MT

value: MD Anderson Hospital and Tumor Institute

value: NCI/DCT/DTP

value: Contrib oncol 42, 1992


title: RE:SN12C [113414hp133a11]

description: Renal cell carcinoma-poor differentiation

value: 3n, Triploid (69)


title: RE:A498 [113410hp133a11]

description: Adenocarcinoma

value: Renal

value: WT

value: National Cancer Institute, NIH


title: CO:SW_620 [113408hp133a11]

description: Carcinoma-undifferentiated

value: Colon

value: M

value: Scott White Clinic

value: A. Leibovitz


title: RE:TK_10 [113415hp133a11]

description: Renal Spindle cell carcinoma

source_name: Renal Spindle cell carcinoma

value: 4n, Tetraploid (92)

value: R.V.Clayman, Washington Univ.School of Medicine


title: CO:HT29 [113406hp133a11]

description: Adenocarcinoma-moderate differentiation

value: F

value: Primary

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor Cells in vitro:115-159, 1975


title: CO:KM12 [113407hp133a11]

description: Adenocarcinome-poor differentiation

source_name: Adenocarcinome

value: yes

value: MT

value: MD Anderson Hospital and Tumor Institute

value: I.J. Fidler, Univ of Texas M.D. Anderson Hospital and Tumor Institute


title: CNS:U251 [113401hp133a11]

description: Glioblastoma-undifferentiated

source_name: Glioblastoma

value: CNS

value: no

value: 2n+, Hyperdiploid (47-57)

value: University of Uppsala, Sweden

value: J Neuropathol Exp Neurol 40:410-427, 1981


title: CNS:SF_295 [113397hp133a11]

description: Glioblastoma-undifferentiated

value: Rad

value: University of California

value: M.L. Rosenblum

value: Acta Neuropathol 75:92-103, 1988


title: ME:MDA_MB_435 [113395hp133a11]

source_name: Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;

value: Melanoma

value: F

value: Pleural effusion

value: R. Cailleau


title: CO:HCT_15 [113405hp133a11]

source_name: Adenocarcinoma

value: Colon

value: yes

value: ATCC

value: ATCC (D.L. Dexter, Roger Williams General Hospital)


title: CNS:SNB_75 [113400hp133a11]

description: Astrocytoma

source_name: Astrocytoma

value: CNS

value: MT

value: NINCDS

value: P.L. Kornblith


title: CO:COLO205 [113402hp133a11]

description: Adenocarcinoma

value: M

value: Ascites

value: 3n, Triploid (69)

value: Denver Medical Hospital

value: G.E. Moore


title: LE:K_562 [113389hp133a11]

description: CML

source_name: CML

value: Leukemia

value: Bisulfan/PiBr

value: no

value: 3n-, Hypotriploid (58-68)

value: University of Tennesse

value: H.T. Holden


title: LE:SR [113388hp133a11]

description: Lymphoma

source_name: Lymphoma

value: SR

value: Y

value: Program Resources, Inc.

value: W.J. Urba, Program Resources, Inc.


title: RE:786_0 [113409hp133a11]

description: Adenocarcinoma

value: Renal

value: yes

value: MT

value: R.D.Williams, Univ. of Iowa


title: CO:HCC_2998 [113403hp133a11]

description: carcinoma

source_name: carcinoma

value: Colon

value: MD Anderson Hospital and Tumor Institute


title: CO:HCT_116 [113404hp133a11]

description: carcinoma-very poorly differentiated

value: M

value: 2n-, Hypodiploid (35-45)

value: Baylor College


title: CNS:SF_539 [113398hp133a11]

description: Glial cell neoplasm

source_name: Glial cell neoplasm

value: CNS

value: F

value: no

value: WT

value: University of California

value: M.L. Rosenblum

value: J Neuropathol Exp Neurol 40:201-229, 1981


title: RE:ACHN [113411hp133a11]

description: Renal cell carcinoma-poor to moderate differentiation

value: ACHN

value: Rad/VB/CCNU/Mto/Pred

value: Southern Research Inst. (T.F. Hogan, Middleton memorial VA hospital)


title: LE:MOLT_4 [113386hp133a21]

source_name: ALL

value: Leukemia

value: PB

value: 4n, Tetraploid (92)

value: Roswell Park Memorial Institute

value: J. Minowada


title: BR:MCF7 [113392hp133a11]

source_name: Adenocarcinoma-mammary gland; breast; metastatic site: pleural effusion;

value: Breast

value: yes

value: Pleural effusion

value: 3n-, Hypotriploid (58-68)

value: Michigan Cancer Foundtion

value: C.M. McGrath


title: LE:RPMI_8226 [113387hp133a11]

description: Myeloma

source_name: Myeloma

value: M

value: no

value: WT

value: G.E. Moore


title: LE:CCRF_CEM [113384hp133a11]

description: ALL

value: F

value: Rad/Mtx/Cyx

value: MT

value: Children's Cancer research Foudation

value: G.E. Foley


title: CNS:SF_268 [113396hp133a11]

description: Glioblastoma-undifferentiated

value: CNS

value: Rad

value: 2n+, Hyperdiploid (47-57)

value: Acta Neuropathol 75:92-103, 1987


title: LE:HL_60 [113385hp133a11]

description: Pro myelocytic leukemia

source_name: Pro myelocytic leukemia

value: Leukemia

value: PBL

value: National Cancer Institute, NIH

value: R.C. Gallo


title: HomoProstate_N_PD_40

city: Rockville

first: Albert

last: Dobi

state: MD

address: 1530 E. Jefferson St

institute: CPDR USU

description: Poorly Differentiated Matched Normal Patient 40

hyb_protocol: The biotin labeled and fragmented aRNA was hybridized to the HG U133A human genechip array (Affymetrix, Santa Clara, CA). Briefly, a 220 µl hybridization solution consisting of: 1M NaCl, 10 mM Tris pH 7.6, 0.005% Triton X-100, 50 pM control Oligo B2 (5’ bioGTCAAGATGCTACCGTTCAG 3’) (Affymetrix); the control cRNA cocktail of: Bio B (150 pM), Bio C (500 pM), Bio D (2.5 nM) and Cre X (10 nM) (American Type Tissue Collection, Manassas,VA and Lofstrand Labs, Gaithersburg, MD), 0.1 mg/ml herring sperm DNA and 0.05 µg/µl of the fragmented labeled sample cRNA was heated to 95°C for 35 min., cooled to 40°C and clarified by centrifugation. Hybridization was at 42°C in a rotisserie hybridization oven (Model 320, Affymetrix) at 60 rpm for 16 hours. Following hybridization, the GeneChip arrays were washed 10 times at 25°C with 6X SSPE-T buffer (1 M NaCl, 0.006 M EDTA, and 0.06 M Na3PO4 , 0.005% Triton X-100, pH 7.6) using the automated fluidics station protocol. GeneChip arrays were incubated at 50°C in 0.5X SSPE-T, 0.005% Triton X-100 for 20 minutes at 60 rpm in the rotisserie oven. GeneChip arrays were stained for 15 minutes at room temperature and at 60 rpm, with streptavidin phycoerythrin (Molecular Probes, Inc., Eugene, OR) stain solution at a final concentration of 10 µg/ml in 6X SSPE-T buffer and 1.0 mg/ml acetylated bovine serum albumin (Sigma). GeneChip arrays were washed twice at room temperature with 6X SSPE-T buffer.

scan_protocol: GeneChip arrays were scanned with the HP GeneArray Scanner (Hewlett-Packard, Santa Clara, CA) controlled by GeneChip 3.1 Software (Affymetrix).

data_processing: Affymetrix GeneChip Microarray Analysis Software, version 3.1 and Affymetrix Micro DB and Data Mining Tool version 2.0 (Affymetrix), Microsoft Excel 2000 (Microsoft, Seattle, WA) and Statistica version 4.1 (Stat Soft, Inc., Tulsa, OK) were used. In the Affymetrix system, the average difference fluorescence is the average of the difference between every perfect match probe cell and its control mismatch probe cell and is directly related to the level of expression of a transcript. A comparative file indicates the relative change in abundance (fold change) for each transcript between a baseline and an experimental sample.

source_name: Poorly Differentiated Matched Normal Sample

label_protocol: Biotinylation was carried out using aRNA by In vitro transcription using MEGA script T7 in vitro Transcription Kit (Ambion, Austin, TX, USA) cDNA and biotinylated UTP and biotinylated CTP (ENZO, Farmingdale, NY, USA)

growth_protocol: Normal and cancer cells were laser capture microdissected (LCM) (Arcturus Pixel 2) by AFIP pathologists from OCT embedded and H&E stained frozen prostate sections of radical prostatectomy specimens (2000 laser shots for one sample). Total RNA was isolated from the LCM samples with the MicroRNA kit (Stratagene, La Jolla, CA), quantified using RiboGreen dye (Molecular Probes, Eugene, OR) and VersaFluor fluorimeter (BioRad, Hercules, CA), and quality tested by quantitative RT-PCR using NKX3.1 and GAPDH primers. Linear RNA amplification was performed using RiboAmp RNA amplification kit (Arcturus, Mountain View, CA). Precisely, 2 nanograms of total RNA from LCM derived epithelial cells of normal as well as tumor tissue from each patient was used for the first round of amplification. During the second round of amplification after cDNA synthesis and purification the samples were biotinylated during in vitro transcription which was used for the GeneChip analysis.

extract_protocol: The biotin labeled cRNA was purified using the QIAGEN RNeasy spin columns (QIAGEN, Valencia, CA). The biotin labeled cRNA was fragmented in a 40 µl reaction mixture containing 40 mM Tris-acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate incubated at 94°C for 35 minutes and then put on ice.

tag: tissue

value: normal prostate

tag: differentiation

value: Poorly Differentiated Matched


title: BR:HS578T [113391hp133a11]

description: Carcinosarcoma-mammary gland; breast

source_name: Carcinosarcoma-mammary gland; breast

tag: tissue of origin

value: Breast

value: yes

value: Primary

value: Naval Bioscience Laboratory

value: A.J. Hackett


title: HomoProstate_T_PD_40

description: Poorly Differentiated Tumor Patient 40

source_name: Poorly Differentiated Tumor Sample

value: prostate tumor

value: Poorly Differentiated


title: CNS:SNB_19 [113399hp133a11]

description: Glioblastoma-undifferentiated

value: CNS

value: M

tag: epithelial

value: no

value: MT

value: NINCDS

value: P.L. Kornblith


title: BR:MDA_MB_231 [113394hp133a11]

source_name: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site: pleural effusion;

value: F

value: Pleural effusion

tag: ploidy

value: 2n+, Hyperdiploid (47-57)

value: MD Anderson Hospital and Tumor Institute

value: R. Cailleau


title: BR:BT_549 [113390hp133a11]

source_name: Papillary infiltrating ductal carcinoma-mammary gland; breast

value: Breast

value: yes

value: Metastasis

value: W. Coutinho; E.Y. Lasfargues


title: OV:NCI_ADR_RES [113393hp133a11]

description: Adenocarcinoma

value: Ovarian

tag: p53 mutation

value: National Cancer Institute, NIH

value: K.Cowan, NCI


title: HomoProstate_N_PD_38

description: Poorly Differentiated Matched Normal Patient 38

value: normal prostate

value: Poorly Differentiated Matched


title: HomoProstate_T_PD_39

description: Poorly Differentiated Tumor Patient 39

value: prostate tumor

value: Poorly Differentiated


title: HomoProstate_N_PD_39

description: Poorly Differentiated Matched Normal Patient 39


title: ME:UACC_62 [113499hp133a11]

description: Melanotic melanoma

source_name: Melanotic melanoma

value: Melanoma

value: no

value: WT

tag: doubling time

value: University of Arizona

value: A. Leibovitz, UACC


title: HomoProstate_T_PD_37

description: Poorly Differentiated Tumor Patient 37


title: HomoProstate_N_PD_37

description: Poorly Differentiated Matched Normal Patient 37


title: HomoProstate_T_PD_36

description: Poorly Differentiated Tumor Patient 36


title: HomoProstate_T_PD_34

description: Poorly Differentiated Tumor Patient 34


title: HomoProstate_N_PD_32

description: Poorly Differentiated Matched Normal Patient 32


title: HomoProstate_N_PD_33

description: Poorly Differentiated Matched Normal Patient 33


title: HomoProstate_T_PD_38

description: Poorly Differentiated Tumor Patient 38


title: HomoProstate_T_PD_33

description: Poorly Differentiated Tumor Patient 33


title: HomoProstate_N_PD_34

description: Poorly Differentiated Matched Normal Patient 34


title: HomoProstate_N_PD_31

description: Poorly Differentiated Matched Normal Patient 31


title: HomoProstate_N_PD_35

description: Poorly Differentiated Matched Normal Patient 35


title: HomoProstate_T_PD_28

description: Poorly Differentiated Tumor Patient 28


title: HomoProstate_T_PD_27

description: Poorly Differentiated Tumor Patient 27


title: HomoProstate_N_PD_28

description: Poorly Differentiated Matched Normal Patient 28


title: HomoProstate_N_PD_29

description: Poorly Differentiated Matched Normal Patient 29


title: HomoProstate_N_PD_26

description: Poorly Differentiated Matched Normal Patient 26


title: HomoProstate_T_PD_30

description: Poorly Differentiated Tumor Patient 30


title: HomoProstate_N_PD_25

description: Poorly Differentiated Matched Normal Patient 2


title: HomoProstate_T_PD_29

description: Poorly Differentiated Tumor Patient 29


title: HomoProstate_T_PD_32

description: Poorly Differentiated Tumor Patient 32


title: HomoProstate_N_PD_30

description: Poorly Differentiated Matched Normal Patient 30


title: HomoProstate_N_PD_27

description: Poorly Differentiated Matched Normal Patient 27


title: HomoProstate_T_PD_25

description: Poorly Differentiated Tumor Patient 25


title: HomoProstate_T_PD_26

description: Poorly Differentiated Tumor Patient 26


title: HomoProstate_T_PD_24

description: Poorly Differentiated Tumor Patient 24


title: HomoProstate_N_PD_24

description: Poorly Differentiated Matched Normal Patient 24


title: HomoProstate_N_PD_22

description: Poorly Differentiated Matched Normal Patient 22


title: HomoProstate_T_PD_23

description: Poorly Differentiated Tumor Patient 23


title: HomoProstate_T_PD_22

description: Poorly Differentiated Tumor Patient 22


title: HomoProstate_N_WD_20

description: Well Differentiated Matched Normal Patient 20

source_name: Well Differentiated Matched Normal Sample

value: Well Differentiated Matched


title: HomoProstate_T_WD_20

description: Well Differentiated Tumor Patient 20

source_name: Well Differentiated Tumor Sample

value: Well Differentiated


title: HomoProstate_N_WD_19

description: Well Differentiated Matched Normal Patient 19


title: HomoProstate_T_WD_19

description: Well Differentiated Tumor Patient 19


title: HomoProstate_N_WD_17

description: Well Differentiated Matched Normal Patient 17


title: HomoProstate_N_PD_23

description: Poorly Differentiated Matched Normal Patient 23


title: HomoProstate_N_WD_14

description: Well Differentiated Matched Normal Patient 14


title: HomoProstate_T_PD_21

description: Poorly Differentiated Tumor Patient 21


title: HomoProstate_N_WD_16

description: Well Differentiated Matched Normal Patient 16


title: HomoProstate_N_PD_21

description: Poorly Differentiated Matched Normal Patient 21


title: HomoProstate_T_WD_16

description: Well Differentiated Tumor Patient 16


title: HomoProstate_T_WD_18

description: Well Differentiated Tumor Patient 18


title: HomoProstate_T_WD_15

description: Well Differentiated Tumor Patient 15


title: HomoProstate_N_WD_13

description: Well Differentiated Matched Normal Patient 13


title: HomoProstate_N_WD_15

description: Well Differentiated Matched Normal Patient 15


title: HomoProstate_T_WD_17

description: Well Differentiated Tumor Patient 17


title: HomoProstate_T_WD_13

description: Well Differentiated Tumor Patient 13


title: HomoProstate_N_WD_11

description: Well Differentiated Matched Normal Patient 11


title: HomoProstate_N_WD_18

description: Well Differentiated Matched Normal Patient 18


title: HomoProstate_T_WD_11

description: Well Differentiated Tumor Patient 11


title: HomoProstate_T_WD_14

description: Well Differentiated Tumor Patient 14


title: HomoProstate_N_WD_12

description: Well Differentiated Matched Normal Patient 12


title: HomoProstate_T_WD_12

description: Well Differentiated Tumor Patient 12


title: HomoProstate_N_WD_10

description: Well Differentiated Matched Normal Patient 0


title: HomoProstate_N_PD_36

description: Poorly Differentiated Matched Normal Patient 36


title: HomoProstate_N_WD_9

description: Well Differentiated Matched Normal Patient 9


title: HomoProstate_T_WD_10

description: Well Differentiated Tumor Patient 10


title: HomoProstate_T_WD_9

description: Well Differentiated Tumor Patient 9


title: HomoProstate_N_WD_8

description: Well Differentiated Matched Normal Patient 8


title: HomoProstate_T_WD_7

description: Well Differentiated Tumor Patient 7


title: HomoProstate_N_WD_7

description: Well Differentiated Matched Normal Patient 7


title: HomoProstate_T_WD_8

description: Well Differentiated Tumor Patient 8


title: FSHD myoblast 3

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: FSHD myoblasts (at ~70% confluence), biological rep3

data_processing: Raw CEL files were processed using Affymetrix Expression Console Software using RMA-Core-DABG

source_name: FSHD myoblast

label_protocol: 1ug of total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 STarrays

growth_protocol: Culture cells on 0.7% gelatin coated dish with growth medium (F10, 20% FBS, P/S) supplemented with bFGF and dexamethasone. At 100% confluent, induce differentiation with differentiation medium (DMEM, 2%HS, P/S, glutamin) followed by 15%HS after 24h.

extract_protocol: total RNA was extracted from cell pellets using Trizol protocol

treatment_protocol: cells were supplied as pellets in trizol

tag: cell type

value: FSHD myoblasts (at ~70% confluence)


title: HomoProstate_N_WD_5

description: Well Differentiated Matched Normal Patient 5


title: HomoProstate_N_WD_2

description: Well Differentiated Matched Normal Patient 2


title: HomoProstate_T_WD_4

description: Well Differentiated Tumor Patient 4


title: HomoProstate_T_WD_1

description: Well Differentiated Tumor Patient 1


title: FSHD myoblast 1

description: FSHD myoblasts (at ~70% confluence), biological rep1

hyb_protocol: Standard Affymetrix WT protocol for Exon 1.0 STarrays


title: FSHD myotube 1

description: FSHD myotubes (after incubation in differentiation medium for 7 days), biological rep1

scan_protocol: Standard Affymetrix WT protocol for Exon 1.0 STarrays

source_name: FSHD myotube


title: HomoProstate_T_WD_5

description: Well Differentiated Tumor Patient 5


title: HomoProstate_T_WD_6

description: Well Differentiated Tumor Patient 6


title: FSHD myotube 2

description: FSHD myotubes (after incubation in differentiation medium for 5 days), biological rep2


title: HomoProstate_N_WD_6

description: Well Differentiated Matched Normal Patient 6


title: FSHD myoblast 2

description: FSHD myoblasts (at ~70% confluence), biological rep2


title: HomoProstate_N_WD_4

description: Well Differentiated Matched Normal Patient 4


title: HomoProstate_N_WD_1

description: Well Differentiated Matched Normal Patient 1


title: FSHD myotube 3

description: FSHD myotubes (after incubation in differentiation medium for 7 days), biological rep3


title: HomoProstate_T_WD_3

description: Well Differentiated Tumor Patient 3


title: HomoProstate_T_WD_2

description: Well Differentiated Tumor Patient 2


title: HomoProstate_T_PD_35

description: Poorly Differentiated Tumor Patient 35


title: HomoProstate_N_WD_3

description: Well Differentiated Matched Normal Patient 3


title: #5612002_Drugtreated_CT

city: Beltsville

first: Robert

last: Li

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

scan_protocol: Axon GenePix 4000B at 5 um resolution

data_processing: The data presented here are average fluorescent intensity from either 4 or 8 perfect match oligos that represent a single unique sequence. These data are usually log transformed and subject to quantile normalization method using the R package before analyzed. see Li & Li, BMC Genomics 2006, 7:234

organism: Bos taurus

label_protocol: Incoporation

growth_protocol: normal Holstein bull calf (2 to 4 months old fed with hay)

extract_protocol: Trizol followed by Qiagen RNeasy mini cleanup

tag: breed

value: Holstein

tag: gender

value: male

value: small intestine


title: HomoProstate_T_PD_31

description: Poorly Differentiated Tumor Patient 31


title: #5656102_Reinfected for 14dpi

source_name: #5656102_Reinfected for 14dpi


title: #5597502_Reinfected for 14dpi

source_name: #5597502_Reinfected for 14dpi


title: #3440302_drugtreated_CT


title: #3392792_reinfected for 14dpi

source_name: #3392792_reinfected for 14dpi


title: #3398302_reinfected for 14dpi

source_name: #3398302_reinfected for 14dpi


title: #3306302_Drugtreated_CT


title: Breast tumor 160

city: Toronto

first: Dong-Yu

last: Wang

address: 610 University Ave

country: Canada

institute: UHN-PMH-OCI

description:
raw data column: 4098316046_F
Breast tumor 160

hyb_protocol: 750 ng of labeled cRNA were applied to Illimuna whole-genome gene expression HumanRef-8 v2 BeadChips for a overnight hybridization at 58°C.

scan_protocol: Signal is developed with streptavidin-Cy3 and the BeadChip is scanned with the Illumina BeadArray Reader.

data_processing: Image data were processed by BeadStudio software using background subtraction and Quantile normalization. The methods to adjust the normalized intensity values see MAQC Consortium’s description [PMID: 16964229]. Log2 expression ratio of a normalized intensity value to the average signal in all samples for each transcript was calculated.

label: Biotin

source_name: Human breast tumor

label_protocol: 250 ng of total RNA were converted to cDNA, followed by an in vitro transcription amplification step to generate biotin-labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Applied Biosystems, Austin, TX).

extract_protocol: RNA was extracted with QIAGEN RNAeasy Micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: Primary tumor


title: Breast tumor 159

description:
raw data column: 4098316046_E
Breast tumor 159


title: Breast tumor 161

description:
raw data column: 4098316046_G
Breast tumor 161


title: Breast tumor 152

description:
raw data column: 1888849006_E
Breast tumor 152


title: Breast tumor 157

description:
raw data column: 4098316046_C
Breast tumor 157


title: Breast tumor 153

description:
raw data column: 1888849006_F
Breast tumor 153


title: Breast tumor 155

description:
raw data column: 4098316046_A
Breast tumor 155


title: Breast tumor 147

description:
raw data column: 1888849005_G
Breast tumor 147


title: Breast tumor 145

description:
raw data column: 1888849005_E
Breast tumor 145


title: Breast tumor 148

description:
raw data column: 1888849006_A
Breast tumor 148


title: Breast tumor 142

description:
raw data column: 1888849005_B
Breast tumor 142


title: Breast tumor 143

description:
raw data column: 1888849005_C
Breast tumor 143


title: Breast tumor 139

description:
raw data column: 4098316013_E
Breast tumor 139


title: Breast tumor 141

description:
raw data column: 4098316013_G
Breast tumor 141


title: Breast tumor 149

description:
raw data column: 1888849006_B
Breast tumor 149


title: Breast tumor 140

description:
raw data column: 4098316013_F
Breast tumor 140


title: Breast tumor 138

description:
raw data column: 4098316013_D
Breast tumor 138


title: Breast tumor 151

description:
raw data column: 1888849006_D
Breast tumor 151


title: Breast tumor 154

description:
raw data column: 1888849006_G
Breast tumor 154


title: Breast tumor 150

description:
raw data column: 1888849006_C
Breast tumor 150


title: Breast tumor 158

description:
raw data column: 4098316046_D
Breast tumor 158


title: Breast tumor 156

description:
raw data column: 4098316046_B
Breast tumor 156


title: Breast tumor 146

description:
raw data column: 1888849005_F
Breast tumor 146


title: Breast tumor 144

description:
raw data column: 1888849005_D
Breast tumor 144


title: Breast tumor 136

description:
raw data column: 4098316013_B
Breast tumor 136


title: Breast tumor 137

description:
raw data column: 4098316013_C
Breast tumor 137


title: Breast tumor 135

description:
raw data column: 4098316013_A
Breast tumor 135


title: Breast tumor 134

description:
raw data column: 4098316007_G
Breast tumor 134


title: Breast tumor 133

description:
raw data column: 4098316007_F
Breast tumor 133


title: Breast tumor 132

description:
raw data column: 4098316007_E
Breast tumor 132


title: Breast tumor 131

description:
raw data column: 4098316007_D
Breast tumor 131


title: Breast tumor 130

description:
raw data column: 4098316007_C
Breast tumor 130


title: Breast tumor 128

description:
raw data column: 4098316007_A
Breast tumor 128


title: Breast tumor 129

description:
raw data column: 4098316007_B
Breast tumor 129


title: Breast tumor 127

description:
raw data column: 1888849036_F
Breast tumor 127


title: Breast tumor 125

description:
raw data column: 1888849036_C
Breast tumor 125


title: Breast tumor 126

description:
raw data column: 1888849036_E
Breast tumor 126


title: Breast tumor 124

description:
raw data column: 1888849036_B
Breast tumor 124


title: Breast tumor 115

description:
raw data column: 1787466039_G
Breast tumor 115


title: Breast tumor 120

description:
raw data column: 1888849028_E
Breast tumor 120


title: Breast tumor 113

description:
raw data column: 1787466039_E
Breast tumor 113


title: Breast tumor 121

description:
raw data column: 1888849028_F
Breast tumor 121


title: Breast tumor 116

description:
raw data column: 1888849028_A
Breast tumor 116


title: Breast tumor 118

description:
raw data column: 1888849028_C
Breast tumor 118


title: Breast tumor 117

description:
raw data column: 1888849028_B
Breast tumor 117


title: Breast tumor 123

description:
raw data column: 1888849036_A
Breast tumor 123


title: Breast tumor 114

description:
raw data column: 1787466039_F
Breast tumor 114


title: Breast tumor 122

description:
raw data column: 1888849028_G
Breast tumor 122


title: #5657802_Drugtreated_CT


title: Breast tumor 119

description:
raw data column: 1888849028_D,1888849036_G
Breast tumor 119 combined with replicates


title: Breast tumor 112

description:
raw data column: 1787466039_D
Breast tumor 112


title: Breast tumor 102

description:
raw data column: 1787466038_A
Breast tumor 102


title: Breast tumor 103

description:
raw data column: 1787466038_B
Breast tumor 103


title: Breast tumor 109

description:
raw data column: 1787466039_A
Breast tumor 109


title: Breast tumor 111

description:
raw data column: 1787466039_C
Breast tumor 111


title: Breast tumor 104

description:
raw data column: 1787466038_C
Breast tumor 104


title: Breast tumor 101

description:
raw data column: 1787466037_G
Breast tumor 101


title: Breast tumor 107

description:
raw data column: 1787466038_F
Breast tumor 107


title: Breast tumor 110

description:
raw data column: 1787466039_B
Breast tumor 110


title: Breast tumor 108

description:
raw data column: 1787466038_G
Breast tumor 108


title: WT control

city: Madrid

first: Sonsoles

last: Hortelano

address: Carretera de Majadahonda-Pozuelo Km 2

country: Spain

institute: ISCIII

description: WT Control (this sample represent  4 replicates)

data_processing: cDNA was used to amplify the gene of interest using specific primer combinations. Data were evaluated by the ΔΔCt method against WT control cells using an on-line template (http://pcrdataanalysis.sabiosciences.com/pcr/arrayanalysis.php). ΔCt values were calculated by subtracting average cycle threshold (Ct) values of housekeeping genes (glucuronidase, beta, Gusb; Heat shock protein 90 alpha (cytosolic), class B member 1, Hsp90ab1; glyceraldehyde-3-phosphate dehydrogenase, Gapdh; actin, beta, Actb; and hypoxanthine guanine phosphoribosyl transferase 1, Hprt1).

label: SYBR Green

organism: Mus musculus

source_name: peritoneal macrophages

label_protocol: RNA was reverse transcribed into cDNA (RT² First Strand Kit, SABiosciences), and the cDNA was used for quantitative PCR analysis. Expression in peritoneal macrophages was analyzed by quantitative Real-Time PCR using SABiosciences RT² SYBR Green Master Mixes. The PCR conditions were 95°C for 10 min followed by 40 cycles of 95°C for 15 sec and 60°C for 1 min. Analyses were performed on an ABI Real-Time PCR System 7900 (Applied Biosystems, Foster City, CA).

growth_protocol: Peritoneal macrophages were elicited by intraperitoneal injection of 2.5 ml 3% thioglycollate in distilled water. Cells were seeded at 1 x 106/cm2 in RPMI containing 10% FBS. Nonadherent cells were removed 2 h after seeding by extensive washing with medium.

extract_protocol: Total RNA was extracted from cells using Trizol reagent (Invitrogen)

treatment_protocol: Peritoneal macrophages were treated with LPS (200ng/ml) for 4h

tag: cell

value: peritoneal macrophages

tag: genotype/variation

tag: treatment

tag: strain


title: Breast tumor 100

description:
raw data column: 1787466037_F
Breast tumor 100


title: Breast tumor 95

description:
raw data column: 1787466037_A
Breast tumor 95


title: WT LPS

description: WT LPS (this sample represent 4 replicates)

value: LPS


title: Breast tumor 105

description:
raw data column: 1787466038_D
Breast tumor 105


title: Breast tumor 106

description:
raw data column: 1787466038_E
Breast tumor 106


title: ARF control

description: ARF Control (this sample represent 4 replicates)

value: ARF deficient


title: ARF LPS

description: ARF LPS (this sample represent 4 replicates)


title: Breast tumor 97

description:
raw data column: 1787466037_C
Breast tumor 97


title: Breast tumor 93

description:
raw data column: 1787466026_E
Breast tumor 93


title: Breast tumor 99

description:
raw data column: 1787466037_E
Breast tumor 99


title: Breast tumor 98

description:
raw data column: 1787466037_D
Breast tumor 98


title: Breast tumor 90

description:
raw data column: 1787466026_B
Breast tumor 90


title: Breast tumor 92

description:
raw data column: 1787466026_D
Breast tumor 92


title: Breast tumor 96

description:
raw data column: 1787466037_B
Breast tumor 96


title: Breast tumor 88

description:
raw data column: 1787466013_E
Breast tumor 88


title: Breast tumor 91

description:
raw data column: 1787466026_C
Breast tumor 91


title: Breast tumor 94

description:
raw data column: 1787466026_G
Breast tumor 94


title: Breast tumor 89

description:
raw data column: 1787466026_A,1888849036_D
Breast tumor 89 combined with replicates


title: Breast tumor 86

description:
raw data column: 1787466013_C
Breast tumor 86


title: Breast tumor 87

description:
raw data column: 1787466013_D
Breast tumor 87


title: Breast tumor 82

description:
raw data column: 1699538161_E
Breast tumor 82


title: Nodal Marginal Zone Lymphoma_00060047

city: Toledo

first: Alberto

last: Arribas

state: Toledo

address: Avda Barber, 30

department: Molecular Pathology Research Unit

institute: Hospital Virgen de la Salud

hyb_protocol: DNA was hybridized on an Agilent Human Genome CGH Microarray Kit 1x44K (Agilent Technologies, Inc., Santa Clara, CA) according to the manufacturer’s instructions.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Normalization and DNA copy number alterations (CNA) were performed using CAPweb version 2.0 from the Curie Institute (http://bioinfo-out.curie.fr/CAPweb)
The background subtraction of microarray data was carried out using GEPAS 4.0 (http://gepas.bioinfo.cipf.es). The dataset was normalized by lowess within-array normalization and quantile between-array normalization.

source_name: Nodal Marginal Zone Lymphoma

label_protocol: Total DNA amplification and labeling were performed according to the standard Agilent protocol. The samples (1 μg DNA) were labeled with Cy5 and the DNA donor pool was labeled with Cy3.

extract_protocol: DNA of frozen-tissue cases was extracted using the standard phenol-chloroform protocol. For CNA, the DNA was hybridized on an Agilent Human Genome CGH Microarray Kit 1 x 44K (Agilent Technologies) following the manufacturer’s instructions. Human female and male pooled gDNA (Promega) was used to normalize the CGH results. Results were considered valuable in 12 cases. The samples (1 μg DNA) were labeled with Cy5 and the DNA donor pool was labeled with Cy3.

tag: tissue origin

value: freshly frozen lymph nodes

source_name: Universal Human Reference DNA from Promega

tag: sample type

value: reference - Human female and male-pooled gDNA


title: Nodal Marginal Zone Lymphoma_02060229


title: Breast tumor 81

description:
raw data column: 1699538161_D
Breast tumor 81


title: Breast tumor 85

description:
raw data column: 1787466013_B
Breast tumor 85


title: Breast tumor 83

description:
raw data column: 1699538161_F
Breast tumor 83


title: Nodal Marginal Zone Lymphoma_02040336


title: Nodal Marginal Zone Lymphoma_02030091


title: Nodal Marginal Zone Lymphoma_00030109


title: Breast tumor 80

description:
raw data column: 1699538161_C,1787466013_G
Breast tumor 80 combined with replicates


title: Breast tumor 79

description:
raw data column: 1699538161_B
Breast tumor 79


title: Nodal Marginal Zone Lymphoma_02050469


title: Nodal Marginal Zone Lymphoma_00021904


title: Nodal Marginal Zone Lymphoma_00011673


title: Nodal Marginal Zone Lymphoma_00000119


title: Breast tumor 76

description:
raw data column: 1699538093_F
Breast tumor 76


title: Nodal Marginal Zone Lymphoma_00011021


title: Breast tumor 84

description:
raw data column: 1699538161_G
Breast tumor 84


title: Nodal Marginal Zone Lymphoma_00020184


title: Nodal Marginal Zone Lymphoma_00011953


title: Breast tumor 75

description:
raw data column: 1699538093_D,1699538093_E
Breast tumor 75 combined with replicates


title: Nodal Marginal Zone Lymphoma_02040450


title: Nodal Marginal Zone Lymphoma_00000927


title: Breast tumor 74

description:
raw data column: 1699538093_C
Breast tumor 74


title: Breast tumor 77

description:
raw data column: 1699538093_G
Breast tumor 77


title: Breast tumor 72

description:
raw data column: 1699538093_A
Breast tumor 72


title: Breast tumor 70

description:
raw data column: 1855529057_D
Breast tumor 70


title: 41

city: Nantes

first: Edouard

last: Hirchaud

address: 8 quai Moncousu

country: France

institute: Plateforme Bioinformatique de Nantes

description: US82400123_251485056798_S01_GE2-v5_95_Feb07_1_4.txt

hyb_protocol: The Whole Human genome (4x44K) Oligo Microarray were hybridized according to the instructions of Agilent protocol (One color-Agilent Microarray 5,5-February 2007) for 17 h at 65 °C . Stabilization and drying solution was used to protect against Ozone.

scan_protocol: Agilent Technologies Scanner G2505B US22502687-GE2-v5_95_Feb07 + Feature Extraction 10.5.1.1

data_processing: The raw data were normalized and scaled with lowess algorithm. The median sample (median of all samples) were used for fitting of a non-linear normalization curve. We used a homemade script R (version 2.11.1) to generate normalized data.

source_name: lymphoma tumor

label_protocol: 250 ng of total RNA was reverse-transcribed according to the instructions of Agilent protocol (2color-Quick Amp-Agilent Microarray-03-2008). Agilent's Low RNA Input Linear Amplification Kit PLUS generates fluorescent cRNA (complimentary RNA) and  uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP.

extract_protocol: Total RNA are isolated from tissues by Chomzynski modified method, with thiocyanate and buffer saturaded phenol, ( P. Chomczynski and N Sacchi : Analytical Biochemistry 162,156-159 (1987).

tag: case (gc is for germinal center; ngc is for none germinal center)

value: non GC


title: Breast tumor 69

description:
raw data column: 1855529057_C
Breast tumor 69

tag: tissue


title: Breast tumor 68

description:
raw data column: 1855529057_B
Breast tumor 68


title: 39

description: US82400123_251485056798_S01_GE2-v5_95_Feb07_1_2.txt


title: 79

description: US82400123_251485056798_S01_GE2-v5_95_Feb07_1_1.txt


title: Breast tumor 73

description:
raw data column: 1699538093_B
Breast tumor 73


title: 80

value: GC


title: 82


title: 40

description: US82400123_251485056798_S01_GE2-v5_95_Feb07_1_3.txt


title: 81


title: 38

value: nGC


title: Breast tumor 71

description:
raw data column: 1855529057_E
Breast tumor 71


title: 76

description: US82400123_251485052738_S01_GE2-v5_95_Feb07_1_1.txt


title: Breast tumor 78

description:
raw data column: 1699538161_A
Breast tumor 78


title: Breast tumor 66

description:
raw data column: 1855529033_D
Breast tumor 66


title: 36

description: US82400123_251485052738_S01_GE2-v5_95_Feb07_1_3.txt


title: Breast tumor 65

description:
raw data column: 1855529033_C,1787466013_F
Breast tumor 65 combined with replicates


title: Breast tumor 67

description:
raw data column: 1855529033_E
Breast tumor 67


title: Breast tumor 64

description:
raw data column: 1855529017_E
Breast tumor 64


title: Breast tumor 63

description:
raw data column: 1855529017_D
Breast tumor 63


title: 77


title: Breast tumor 62

description:
raw data column: 1855529017_C
Breast tumor 62


title: Breast tumor 59

description:
raw data column: 1855529010_D
Breast tumor 59


title: Breast tumor 60

description:
raw data column: 1855529010_E
Breast tumor 60


title: 78

description: US82400123_251485052738_S01_GE2-v5_95_Feb07_1_4.txt


title: 35


title: Breast tumor 61

description:
raw data column: 1855529017_B
Breast tumor 61


title: Breast tumor 57

description:
raw data column: 1855529010_B
Breast tumor 57


title: 34

description: US82400123_251485052737_S01_GE2-v5_95_Feb07_1_4.txt


title: 31

description: US82400123_251485052737_S01_GE2-v5_95_Feb07_1_1.txt


title: Breast tumor 55

description:
raw data column: 1855529004_D
Breast tumor 55


title: 74

description: US82400123_251485052737_S01_GE2-v5_95_Feb07_1_3.txt


title: Breast tumor 58

description:
raw data column: 1855529010_C
Breast tumor 58


title: 32

description: US82400123_251485052737_S01_GE2-v5_95_Feb07_1_2.txt


title: 72


title: Breast tumor 56

description:
raw data column: 1855529004_E
Breast tumor 56


title: 33


title: 73


title: 29

description: US82400123_251485052736_S01_GE2-v5_95_Feb07_1_3.txt


title: 71

description: US82400123_251485052736_S01_GE2-v5_95_Feb07_1_4.txt


title: 70


title: 30


title: Breast tumor 51

description:
raw data column: 1699538091_E
Breast tumor 51


title: Breast tumor 53

description:
raw data column: 1855529004_B
Breast tumor 53


title: Breast tumor 52

description:
raw data column: 1699538091_F
Breast tumor 52


title: 28

description: US82400123_251485052736_S01_GE2-v5_95_Feb07_1_2.txt


title: Breast tumor 54

description:
raw data column: 1855529004_C,1787466026_F
Breast tumor 54 combined with replicates


title: Breast tumor 50

description:
raw data column: 1699538091_D
Breast tumor 50


title: Breast tumor 48

description:
raw data column: 1699538091_B
Breast tumor 48


title: 68

description: US82400123_251485052736_S01_GE2-v5_95_Feb07_1_1.txt


title: 75

description: US82400123_251485052737_S01_GE2-v5_95_Feb07_1_4.txt


title: Breast tumor 47

description:
raw data column: 1699538091_A
Breast tumor 47


title: Breast tumor 46

description:
raw data column: 1699538090_G
Breast tumor 46


title: Breast tumor 49

description:
raw data column: 1699538091_C
Breast tumor 49


title: Breast tumor 45

description:
raw data column: 1699538090_F
Breast tumor 45


title: 27


title: Breast tumor 44

description:
raw data column: 1699538090_E
Breast tumor 44


title: 26

description: US82400123_251485052734_S01_GE2-v5_95_Feb07_1_4.txt


title: 66

description: US82400123_251485052734_S01_GE2-v5_95_Feb07_1_3.txt


title: 67


title: Breast tumor 42

description:
raw data column: 1699538090_C
Breast tumor 42


title: Breast tumor 43

description:
raw data column: 1699538090_D
Breast tumor 43


title: Breast tumor 39

description:
raw data column: 1699538089_G
Breast tumor 39


title: Breast tumor 41

description:
raw data column: 1699538090_B
Breast tumor 41


title: 24

description: US82400123_251485052734_S01_GE2-v5_95_Feb07_1_2.txt


title: 64

description: US82400123_251485052734_S01_GE2-v5_95_Feb07_1_1.txt


title: 25


title: 65


title: Breast tumor 36

description:
raw data column: 1699538089_D
Breast tumor 36


title: Breast tumor 40

description:
raw data column: 1699538090_A
Breast tumor 40


title: 62

description: US82400123_251485052733_S01_GE2-v5_95_Feb07_1_3.txt


title: Breast tumor 38

description:
raw data column: 1699538089_F
Breast tumor 38


title: 22

description: US82400123_251485052733_S01_GE2-v5_95_Feb07_1_4.txt


title: Breast tumor 34

description:
raw data column: 1699538089_B
Breast tumor 34


title: 21


title: 63


title: Breast tumor 31

description:
raw data column: 1699538083_E,1699538083_F
Breast tumor 31 combined with replicates


title: 23


title: Breast tumor 37

description:
raw data column: 1699538089_E
Breast tumor 37


title: 61

description: US82400123_251485052733_S01_GE2-v5_95_Feb07_1_2.txt


title: 20


title: 19

description: US82400123_251485052733_S01_GE2-v5_95_Feb07_1_1.txt


title: Breast tumor 35

description:
raw data column: 1699538089_C
Breast tumor 35


title: 60


title: 59

description: US82400123_251485043092_S01_GE2-v5_95_Feb07_1_4.txt


title: Breast tumor 30

description:
raw data column: 1699538083_C,1699538083_D
Breast tumor 30 combined with replicates


title: Breast tumor 33

description:
raw data column: 1699538089_A
Breast tumor 33


title: 18


title: Breast tumor 25

description:
raw data column: 1699538082_C
Breast tumor 25


title: 57

description: US82400123_251485043092_S01_GE2-v5_95_Feb07_1_2.txt


title: Breast tumor 26

description:
raw data column: 1699538082_E,1699538082_F
Breast tumor 26 combined with replicates


title: Breast tumor 27

description:
raw data column: 1699538082_G
Breast tumor 27


title: Breast tumor 29

description:
raw data column: 1699538083_B
Breast tumor 29


title: 17

description: US82400123_251485043092_S01_GE2-v5_95_Feb07_1_3.txt


title: 16


title: Breast tumor 23

description:
raw data column: 1825371099_D
Breast tumor 23


title: 58


title: Breast tumor 24

description:
raw data column: 1825371099_E,1699538082_A
Breast tumor 24 combined with replicates


title: Breast tumor 28

description:
raw data column: 1699538083_A
Breast tumor 28


title: Breast tumor 21

description:
raw data column: 1825371099_B
Breast tumor 21


title: 55

description: US82400123_251485043091_S01_GE2-v5_95_Feb07_1_4.txt


title: 56

description: US82400123_251485043092_S01_GE2-v5_95_Feb07_1_1.txt


title: 13

description: US82400123_251485043091_S01_GE2-v5_95_Feb07_1_3.txt


title: Breast tumor 32

description:
raw data column: 1699538083_G
Breast tumor 32


title: Breast tumor 20

description:
raw data column: 1825371097_E
Breast tumor 20


title: 14


title: 37

description: US82400123_251485052738_S01_GE2-v5_95_Feb07_1_4.txt


title: Breast tumor 22

description:
raw data column: 1825371099_C
Breast tumor 22


title: Breast tumor 16

description:
raw data column: 1825371087_E
Breast tumor 16


title: Breast tumor 19

description:
raw data column: 1825371097_D
Breast tumor 19


title: 51

description: US82400123_251485043090_S01_GE2-v5_95_Feb07_1_3.txt


title: 12

description: US82400123_251485043091_S01_GE2-v5_95_Feb07_1_1.txt


title: 10


title: Breast tumor 12

description:
raw data column: 1825371086_E
Breast tumor 12


title: Breast tumor 17

description:
raw data column: 1825371097_B
Breast tumor 17


title: 54


title: Breast tumor 15

description:
raw data column: 1825371087_D
Breast tumor 15


title: Breast tumor 14

description:
raw data column: 1825371087_C
Breast tumor 14


title: Breast tumor 18

description:
raw data column: 1825371097_C
Breast tumor 18


title: 11

description: US82400123_251485043090_S01_GE2-v5_95_Feb07_1_4.txt


title: Breast tumor 11

description:
raw data column: 1825371086_D
Breast tumor 11


title: Breast tumor 13

description:
raw data column: 1825371087_B
Breast tumor 13


title: 9

description: US82400123_251485043090_S01_GE2-v5_95_Feb07_1_2.txt


title: 53


title: Breast tumor 10

description:
raw data column: 1825371086_C
Breast tumor 10


title: 15

description: US82400123_251485043092_S01_GE2-v5_95_Feb07_1_1.txt


title: 52


title: 69

description: US82400123_251485052736_S01_GE2-v5_95_Feb07_1_2.txt


title: 8

description: US82400123_251485043090_S01_GE2-v5_95_Feb07_1_1.txt


title: 50


title: Breast tumor 9

description:
raw data column: 1825371086_B
Breast tumor 9


title: 7

description: US82400123_251485043089_S01_GE2-v5_95_Feb07_1_4.txt


title: 49


title: Breast tumor 7

description:
raw data column: 1825371085_D
Breast tumor 7


title: Breast tumor 6

description:
raw data column: 1825371085_C
Breast tumor 6


title: 47

description: US82400123_251485043089_S01_GE2-v5_95_Feb07_1_3.txt


title: Breast tumor 5

description:
raw data column: 1825371085_B
Breast tumor 5


title: 5

description: US82400123_251485043089_S01_GE2-v5_95_Feb07_1_2.txt


title: 48


title: 6


title: Breast tumor 4

description:
raw data column: 1825371052_E
Breast tumor 4


title: Breast tumor 8

description:
raw data column: 1825371085_E
Breast tumor 8


title: Breast tumor 2

description:
raw data column: 1825371052_C
Breast tumor 2


title: Breast tumor 3

description:
raw data column: 1825371052_D
Breast tumor 3


title: Breast tumor 1

description:
raw data column: 1825371052_B, 1699538091_H
Breast tumor 1 combined with replicates


title: 4

description: US82400123_251485043088_S01_GE2-v5_95_Feb07_1_4.txt


title: 45


title: 44

description: US82400123_251485043088_S01_GE2-v5_95_Feb07_1_3.txt


title: UHRR-29

description: replicate 29

data_processing: Image data were processed by BeadStudio software using background subtraction and Quantile normalization.

source_name: Stratagene Universal Human Reference RNA (Catalog #740000)

extract_protocol: Statagene Universal Reference RNA

value: Reference RNA


title: 3


title: UHRR-30

description: replicate 30


title: UHRR-28

description: replicate 28


title: 46


title: 2

description: US82400123_251485043088_S01_GE2-v5_95_Feb07_1_2.txt


title: 42

description: US82400123_251485043088_S01_GE2-v5_95_Feb07_1_1.txt


title: UHRR-23

description: replicate 23


title: UHRR-25

description: replicate 25


title: UHRR-22

description: replicate 22


title: 43


title: UHRR-27

description: replicate 27


title: UHRR-26

description: replicate 26


title: UHRR-21

description: replicate 21


title: UHRR-20

description: replicate 20


title: UHRR-15

description: replicate 15


title: UHRR-14

description: replicate 14


title: UHRR-19

description: replicate 19


title: UHRR-13

description: replicate 13


title: UHRR-16

description: replicate 16


title: UHRR-18

description: replicate 18


title: UHRR-12

description: replicate 12


title: UHRR-24

description: replicate 24


title: UHRR-8

description: replicate 8


title: UHRR-17

description: replicate 17


title: UHRR-6

description: replicate 6


title: UHRR-10

description: replicate 10


title: UHRR-11

description: replicate 11


title: UHRR-7

description: replicate 7


title: lung of Nfibf/f, Dermo1-Cre animal, biological rep1

city: buffalo

first: Dan

address: Elm & Carlton Streets

institute: RPCI

description: gene expression data from Nfibf/f, Dermo1-Cre lung

hyb_protocol: Biotinylated cRNA were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays.

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

data_processing: MAS5.0 algorithm in the Affy package of Bioconductor in the R statistical computing enviroment was used to generate expression summary values, followed by trimmed mean global normalization.

source_name: mouse lung E18.5

label_protocol: Total RNA was subjected to the standard Affymetrix labeling protocol to obtain biotinylated cRNA.

extract_protocol: Total RNA was extracted from Nfibf/f and Nfibf/f, Dermo1-Cre lungs at E18.5 using TRIzol (Invitrogen, Carlsbad, CA) and then purified using the RNeasy Mini kit (Qiagen, Valencia, CA).

value: fetal lung

tag: genotype

value: Nfibf/f, Dermo1-Cre

tag: age


title: UHRR-3

description: replicate 3


title: lung of Nfibf/f, Dermo1-Cre animal, biological rep3


title: UHRR-2

description: replicate 2


title: UHRR-4

description: replicate 4


title: 1


title: lung of Nfibf/f, Dermo1-Cre animal, biological rep2


title: lung of Nfibf/f animal, biological rep3

description: gene expression data from Nfibf/f lung

value: Nfibf/f


title: UHRR-1

description: replicate 1


title: UHRR-5

description: replicate 5


title: lung of Nfibf/f animal, biological rep1

description: gene expression data from Nfibf/f lung


title: lung of Nfibf/f animal, biological rep2

description: gene expression data from Nfibf/f lung