title: RAW 264.7, RANKL + M-CSF

status: Public on Jun 23 2010

type: RNA

city: Rehovot

first: Omer

last: Barad

address: Herzel

country: Israel

institute: Weizmann Institute of Science

description: osteoclast differentiation of RAW 264.7 transfected with control vector

hyb_protocol: As per standard Affymetrix protocol for the Mouse 1.0ST arrays.

scan_protocol: Arrays were scanned on a DNA microarray Agilent Scanner

data_processing: Quantile normalisation and Robust Multichip Average (RMA) background correction adjusting for probe sequence (Partek Software) was used to generate gene expression levels from the Mouse Gene 1.0ST arrays.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: RAW 264.7, RANKL + M-CSF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for the Mouse 1.0ST arrays from 100ng total RNA.

extract_protocol: RNeasy (Qiagen)

tag: cell line


title: RAW 264.7, RANKL + M-CSF, miR-155

description: osteoclast differentiation of RAW 264.7 transfected with miR-155 expressing vector

source_name: RAW 264.7, RANKL + M-CSF, miR-155


title: HCC LiC.367T

status: Public on Jun 18 2010

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description: To export to gene expression data based on unique gene, we use Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 2 of the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin.

organism: Homo sapiens

source_name: hepatocellular carcinoma

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using RiboGreen were measured (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide

tag: biological source

value: hepatocellular carcinoma


title: HCC LiC.366T


title: HCC LiC.365T


title: HCC LiC.361T


title: HCC LiC.368T


title: HCC LiC.360T


title: RAW 264.7, Unstimulated

description: RAW 264.7 transfected with control vector

scan_protocol: Arrays were scanned on an DNA microarray Agilent Scanner

source_name: RAW 264.7, Unstimulated


title: HCC LiC.363T


title: HCC LiC.362T


title: HCC LiC.359T


title: HCC LiC.364T


title: HCC LiC.369T


title: RAW 264.7, Unstimulated, miR-155

description: RAW 264.7 transfected with miR-155 expressing vector

source_name: RAW 264.7, Unstimulated, miR-155


title: HCC LiC.357T


title: HCC LiC.355T


title: HCC LiC.354T


title: HCC LiC.353T


title: HCC LiC.358T


title: HCC LiC.356T


title: HCC LiC.352T


title: HCC LiC.460T


title: HCC LiC.456T


title: HCC LiC.451T


title: HCC LiC.458T


title: HCC LiC.453T


title: HCC LiC.454T


title: HCC LiC.455T


title: HCC LiC.446T


title: HCC LiC.452T


title: HCC LiC.448T


title: HCC LiC.459T


title: HCC LiC.351T


title: HCC LiC.447T


title: HCC LiC.450T


title: HCC LiC.449T


title: HCC LiC.445T


title: HCC LiC.443T


title: HCC LiC.441T


title: HCC LiC.444T


title: HCC LiC.442T


title: HCC LiC.440T


title: HCC LiC.457T


title: HCC LiC.437T


title: HCC LiC.428T


title: HCC LiC.436T


title: HCC LiC.438T


title: HCC LiC.435T


title: HCC LiC.423T


title: HCC LiC.425T


title: HCC LiC.439T


title: HCC LiC.434T


title: HCC LiC.430T


title: HCC LiC.431T


title: HCC LiC.424T


title: HCC LiC.422T


title: HCC LiC.429T


title: HCC LiC.370T


title: HCC LiC.432T


title: HCC LiC.426T


title: HCC LiC.410T


title: HCC LiC.421T


title: HCC LiC.427T


title: HCC LiC.407T


title: HCC LiC.405T


title: HCC LiC.418T


title: HCC LiC.414T


title: HCC LiC.404T


title: HCC LiC.417T


title: HCC LiC.419T


title: HCC LiC.408T


title: HCC LiC.420T


title: HCC LiC.409T


title: HCC LiC.416T


title: HCC LiC.415T


title: HCC LiC.412T


title: HCC LiC.340T


title: HCC LiC.413T


title: HCC LiC.411T


title: HCC LiC.402T


title: HCC LiC.406T


title: HCC LiC.333T


title: HCC LiC.403T


title: HCC LiC.334T


title: HCC LiC.336T


title: HCC LiC.401T


title: HCC LiC.338T


title: HCC LiC.331T


title: HCC LiC.332T


title: HCC LiC.330T


title: HCC LiC.337T


title: HCC LiC.339T


title: HCC LiC.329T


title: HCC LiC.323T


title: HCC LiC.324T


title: HCC LiC.433T


title: HCC LiC.326T


title: HCC LiC.335T


title: YX_U133_2_14786T

status: Public on Jun 17 2010

city: New York

first: Don

middle: X

last: Nguyen

state: NY

address: 1275 York Box 116

department: Cancer Biology and Genetics

country: USA

institute: MSKCC

hyb_protocol: standard

scan_protocol: standard

data_processing: RMA

label: Biotin

source_name: Brain met

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Brain met tissue

extract_protocol: Rneasy qiagen kit.

treatment_protocol: Frozen

tag: Brain met from lung adenocarcinoma patient


title: HCC LiC.322T


title: HCC LiC.328T


title: YX_U133_2_15922T


title: YX_U133_2_14770T


title: HCC LiC.327T


title: YX_U133_2_111014T


title: YX_U133_2_112056T


title: HCC LiC.321T


title: YX_U133_2_14595T


title: YX_U133_2_106017T


title: YX_U133_2_105400T


title: YX_U133_2_105786T


title: YX_U133_2_103756T


title: YX_U133_2_104640T


title: YX_U133_2_104449T


title: YX_U133_2_102520T


title: YX_U133_2_102466T


title: NCI_U133A_8M


title: YX_U133_2_102206T


title: YX_U133_2_102385T


title: YX_U133_2_100874T


title: NCI_U133A_7M


title: YX_U133_2_104882T


title: NCI_U133A_4M


title: NCI_U133A_3M


title: NCI_U133A_6M


title: NCI_U133A_2M


title: NCI_U133A_5M


title: BMDCs-uninfected-24hr-sorted-rep1

status: Public on Jun 15 2010

city: Paris

first: Eric

last: Prina

address: 25 rue du Dr Roux

department: Parasitology and Mycology

country: France

institute: Institut Pasteur

hyb_protocol: GeneChip hybridizations were performed according to the Affymetrix protocol.

scan_protocol: GeneChipScanner (GSC) 3000 was used with GeneChip Operating Software (GCOS).

data_processing: QC assessment of Affymetrix recommended QC metrics was done using the AffyGCQC program[Osorio-y-Fortéa et al., 2008]. Data processing, background correction, normalization and signal quantification were carried out using the GC-Robust Multiarray Analysis (GC-RMA) algorithm.

source_name: Bone marrow-derived dendritic cells, uninfected controls, 24h sorted

label_protocol: Affymetrix two-cycle labeling protocol

growth_protocol: On day 0, bone marrow cells were seeded at 2x106 cells per 100 mm-diameter bacteriological grade Petri dish (Falcon, Becton Dickinson Labware) in 10 ml of Iscove’s modified Dulbecco’s medium (IMDM; BioWhittaker Europe) supplemented with 10% heat-inactivated fetal calf serum (FCS; Dutscher), 1.5% supernatant from a J558 cell line producing murine GM-CSF (Zal et al., 1994), 50 U/ml penicillin, 50 µg/ml streptomycin, 50 µM 2-mercaptoethanol and 2 mM glutamine (complete IMDM). Cultures were incubated at 37°C in a humidified atmosphere with 7% CO2. On day 3, 10 ml of complete IMDM was added. On day 6, suspended cells and loosely adherent cells were harvested using prewarmed 1% EDTA in Dulbecco’s PBS without Ca2+ and Mg2+ (Biochrom AG). Recovered cells were further cultured in the same conditions as above, except that complete IMDM was supplemented with 10% of the primary culture supernatant. On day 10, cells were harvested with EDTA as above, and distributed in hydrophobic 6-well plates (Greiner) at a concentration of 9x105 cells/well in 3 ml complete IMDM. On day 13, 2 ml of medium was removed from each well and replaced by 2 ml of fresh medium.

extract_protocol: Total RNA was extracted from biological replicates using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s instructions. Evaluation of RNA quality was performed by optical density measurement and by electrophoresis on a Lab-on-a-chip product using the Agilent 2100 Bioanalyzer (Agilent). RNA was quantified using Nanodrop (Kisker).

treatment_protocol: On day 14, DCs were infected or not with L. amazonensis amastigotes at parasite/DC ratios of 4/1. The samples were gently pipetted to dissociate DC clusters and to promote contact between microorganisms and DCs. Infected cells and uninfected cells (controls run in parallel) were then placed at 34°C for 24 hours. After staining with the PE-Cy5 stained M5/114 mAb, DCs were sorted using the BD FACSDiva software (BD Biosciences). The sorter was equipped with 405, 488 and 633 nm laser excitation wavelengths. PE-Cy5 and DsRed2 fluorescences were collected through 695/40 and 576/26 bandpass filters respectively. Forward and side laser scatter were displayed on a linear scale, and used to discard cell debris. To avoid the sorting of cell doublets or cell aggregates, single cells were sequentially selected on SSC-H/SSC-W and FSC-H/FSC-W dot plots. Infected DCs were sorted by selecting cells expressing both MHC Class II molecules and DsRed2 (M5/114 PE-Cy5/DsRed2 dot plot).

tag: strain

value: BALB/c

tag: gender

value: Female

tag: age

value: 8 weeks

tag: origin

value: bone marrow cells

tag: culture

value: 14 days in vitro with GM-CSF


title: BMDCs-infected-24hr-sorted-rep1

source_name: Bone marrow-derived dendritic cells, infected aLV79, 24h sorted

tag: infection

value: aLV79 for 24 hours


title: NCI_U133A_1M


title: BMDCs-uninfected-24hr-sorted-rep2


title: BMDCs-uninfected-24hr-sorted-rep3


title: HCC LiC.325T


title: HES2-P99+17 -ASC

status: Public on Jun 10 2010

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

description: HES2 HESC P99+17 in KOSR (no ASC)

hyb_protocol: llumina Human 6 BeadChips (V3) were hybridized, washed, stained and scanned according to Illuminas protocol

scan_protocol: Processed arrays were read using Illumina BeadReader according to the manufacturer's instructions.

data_processing: Data were first extracted with Illumina BeadStudio software without normalisation.  Data was then uploaded into R, where RMA background adjustment (affy package) and Quantile normalisation (normalize.quantiles) was performed

source_name: Embryonic Stem Cells

label_protocol: Targets were prepared from 200 ng total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791)

extract_protocol: RNA samples were prepared using Qiagen RNeasy Micro Kit (Qiagen) and then assayed using the Agilent Systems Bioanalyzer 2100 to ensure that high-quality RNA was used for the array experiments.

tag: cell type

value: Embryonic Stem Cells

value: 17 passages


title: BMDCs-infected-24hr-sorted-rep2


title: YX_U133_2_112761T


title: HES2-P99+17 +ASC

description: HES2 HESC P99+17 in KOSR (includes ASC)


title: HES2-P99+20 -ASC

description: HES2 HESC P99+20 in KOSR (no ASC)

value: 20 passages


title: HES2-P99+19 -ASC

description: HES2 HESC P99+19 in KOSR (no ASC)

value: 19 passages


title: HES2-P99+20 +ASC

description: HES2 HESC P99+20 in KOSR (includes ASC)


title: SCLC1997

status: Public on Jun 12 2010

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: protocols according to manufacturer (Enzo Life Sciences or www.Agilent.com

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing:
Dewaving: The data have been de-waved as described in Van de Wiel et al. (2009) using the R package "NoWaves". This is available from www.few.vu.nl/~mavdwiel/nowaves.html. Agilent 105K normals were used as calibration.
Normalization: mode normalization

Segmentation: R-package DNAcopy (Olshen et al., 2004) using default settings. This is available from www.bioconductor.org.

van de Wiel MA, Brosens R, Eilers PHC, Kumps C, Meijer GA, Menten B, Sistermans E, Speleman F, Timmerman ME, Ylstra B (2009). Smoothing waves in array CGH tumor profiles. Bioinformatics,  25, 1099-1104.
Olshen, A.B., E.S. Venkatraman, R. Lucito, and M. Wigler (2004). Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557{572.

molecule: genomic DNA

source_name: DNA from formalin fixed paraffin embedded(FFPE) NSCLC sample SCLC1997

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

value: female

tag: history

value: SCLC stage ED nine years.

source_name: Pooled DNA from the blood of 18 normal individuals

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: reference

value: female reference DNA


title: NCI_U133A_9M


title: Cry-Cre E2F1-/- E2F2-/- E2F3f/f E17.5_27

city: Boston

first: Pamela

middle: L.

last: Wenzel

state: MA

address: 300 Longwood Ave

department: Hematology/Oncology

institute: Children's Hospital Boston

description: Gene expression data from lenses microdissected from Cry-Cre E2F1-/- E2F2-/- E2F3f/f E17.5 murine embryos

hyb_protocol: All steps of GeneChip hybridization were performed by the MicroArray Shared Resource (MASR) for the OSU Comprehensive Cancer Center (OSUCCC) according to standard operating procedures (SOP) following the recommendations provided by Affymetrix.

scan_protocol: Scanning was performed by the MicroArray Shared Resource (MASR) for the OSU Comprehensive Cancer Center (OSUCCC) according to standard operating procedures (SOP) following the recommendations provided by Affymetrix.

data_processing: The data were quantile normalized by RMAExpress using background adjustment and median polish summarization. Signal intensities provided in the matrix table were exported in log scale. Data were subsequently imported into the BRB Array Tools plugin for Microsoft Excel for analysis.

source_name: Lens TKO sample at E17.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Embryos or pups were collected from timed pregnancies in which parental contribution would result in offspring with the E2F2-/- genotype or multiple combinations of wild type or null alleles of E2F1, E2F2, and E2F3 in the lens of the eye.

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

treatment_protocol: Both lenses from the mouse were dissected with 18-gauge needles under a microscope and immediately transferred to TRIzol. Lenses were then homogenized and processed for RNA extraction.

tag: tissue

value: lens

value: epithelial cells

tag: developmental stage

value: embryo

tag: genotype/variation

value: triply-deficient for E2F1, E2F2, E2F3


title: Cry-Cre E2F1-/- E2F2-/- E2F3f/f E17.5_26


title: Cry-Cre E2F1-/- E2F2-/- E2F3f/f P0_21

description: Gene expression data from lenses microdissected from Cry-Cre E2F1-/- E2F2-/- E2F3f/f P0 (newborn) murine pups

source_name: Lens TKO sample at P0

value: newborn


title: HES2-P99+19 +ASC

description: HES2 HESC P99+19 in KOSR (includes ASC)


title: Cry-Cre E2F1-/- E2F2-/- E2F3f/f E17.5_24


title: Cry-Cre E2F1-/- E2F2-/- E2F3f/f P0_17


title: SCLC2008

source_name: DNA from formalin fixed paraffin embedded(FFPE) NSCLC sample SCLC2008


title: Cry-Cre E2F1-/- E2F2-/- E2F3f/f E17.5_28


title: Cry-Cre E2F1-/- E2F2-/- E2F3f/f P0_22


title: Cry-Cre E2F1-/- E2F2-/- E2F3f/f P0_19


title: Cry-Cre E2F1-/- E2F2-/- E2F3f/f E17.5_25


title: E2F2-/- E17.5_10

description: Gene expression data from lenses microdissected from E2F2-/- E17.5 murine embryos

source_name: Lens control sample at E17.5

value: control


title: E2F2-/- P0_06

description: Gene expression data from lenses microdissected from E2F2-/- P0 (newborn) murine pups

source_name: Lens control sample at P0


title: E2F2-/- P0_07


title: Cry-Cre E2F1-/- E2F2-/- E2F3f/f P0_18


title: E2F2-/- P0_08


title: E2F2-/- P0_05


title: E2F2-/- E17.5_11


title: E2F2-/- E17.5_15


title: GT4 with array type poplar from Affymetrix

status: Public on Jun 05 2010

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Populus tremula x Populus alba

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: stem - 10-L potted in a mixture of blond and brown peat, horse manure, heather and disinfected compost (pH 5.8). Cuttings were grown in a greenhouse under controlled temperature (18-20°C) and natural light.

extract_protocol: Pool of extract, 33T4:1ug, 39T4:1ug.

tag: harvest date

value: stem


title: E2F2-/- E17.5_13


title: E2F2-/- P0_01


title: FT3 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 24T3:1ug, 29T3:1ug.


title: E2F2-/- E17.5_12


title: DT2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 13T2:1ug, 17T2:1ug.


title: ET3 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 21T3:1ug, 30T3:1ug.


title: JT5 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 48T5:1ug, 53T5:1ug.


title: CT2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 9T2:1ug, 16T2:1ug.


title: Granta.siNTC

status: Public on Jun 03 2010

city: Heidelberg

first: Alexandra

last: Farfsing

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: Labeled, amplified material (700 to 1250 ng per array) was hybridized to the Illumina Human whole genome Sentrix-6 V2 BeadChip® array according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430.

data_processing: Raw data extraction was done using the beadarray R package (svn release 1.7.0) from bioconductor.org. Bead outliers were removed when their expression value dropped below a threshold: the imaging system background, non-specific binding and cross hybridization signal. Individual bead types were flagged as filtered when their bead replicate count dropped below 17. All data was used for the mean expression value calculation within beadarray. Finally, we excluded a bead type when the bead type’s filter flag was set across all samples. Data analysis was done by variance stabilizing and spline normalizing the signals using the algorithms from the lumi R package (release 1.1.0) from bioconductor.org.

source_name: Granta.siNTC (non-template control)

label_protocol: Labeling was achieved by use of the incorporation of biotin-16-UTP.

growth_protocol: Mec1, Mec2, Granta were cultured in DMEM medium. Eheb, JVM, Jeko and LCL-WEI were cultured in RPMI medium.

extract_protocol: RNA  was isolated from the freshly islolated B-cells using the RNeasy kit (Qiagen, Hilden, Germany). RNA quality and concentration were assessed with the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: disease

value: chronic lymphocytic leukemia

value: CLL cell line


title: HT4 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 36T4:1ug, 43T4:1ug.


title: IT5 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 46T5:1ug, 55T5:1ug.


title: JVM2.pCMV_CCDC50

tag: cell line

value: mantle cell lymphoma

value: MCL cell line


title: JVM2.siCCDC50


title: Granta.siCCDC50


title: AT1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 3T1:1ug, 8T1:1ug.


title: JVM2.siNTC

source_name: JVM2.siNTC (non-template control)


title: BT1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 4T1:1ug, 7T1:1ug.


title: Granta.pCMV_CCDC50


title: JVM2.pCMV


title: Granta.CMV


title: Granta-519

source_name: CLL cell line

tag: isolate

value: cell line 3


title: Mec-2

value: cell line 2


title: Jeko-1

source_name: MCL cell line

value: cell line 4


title: Eheb

value: Eheb

value: cell line 6


title: Mec-1

value: cell line 1


title: LCL-WEI

source_name: control cell line

value: LCL-WEI

value: normal

value: lymphoblastoid non-tumor cell line

value: cell line 7


title: JVM-2

value: cell line 5


title: MCL 2039/99

source_name: Primary MCL

growth_protocol: B-cells of MCL and CLL patients were isolated from peripheral blood using ficoll gradient protocoll.

value: B lymphocytes

value: Primary MCL

value: MCL patient 5


title: MCL 19656/01

value: MCL patient 4


title: MCL 16866/98

value: mantle cell lymphoma

value: MCL patient 3


title: MCL H2568/97

value: MCL patient 2


title: CD19.male_repeat

source_name: Healthy Control cells

value: Healthy Control cells

value: CD19 healthy Donor male


title: CD19.female_repeat

value: CD19 healthy Donor female


title: MCL 28631/01

value: MCL patient 6


title: CLL.12.8

source_name: Primary CLL

value: chronic lymphocytic leukemia

value: Primary CLL

value: CLL patient 16


title: CLL.12.3

value: CLL patient 15


title: CLL.12.34

value: CLL patient 23


title: CLL.13.1.II

value: CLL patient 10


title: CLL.13.44

value: B lymphocytes

value: CLL patient 24


title: CLL.13.40

value: CLL patient 14


title: CLL.13.2

value: CLL patient 21


title: CLL.12.2

value: CLL patient 6


title: CLL.12.1

value: CLL patient 5


title: CLL.17.15

value: CLL patient 8


title: CLL.13.25

value: CLL patient 11


title: CLL.17.12

value: CLL patient 3


title: CD19.pool

value: normal

value: Healthy Control cells

value: CD19 healthy Donor pool


title: CLL.17.14

value: chronic lymphocytic leukemia

value: Primary CLL

value: CLL patient 4


title: CLL.13.1.I

value: CLL patient 9


title: CD19.pool_repeat


title: CD19.female

value: CD19 healthy Donor female


title: CLL.17.11

value: B lymphocytes

value: CLL patient 7


title: CD19.male

value: CD19 healthy Donor male


title: CLL.13.45

value: CLL patient 12


title: Blood from colon cancer patient HRCRC-99

status: Public on Jun 01 2010

city: Daejon

first: Seon-Young

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

description: Hybridized to SNP 5.0 array

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: BRLMM-P algorithm was applied to obtain call and signal intensities

source_name: blood

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: disease state

value: colon cancer

value: blood

tag: histoculture drug response assay

value: CAPE = 30

value: FLOX = 12

value: FLIRI = 13


title: Blood from colon cancer patient HRCRC-96

description: Hybridized to SNP 5.0 array

value: CAPE = 42

value: FLOX = 40

value: FLIRI = 29


title: Blood from colon cancer patient HRCRC-90

description: Hybridized to SNP 5.0 array

value: CAPE = 27

value: FLOX = 45

value: FLIRI = 18


title: Blood from colon cancer patient HRCRC-87

description: Hybridized to SNP 5.0 array

value: CAPE = 36

value: FLOX = 41

value: FLIRI = 34


title: Blood from colon cancer patient HRCRC-85

description: Hybridized to SNP 5.0 array

value: FL = 4

value: CAPE = 31

value: FLOX = 35

value: FLIRI = 5


title: Blood from colon cancer patient HRCRC-95

description: Hybridized to SNP 5.0 array

value: colon cancer

value: blood

value: CAPE = 38

value: FLOX = 32

value: FLIRI = 35


title: Blood from colon cancer patient HRCRC-86

description: Hybridized to SNP 5.0 array

value: FL = 5

value: CAPE = 6

value: FLOX = 28

value: FLIRI = 7


title: Blood from colon cancer patient HRCRC-89

description: Hybridized to SNP 5.0 array

value: CAPE = 41

value: FLIRI = 13


title: Blood from colon cancer patient HRCRC-80

description: Hybridized to SNP 5.0 array

value: FL = 2

value: CAPE = 5

value: FLOX = 2


title: Blood from colon cancer patient HRCRC-93

description: Hybridized to SNP 5.0 array

value: CAPE = 10

value: FLOX = 33

value: FLIRI = 12


title: Blood from colon cancer patient HRCRC-75

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 19

value: FLOX = 22

value: FLIRI = 33


title: Blood from colon cancer patient HRCRC-81

description: Hybridized to SNP 5.0 array

value: blood

value: FL = 8

value: FLOX = 11

value: FLIRI = 5


title: Blood from colon cancer patient HRCRC-84

description: Hybridized to SNP 5.0 array

value: CAPE = 36

value: FLOX = 38

value: FLIRI = 4


title: Blood from colon cancer patient HRCRC-76

description: Hybridized to SNP 5.0 array

value: CAPE = 42

value: FLOX = 47

value: FLIRI = 25


title: Blood from colon cancer patient HRCRC-92

description: Hybridized to SNP 5.0 array

value: CAPE = 26

value: FLOX = 13

value: FLIRI = 49


title: Blood from colon cancer patient HRCRC-8

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 23

value: FLOX = 44

value: FLIRI = 57


title: Blood from colon cancer patient HRCRC-83

description: Hybridized to SNP 5.0 array

value: blood

value: FL = 5

value: CAPE = 10

value: FLIRI = 6


title: Blood from colon cancer patient HRCRC-94

description: Hybridized to SNP 5.0 array

value: CAPE = 11

value: FLOX = 17

value: FLIRI = 15


title: Blood from colon cancer patient HRCRC-78

description: Hybridized to SNP 5.0 array

value: CAPE = 19

value: FLOX = 33


title: Blood from colon cancer patient HRCRC-77

description: Hybridized to SNP 5.0 array

value: CAPE = 5

value: FLOX = 21

value: FLIRI = 4


title: Blood from colon cancer patient HRCRC-82

description: Hybridized to SNP 5.0 array

value: CAPE = 12

value: FLOX = 7

value: FLIRI = 16


title: Blood from colon cancer patient HRCRC-70

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 28

value: FLOX = 13

value: FLIRI = 35


title: Blood from colon cancer patient HRCRC-79

description: Hybridized to SNP 5.0 array

value: blood

value: FLOX = 11

value: FLIRI = 45


title: Blood from colon cancer patient HRCRC-72

description: Hybridized to SNP 5.0 array

value: CAPE = 38

value: FLOX = 52

value: FLIRI = 42


title: Blood from colon cancer patient HRCRC-88

description: Hybridized to SNP 5.0 array

value: FL = 9

value: CAPE = 13

value: FLOX = 6

value: FLIRI = 11


title: Blood from colon cancer patient HRCRC-7

description: Hybridized to SNP 5.0 array

value: CAPE = 39

value: FLOX = 33

value: FLIRI = 32


title: Blood from colon cancer patient HRCRC-91

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 55

value: FLOX = 54

value: FLIRI = 67


title: Blood from colon cancer patient HRCRC-73

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 5

value: FLOX = 18

value: FLIRI = 5


title: Blood from colon cancer patient HRCRC-69

description: Hybridized to SNP 5.0 array

value: CAPE = 28

value: FLOX = 35

value: FLIRI = 17


title: Blood from colon cancer patient HRCRC-66

description: Hybridized to SNP 5.0 array

value: CAPE = 11

value: FLOX = 52

value: FLIRI = 59


title: Blood from colon cancer patient HRCRC-71

description: Hybridized to SNP 5.0 array

value: CAPE = 8

value: FLIRI = 10


title: Blood from colon cancer patient HRCRC-59

description: Hybridized to SNP 5.0 array

value: FL = 6

value: CAPE = 6

value: FLOX = 21

value: FLIRI = 26


title: Blood from colon cancer patient HRCRC-57

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = NA

value: FLOX = 13

value: FLIRI = 13


title: Blood from colon cancer patient HRCRC-58

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 39

value: FLOX = 63

value: FLIRI = 46


title: Blood from colon cancer patient HRCRC-53

description: Hybridized to SNP 5.0 array

value: CAPE = 36

value: FLOX = 31


title: Blood from colon cancer patient HRCRC-49

description: Hybridized to SNP 5.0 array

value: CAPE = 28

value: FLOX = 41

value: FLIRI = 23


title: Blood from colon cancer patient HRCRC-50

description: Hybridized to SNP 5.0 array

value: CAPE = 19

value: FLOX = 35


title: Blood from colon cancer patient HRCRC-61

description: Hybridized to SNP 5.0 array

value: FL = 9

value: FLOX = 14

value: FLIRI = 8


title: Blood from colon cancer patient HRCRC-6

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 26

value: FLOX = 74

value: FLIRI = 76


title: Blood from colon cancer patient HRCRC-62

description: Hybridized to SNP 5.0 array

value: blood

value: FL = 6

value: CAPE = 23

value: FLOX = 5

value: FLIRI = 19


title: Blood from colon cancer patient HRCRC-54

description: Hybridized to SNP 5.0 array

value: CAPE = 8

value: FLOX = 31


title: Blood from colon cancer patient HRCRC-68

description: Hybridized to SNP 5.0 array

value: FLOX = 41

value: FLIRI = 18


title: Blood from colon cancer patient HRCRC-52

description: Hybridized to SNP 5.0 array

value: CAPE = 16

value: FLOX = 48

value: FLIRI = 17


title: Blood from colon cancer patient HRCRC-51

description: Hybridized to SNP 5.0 array

value: CAPE = 6

value: FLOX = 10

value: FLIRI = 15


title: Blood from colon cancer patient HRCRC-5

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 37

value: FLOX = 70

value: FLIRI = 65


title: Blood from colon cancer patient HRCRC-44

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 9

value: FLOX = 22

value: FLIRI = 41


title: Blood from colon cancer patient HRCRC-46

description: Hybridized to SNP 5.0 array

value: CAPE = 26

value: FLOX = 26

value: FLIRI = 26


title: Blood from colon cancer patient HRCRC-42

description: Hybridized to SNP 5.0 array

value: CAPE = 51

value: FLOX = 51

value: FLIRI = 51


title: Blood from colon cancer patient HRCRC-45

description: Hybridized to SNP 5.0 array

value: CAPE = 20

value: FLOX = 20

value: FLIRI = 16


title: Blood from colon cancer patient HRCRC-47

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 42

value: FLOX = 45

value: FLIRI = 35


title: Blood from colon cancer patient HRCRC-43

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 21

value: FLOX = 10

value: FLIRI = 43


title: Blood from colon cancer patient HRCRC-40

description: Hybridized to SNP 5.0 array

value: CAPE = 40

value: FLOX = 43

value: FLIRI = 49


title: Blood from colon cancer patient HRCRC-38

description: Hybridized to SNP 5.0 array

value: CAPE = 49

value: FLOX = 49

value: FLIRI = 47


title: Blood from colon cancer patient HRCRC-39

description: Hybridized to SNP 5.0 array

value: CAPE = 7

value: FLOX = 35

value: FLIRI = 38


title: Blood from colon cancer patient HRCRC-33

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 37

value: FLIRI = 55


title: Blood from colon cancer patient HRCRC-64

description: Hybridized to SNP 5.0 array

value: CAPE = 5

value: FLOX = 30

value: FLIRI = 13


title: Blood from colon cancer patient HRCRC-36

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 17

value: FLOX = 51

value: FLIRI = 35


title: Blood from colon cancer patient HRCRC-37

description: Hybridized to SNP 5.0 array

value: FLOX = 39

value: FLIRI = 18


title: Blood from colon cancer patient HRCRC-4

description: Hybridized to SNP 5.0 array

value: CAPE = 38

value: FLOX = 80

value: FLIRI = 80


title: Blood from colon cancer patient HRCRC-35

description: Hybridized to SNP 5.0 array

value: CAPE = 4

value: FLOX = 16

value: FLIRI = 15


title: Blood from colon cancer patient HRCRC-34

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 49

value: FLOX = 25

value: FLIRI = 46


title: Blood from colon cancer patient HRCRC-30

description: Hybridized to SNP 5.0 array

value: CAPE = 13

value: FLOX = 35

value: FLIRI = 26


title: Blood from colon cancer patient HRCRC-3

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 59

value: FLOX = 70

value: FLIRI = 38


title: Blood from colon cancer patient HRCRC-29

description: Hybridized to SNP 5.0 array

value: CAPE = 20

value: FLOX = 21

value: FLIRI = 10


title: Blood from colon cancer patient HRCRC-26

description: Hybridized to SNP 5.0 array

value: CAPE = 37

value: FLOX = 17

value: FLIRI = 16


title: Blood from colon cancer patient HRCRC-27

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 7

value: FLOX = 12

value: FLIRI = 31


title: Blood from colon cancer patient HRCRC-25

description: Hybridized to SNP 5.0 array

value: CAPE = 17

value: FLOX = 13

value: FLIRI = 46


title: Blood from colon cancer patient HRCRC-22

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 24

value: FLOX = 36

value: FLIRI = 22


title: Blood from colon cancer patient HRCRC-20

description: Hybridized to SNP 5.0 array

value: CAPE = 25

value: FLOX = 22

value: FLIRI = 25


title: Blood from colon cancer patient HRCRC-24

description: Hybridized to SNP 5.0 array

value: CAPE = 31

value: FLOX = 26

value: FLIRI = 20


title: Blood from colon cancer patient HRCRC-19

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 45

value: FLIRI = 18


title: Blood from colon cancer patient HRCRC-17

description: Hybridized to SNP 5.0 array

value: CAPE = 38

value: FLOX = 77

value: FLIRI = 52


title: Blood from colon cancer patient HRCRC-23

description: Hybridized to SNP 5.0 array

value: CAPE = 64

value: FLOX = 52


title: Blood from colon cancer patient HRCRC-2

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 8

value: FLOX = 45

value: FLIRI = 30


title: Blood from colon cancer patient HRCRC-21

description: Hybridized to SNP 5.0 array

value: CAPE = 15

value: FLOX = 20

value: FLIRI = 31


title: Blood from colon cancer patient HRCRC-16

description: Hybridized to SNP 5.0 array

value: CAPE = 33

value: FLOX = 44

value: FLIRI = 38


title: Blood from colon cancer patient HRCRC-18

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 36

value: FLOX = 63

value: FLIRI = 5


title: Blood from colon cancer patient HRCRC-120

description: Hybridized to SNP 5.0 array

value: FL = 6

value: CAPE = 28

value: FLOX = 12

value: FLIRI = 4


title: Blood from colon cancer patient HRCRC-123

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 30

value: FLOX = 35

value: FLIRI = 12


title: Blood from colon cancer patient HRCRC-119

description: Hybridized to SNP 5.0 array

value: FL = 3

value: CAPE = 41

value: FLOX = 20


title: Blood from colon cancer patient HRCRC-14

description: Hybridized to SNP 5.0 array

value: CAPE = 31

value: FLOX = 78

value: FLIRI = 62


title: Blood from colon cancer patient HRCRC-13

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 33

value: FLOX = 39

value: FLIRI = 36


title: Blood from colon cancer patient HRCRC-116

description: Hybridized to SNP 5.0 array

value: CAPE = 16

value: FLOX = 24

value: FLIRI = 7


title: Blood from colon cancer patient HRCRC-112

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 12

value: FLOX = 5

value: FLIRI = 18


title: Blood from colon cancer patient HRCRC-117

description: Hybridized to SNP 5.0 array

value: CAPE = 6

value: FLOX = 17

value: FLIRI = 9


title: Blood from colon cancer patient HRCRC-15

description: Hybridized to SNP 5.0 array

value: CAPE = 19

value: FLOX = 56

value: FLIRI = 23


title: Blood from colon cancer patient HRCRC-113

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 29


title: fat_diet_lung_1713

city: Durham

first: Yuh-Chin

middle: Tony

last: Huang

state: NC

address: Erwin Rd

department: Medicine

institute: Duke University Medical Center

description: no additional information

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: MAS 5.0

source_name: WT mouse high fat diet lung rep 2 (1713)

label_protocol: Affymetrix biotin

extract_protocol: Qiagen RNeasy

value: lung

tag: sample number


title: Blood from colon cancer patient HRCRC-111

description: Hybridized to SNP 5.0 array

value: CAPE = 35

value: FLOX = 43

value: FLIRI = 50


title: Blood from colon cancer patient HRCRC-32

description: Hybridized to SNP 5.0 array

value: CAPE = 30

value: FLOX = 12

value: FLIRI = 30


title: fat_diet_lung_1715

description: no additional information

source_name: WT mouse high fat diet lung rep 3 (1715)


title: control_lung_1321

description: no additional information

source_name: WT mouse control lung rep 2 (1321)


title: Blood from colon cancer patient HRCRC-118

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 24

value: FLOX = 25

value: FLIRI = 35


title: fat_diet_lung_1711

description: no additional information

source_name: WT mouse high fat diet lung rep 1 (1711)


title: Blood from colon cancer patient HRCRC-11

description: Hybridized to SNP 5.0 array

value: CAPE = 63

value: FLOX = 67

value: FLIRI = 42


title: Blood from colon cancer patient HRCRC-115

description: Hybridized to SNP 5.0 array

value: FL = 9

value: CAPE = 12

value: FLOX = 15

value: FLIRI = 28


title: Blood from colon cancer patient HRCRC-114

description: Hybridized to SNP 5.0 array

value: colon cancer

value: FLOX = 39

value: FLIRI = 4


title: control_lung_1317

description: no additional information

source_name: control diet lung WT rep 1

value: lung


title: control_lung_1391

description: no additional information

source_name: WT mouse control lung rep 3 (1391)


title: Blood from colon cancer patient HRCRC-105

description: Hybridized to SNP 5.0 array

value: FLIRI = 15


title: Blood from colon cancer patient HRCRC-110

description: Hybridized to SNP 5.0 array

value: CAPE = 40


title: Blood from colon cancer patient HRCRC-106

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 7

value: FLOX = 4

value: FLIRI = 6


title: Blood from colon cancer patient HRCRC-109

description: Hybridized to SNP 5.0 array

value: CAPE = 19

value: FLOX = 32


title: Differentiated Hind Limb Satellite Cells 3

city: Pittsburgh

first: John

middle: Michael

last: Krill-Burger

state: PA

address: Rm. WG21.3 Shadyside Hospital

institute: University of Pittsburgh Medical Center

description: Biotinylated cRNA probe is prepared and hybridization is carried out following the CodeLink protocols and reagents

hyb_protocol: CodeLink™ fragmentation buffer was added to the cRNA (5ul buffer/10ug cRNA) and incubated 20 minutes at 94C. Fragmented cRNA was suspended in hybridization solution containing nuclease-free water such that 250ul loading volume per array contained 10ug of cRNA. The solution was vortexed, heated (5 minutes at 90C) and transferred to ice prior to loading. Each slide contained a removable plastic hybridization chamber with an infusion port that was sealed immediately after loading. Microarrays were placed in a mixing incubator (Innova 4080 Shaking incubator, New Brunswick Scientific Co., Edison, NJ) for 18 hours, 300 rpm at 37C. CodeLink arrays were selected because of their high sensitivity and low error rate compared to other platforms especially regarding transcripts expressed at low copy numbers (73). After hybridization, arrays were individually taken from the incubator and their hybridization chambers were removed. The slides were placed in a reservoir containing 0.75X TNT (0.1M Tris-HCl, pH 7.6, 0.15 M NaCl, 0.05% Tween-20) for a 1 hour high-stringency wash at 46C. The arrays were incubated in Streptavidin Alexa Fluor 647 (Molecular Probes, Eugene, OR) for 30 minutes (0.2% Alexafluor-647 in TNB=0.1 M Tris-HCl, 0.15 M NaCl, 0.5% NEN Blocking Reagent, pH 7.6 (Perkin Elmer, Boston, MA). Slides were subsequently washed (1XTNT-5 min. each of 4 washes at RT; 0.1% SSC and 0.05% Tween20, 30 sec. at RT) and dried by low speed centrifugation.

scan_protocol: Slides were scanned using a 4000B GenePix scanner (Axon Instruments, Foster City, CA) that was calibrated prior to each use. Laser scanning parameters were set at 635 nm, PMT voltage at 600, resolution of 10 microns and the scan area adjusted for the entire array. Analysis of the array image was configured using the CodeLink™ Expression Analysis software (version 5.0). The program generates raw intensity outputs for each spot by segmentation and detection of spot intensity versus surrounding background. Data for each spot was determined as intensity per pixel within the probe zone after local background subtraction. The data for the array were then generated as both raw intensity values and normalized for the large dynamic range by dividing each spot by the overall median intensity value for that array. Values derived from poor or questionable spot profiles were removed from further computation as were all manufacturing errors designated by the CodeLink™ manufacturing spot report.

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 11.139 and the normalized threshold value for this array is 0.103. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Adult Male Mouse

label_protocol: In vitro transcription (IVT) of total RNA utilized the CodeLink™ Target Preparation Protocol (GE CodeLink™ Microarray System, Piscataway, NJ) as previously described (38). Briefly, 5 micrograms of purified RNA underwent cDNA synthesis using Invitrogen First and Second strand cDNA kits (Invitrogen, Austin,TX). Six bacterial control mRNAs were amplified in parallel to serve as fiducial markers and for intensity normalization during microarray scanning. Purification of double-stranded cDNA was performed using the QIAquick purification kit (Qiagen, Germantown, MD) and cRNA was synthesized via reverse transcriptase (Ambion, Austin, TX) in biotin-11-UTP (Perkin Elmer; Boston, MA) by incubation for 14 hours in a water bath at 37C. Biotin-labeled cRNA was recovered using an RNeasy Mini kit (Qiagen, Germantown, MD) and quantitation of the cRNA was performed by UV spectrophotometry at 260 nm. Confirmation of cRNA diversity was obtained using the Bioanalyzer 2100 to generate an electrophoretogram for each IVT reaction substrate which was characterized regarding sample yield, integrity and size diversity against a calibrated laboratory RNA standard. Based on evaluation of bacterial sequences incorporated as controls in the IVT assay, this step resulted in amplification of mRNA by only 50 to 100-fold thereby reducing the potential for errors associated with primer specific exponential amplification (77).

growth_protocol: Muscles of the anterior and superficial posterior compartments were separately dissected, removed aseptically, pooled and finely minced with iris scissors to form a suspension which was seeded on multiple 100mm tissue culture dishes and left undisturbed overnight in an incubator at 37°C. Each plate contained 10 mls of growth media comprising Ham’s F10C (calcium=1.2mM, Sigma, St. Louis, MO), bovine basic fibroblast growth factor (bFGF: 6.6 ng/ml)(Sigma, St. Louis, MO), 200 ul chick embryo extract (CEE) (Invitrogen, Carlsbad, CA), and 10 ul fungizone (Gibco BRL, Gaithersburg MD). The muscle suspension was transferred to a 15ml conical tube on ice, triturated and vortexed vigorously for 30 seconds. The tubes were then centrifuged at low speed (Jouan BH-12: 1000 rpm x 5 min at 4C), the supernatant removed and the pellet resuspended in growth media for transfer to a 100mm dish. The plates were incubated overnight at 37°C and received supplemental feeding after 12 hours (66ng bFGF, 200ul CEE). The entire procedure beginning with trituration, was repeated each day for 5 days including preplating on plastic plates to remove fibroblasts. Eventually, a mix of purified myoblast clones remained that were seeded on denatured collagen (0.07% gelatin, Difco, Kansas City, MO) coated plates. All subsequent media exchanges (every 12 hours) involved complete growth media replacement but without chick embryo extract and these plates were expanded to a density of 0.8 x 106 cells/plate. The myoblasts were rinsed twice in PBS and "switched" to a differentiation media of F10C containing 1mM insulin and a horse serum concentration of 10% (Hyclone lot # AFG5429, Logan, UT) without FGF supplementation. These cultures were left undisturbed for 72 hours to undergo differentiation at which time they were harvested for RNA isolation.

extract_protocol: Frozen tissue specimens were transferred to 15 ml tubes (Sarstedt, Inc. Newton, NC) containing a ten-fold volume of TRIzol based on tissue weight (1ml/0.1mg; Life Technologies/Gibco, Gaithersburg,MD) and subjected to RNA purification as previously described (38). Homogenization was performed in these tubes followed by incubation at room temperature to permit complete dissociation of nucleoprotein complexes. Addition of 0.2 ml of chloroform per 1 ml of TRIzol reagent and centrifugation was performed to allow phase separation of the RNA. Total RNA was precipitated by mixing the aqueous phase with isopropanol. Samples were subsequently incubated, centrifuged and the supernatant removed. The pellet was washed with 75% ethanol, vortexed, centrifuged and air-dried followed by reconstitution in 100 ul of nuclease free water. For cultured cells, TRIzol was added directly to culture plates (5mls/100mm plate) after they were rinsed with ice cold PBS. The cells were harvested with a cell scraper into 15 ml tubes followed by homogenization. The aqueous layer was collected after organic phase separation as previously described and RNA was precipitated, washed with ethanol and resuspended in nuclease-free water as for the whole muscles. Criteria for inclusion in microarray studies was a spectrophotometric absorption ratio 260/280>1.8 (NanoDrop, Wilmington, DE) and RIN value >0.8 via electrophoretic analysis (Agilent Bioanalyzer 2100; Agilent Technologies, Santa Clara, CA).

tag: Swiss Webster Adult Male Mouse


title: Blood from colon cancer patient HRCRC-108

description: Hybridized to SNP 5.0 array

value: CAPE = 31

value: FLOX = 16

value: FLIRI = 31


title: Differentiated Hind Limb Satellite Cells 1

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 6.797 and the normalized threshold value for this array is 0.372. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.


title: Differentiated Hind Limb Satellite Cells 2

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 15.003 and the normalized threshold value for this array is 0.267. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

label_protocol: In vitro transcription (IVT) of total RNA utilized the CodeLink™ Target Preparation Protocol  (GE CodeLink™ Microarray System, Piscataway, NJ) as previously described (38).  Briefly, 5 micrograms of purified RNA underwent cDNA synthesis using Invitrogen First and Second strand cDNA kits (Invitrogen, Austin,TX). Six bacterial control mRNAs were amplified in parallel to serve as fiducial markers and for intensity normalization during microarray scanning. Purification of double-stranded cDNA was performed using the QIAquick purification kit (Qiagen, Germantown, MD) and cRNA was synthesized via reverse transcriptase (Ambion, Austin, TX) in biotin-11-UTP (Perkin Elmer; Boston, MA) by incubation for 14 hours in a water bath at 37C. Biotin-labeled cRNA was recovered using an RNeasy Mini kit (Qiagen, Germantown, MD) and quantitation of the cRNA was performed by UV spectrophotometry at 260 nm. Confirmation of cRNA diversity was obtained using the Bioanalyzer 2100 to generate an electrophoretogram for each IVT reaction substrate which was characterized regarding sample yield, integrity and size diversity against a calibrated laboratory RNA standard. Based on evaluation of bacterial sequences incorporated as controls in the IVT assay, this step resulted in amplification of mRNA by only 50 to 100-fold thereby reducing the potential for errors associated with primer specific exponential amplification (77).


title: Mouse 438 Nerve Stimulated EDL Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 6.940 and the normalized threshold value for this array is 0.3. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 438_Stimulated EDL Muscle

tag: Adult male Swiss Webster mice (30-35 g) (Harlan, Indianapolis, IN) were maintained in a controlled environment with a 12:12-hrs light-dark cycle and food and water administered ad libitum. Experiments were performed on mice anesthetized to a deep plane of surgical anesthesia with an intraperitoneal injection of pentobarbital sodium (50 mg/kg). Additional doses were administered as necessary by monitoring respiration and heart rate in each animal. Core temperature of the animals was maintained at 37ºC using a temperature controlled environmental chamber and monitored via a rectal temperature probe. Surgical preparations comprised a small incision (0.5 cm) proximal to the iliac crest to expose the sciatic nerve as previously described (65). In brief, a pair of bipolar hook electrodes was implanted adjacent to the nerve and the wound was sealed with cyanoacrylate glue. The hindlimb was subsequently immobilized by positioning the animal prone on a plexiglass platform fitted with a patellar brace to fix the knee. The animal was positioned with the chest wall over an aperture designed to fit physiologic sensors built into the platform. A length of 2.0 silk suture was attached to the Achilles tendon proximal to the calcaneous process and this ligature was then connected to a force transducer (Grass FT10; Astromed Inc, West Warwick, RI) to record the performance of the gastrocnemius-plantarus-soleus muscle group throughout the stimulation time course. Prior to each experiment, the voltage-force relation was determined to establish supramaximal stimulation conditions and the length-tension relation was determined to set the resting length for maximum twitch tension development. Contractions were induced by sciatic nerve stimulation using a Grass S48 stimulator (0.5 msec duration, 2-5 volts). The muscles were allowed to rest 15 minutes after these preliminary studies to allow for full metabolic recovery at physiologic temperatures (82). Supramaximal stimulation was applied at a rate of 10 Hz, the standard frequency employed in previous studies but for a shorter duration (4 hours) (34, 35, 67, 68). Force was digitally captured using an AT MIO 16E A/D board and software (National Instruments, Austin, TX) and analyzed using custom MatLab software (MathWorks, Natick, MA) (31). Following cessation of the stimulation period, test twitches were evaluated to confirm muscle recovery in each animal prior to tissue harvest. At the end of each experiment the EDL and soleus muscles were carefully dissected and either flash frozen in liquid nitrogen and stored at -80ºC for later analysis of mRNA expression or fixed at resting length in 10% neutral buffered formalin for histological processing.


title: Blood from colon cancer patient HRCRC-107

description: Hybridized to SNP 5.0 array

value: FL = 7

value: CAPE = 35

value: FLOX = 6


title: Proliferating Hind Limb Muscle Satellite Cells 2

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 10.897 and the normalized threshold value for this array is 0.164. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

growth_protocol: Muscles of the anterior and superficial posterior compartments were separately dissected, removed aseptically, pooled and finely minced with iris scissors to form a suspension which was seeded on multiple 100mm tissue culture dishes and left undisturbed overnight in an incubator at 37°C. Each plate contained 10 mls of growth media comprising Ham’s F10C (calcium=1.2mM, Sigma, St. Louis, MO), bovine basic fibroblast growth factor (bFGF: 6.6 ng/ml)(Sigma, St. Louis, MO), 200 ul chick embryo extract (CEE) (Invitrogen, Carlsbad, CA), and 10 ul fungizone (Gibco BRL, Gaithersburg MD). The muscle suspension was transferred to a 15ml conical tube on ice, triturated and vortexed vigorously for 30 seconds. The tubes were then centrifuged at low speed (Jouan BH-12: 1000 rpm x 5 min at 4C), the supernatant removed and the pellet resuspended in growth media for transfer to a 100mm dish. The plates were incubated overnight at 37°C and received supplemental feeding after 12 hours (66ng bFGF, 200ul CEE). The entire procedure beginning with trituration, was repeated each day for 5 days including preplating on plastic plates to remove fibroblasts. Eventually, a mix of purified myoblast clones remained that were seeded on denatured collagen (0.07% gelatin, Difco, Kansas City, MO) coated plates. All subsequent media exchanges (every 12 hours) involved complete growth media replacement but without chick embryo extract and these plates were expanded to a density of 0.8 x 106 cells/plate and the myoblasts were harvested for analysis.


title: Proliferating Hind Limb Muscle Satellite Cells 3

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 13.171 and the normalized threshold value for this array is 0.121. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.


title: Mouse 438 Control Contralateral Unstimulated EDL Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 6.714 and the normalized threshold value for this array is 0.346. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 438_Control

tag: The contralateral muscle on the non-stimulated side of the animal provides a control that is genetically identical and subjected to the same circulating plasma hormones and growth factors.


title: Proliferating Hind Limb Muscle Satellite Cells 1

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 8.058 and the normalized threshold value for this array is 0.263. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.


title: Mouse 197 Control Contralateral Unstimulated EDL Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 7.941 and the normalized threshold value for this array is 0.208. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 197_Control EDL Muscle


title: Mouse 440 Control Contralateral Unstimulated EDL Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 6.701 and the normalized threshold value for this array is 0.631. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 440_Control Muscle


title: Mouse 440 Nerve Stimulated EDL Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 7.378 and the normalized threshold value for this array is 0.379. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 440_Stimulated EDL Muscle

tag: Adult male Swiss Webster mice (30-35 g) (Harlan, Indianapolis, IN) were maintained in a controlled environment with a 12:12-hrs light-dark cycle and food and water administered ad libitum.  Experiments were performed on mice anesthetized to a deep plane of surgical anesthesia with an intraperitoneal injection of pentobarbital sodium (50 mg/kg). Additional doses were administered as necessary by monitoring respiration and heart rate in each animal. Core temperature of the animals was maintained at 37ºC using a temperature controlled environmental chamber and monitored via a rectal temperature probe.  Surgical preparations comprised a small incision (0.5 cm) proximal to the iliac crest to expose the sciatic nerve as previously described (65). In brief, a pair of bipolar hook electrodes was implanted adjacent to the nerve and the wound was sealed with cyanoacrylate glue. The hindlimb was subsequently immobilized by positioning the animal prone on a plexiglass platform fitted with a patellar brace to fix the knee. The animal was positioned with the chest wall over an aperture designed to fit physiologic sensors built into the platform.  A length of 2.0 silk suture was attached to the Achilles tendon proximal to the calcaneous process and this ligature was then connected to a force transducer (Grass FT10; Astromed Inc, West Warwick, RI) to record the performance of the gastrocnemius-plantarus-soleus muscle group throughout the stimulation time course.  Prior to each experiment, the voltage-force relation was determined to establish supramaximal stimulation conditions and the length-tension relation was determined to set the resting length for maximum twitch tension development. Contractions were induced by sciatic nerve stimulation using a Grass S48 stimulator (0.5 msec duration, 2-5 volts). The muscles were allowed to rest 15 minutes after these preliminary studies to allow for full metabolic recovery at physiologic temperatures (82).  Supramaximal stimulation was applied at a rate of 10 Hz, the standard frequency employed in previous studies but for a shorter duration (4 hours) (34, 35, 67, 68).   Force was digitally captured using an AT MIO 16E A/D board and software (National Instruments, Austin, TX) and analyzed using custom MatLab software (MathWorks, Natick, MA) (31). Following cessation of the stimulation period, test twitches were evaluated to confirm muscle recovery in each animal prior to tissue harvest.  At the end of each experiment the EDL and soleus muscles were carefully dissected and either flash frozen in liquid nitrogen and stored at -80ºC for later analysis of mRNA expression or fixed at resting length in 10% neutral buffered formalin for histological processing.


title: Mouse 183 Control Contralateral Unstimulated EDL Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 8.02 and the normalized threshold value for this array is 0.198. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse Mouse 183_Control Muscle


title: Mouse 183 Nerve Stimulated EDL Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 9.518 and the normalized threshold value for this array is 0.141. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 183_Stimulated EDL Muscle


title: Mouse 197 Nerve Stimulated EDL Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 8.595 and the normalized threshold value for this array is 0.181. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Mouse 197_Stimulated EDL Muscle


title: Mouse 438 Control Contralateral Unstimulated Soleus Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 29.866 and the normalized threshold value for this array is 0.640. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 438_Control Muscle

growth_protocol: The soleus muscle contralateral to the side of stimulous provides a control that is genetically identical and subjected to the same circulating plasma hormones and growth factors.

tag: Swiss Webster Male Mouse


title: Mouse 438 Nerve Stimulated Soleus Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 63.116 and the normalized threshold value for this array is 1.053. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 438_Stimulated Soleus Muscle

growth_protocol: Adult male Swiss Webster mice (30-35 g) (Harlan, Indianapolis, IN) were maintained in a controlled environment with a 12:12-hrs light-dark cycle and food and water administered ad libitum. Experiments were performed on mice anesthetized to a deep plane of surgical anesthesia with an intraperitoneal injection of pentobarbital sodium (50 mg/kg). Additional doses were administered as necessary by monitoring respiration and heart rate in each animal. Core temperature of the animals was maintained at 37ºC using a temperature controlled environmental chamber and monitored via a rectal temperature probe. Surgical preparations comprised a small incision (0.5 cm) proximal to the iliac crest to expose the sciatic nerve as previously described (65). In brief, a pair of bipolar hook electrodes was implanted adjacent to the nerve and the wound was sealed with cyanoacrylate glue. The hindlimb was subsequently immobilized by positioning the animal prone on a plexiglass platform fitted with a patellar brace to fix the knee. The animal was positioned with the chest wall over an aperture designed to fit physiologic sensors built into the platform. A length of 2.0 silk suture was attached to the Achilles tendon proximal to the calcaneous process and this ligature was then connected to a force transducer (Grass FT10; Astromed Inc, West Warwick, RI) to record the performance of the gastrocnemius-plantarus-soleus muscle group throughout the stimulation time course. Prior to each experiment, the voltage-force relation was determined to establish supramaximal stimulation conditions and the length-tension relation was determined to set the resting length for maximum twitch tension development. Contractions were induced by sciatic nerve stimulation using a Grass S48 stimulator (0.5 msec duration, 2-5 volts). The muscles were allowed to rest 15 minutes after these preliminary studies to allow for full metabolic recovery at physiologic temperatures (82). Supramaximal stimulation was applied at a rate of 10 Hz, the standard frequency employed in previous studies but for a shorter duration (4 hours) (34, 35, 67, 68). Force was digitally captured using an AT MIO 16E A/D board and software (National Instruments, Austin, TX) and analyzed using custom MatLab software (MathWorks, Natick, MA) (31). Following cessation of the stimulation period, test twitches were evaluated to confirm muscle recovery in each animal prior to tissue harvest. At the end of each experiment the EDL and soleus muscles were carefully dissected and either flash frozen in liquid nitrogen and stored at -80ºC for later analysis of mRNA expression or fixed at resting length in 10% neutral buffered formalin for histological processing.


title: Mouse 440 Nerve Stimulated Soleus Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 25.175 and the normalized threshold value for this array is 0.477. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 440_Stimulated Soleus Muscle


title: Blood from colon cancer patient HRCRC-100

description: Hybridized to SNP 5.0 array

data_processing: BRLMM-P algorithm was applied to obtain call and signal intensities

source_name: blood

value: colon cancer

value: FL = 5

value: CAPE = 44

value: FLOX = 2

value: FLIRI = 36


title: Blood from colon cancer patient HRCRC-102

description: Hybridized to SNP 5.0 array

value: blood

value: CAPE = 32

value: FLOX = 37

value: FLIRI = 29


title: Mouse 443 Control Contralateral Unstimulated Soleus Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 42.161 and the normalized threshold value for this array is 0.839. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 443_Control Muscle


title: Mouse 440 Control Contralateral Unstimulated Soleus Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 33.363 and the normalized threshold value for this array is 0.706. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.


title: Mouse 183 Nerve Stimulated Soleus Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 55.558 and the normalized threshold value for this array is 1.058. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 183_Stimulated Soleus Muscle


title: Blood from colon cancer patient HRCRC-103

description: Hybridized to SNP 5.0 array

value: FL = 6

value: CAPE = 13

value: FLOX = 10

value: FLIRI = 17


title: Mouse 443 Nerve Stimulated Soleus Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 39.724 and the normalized threshold value for this array is 0.859. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 443_Stimulated Soleus Muscle


title: Mouse 183 Control Contralateral Unstimulated Soleus Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 49.417 and the normalized threshold value for this array is 1.036. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 183_Control Muscle


title: Mouse 191 Nerve Stimulated Soleus Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 26.878 and the normalized threshold value for this array is 0.522. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 191_Stimulated Soleus Muscle


title: Blood from colon cancer patient HRCRC-101

description: Hybridized to SNP 5.0 array

value: CAPE = 29

value: FLOX = 5

value: FLIRI = 4


title: Mouse 191 Control Contralateral Unstimulated Soleus Muscle

data_processing: Raw intensities were normalized by CodeLink software based on global median for each array. CodeLink also calculated a threshold value based on the negative controls. The raw threshold value for this array is 82.531 and the normalized threshold value for this array is 1.376. To obtain the same data set we used for analysis, the normalized threshold value must be subtracted from each probe in the "value" column.

source_name: Swiss Webster Male Mouse 191_Control Muscle


title: HF4 vs. HF4-REV 309376

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
HF4 vs HF4-REV
Date:2007/06/21

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 16 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : vsn, Intraslide norm. : none, Background norm. : none, Software used : rscript --> VALUE data obtained from log of processed Red signal/processed Green signal.

label_protocol: Ambion

extract_protocol: Qiagen

tag: subject

value: epididymal fat

tag: diet

value: high fat diet


title: HF3-REV vs. HF3 40993

description:
HF3-REV vs HF3
Date:2007/06/21

tag: tissue


title: STD vs. HF0 40988

description:
STD vs HF0
Date:2007/06/21

source_name: STD

value: STD


title: HF3 vs. HF0 309381

description:
HF3 vs HF0
Date:2007/06/20


title: HF4 vs. HF3 309379

description:
HF4 vs HF3
Date:2007/06/21


title: HF1 vs. HF0 309380

description:
HF1 vs HF0
Date:2007/06/20


title: HF4 vs. HF1 309385

description:
HF4 vs HF1
Date:2007/06/20


title: HF4-REV vs. HF4 40994

description:
HF4-REV vs HF4
Date:2007/06/21


title: HF3 vs. HF1 309384

description:
HF3 vs HF1
Date:2007/06/20


title: HF3 vs. HF3-REV 309316

description:
HF3 vs HF3-REV
Date:2007/06/21


title: HF1 vs. HF4 40996

description:
HF1 vs HF4
Date:2007/06/20


title: HF1 vs. HF3 40931

description:
HF1 vs HF3
Date:2007/06/20


title: HF1-REV vs. HF1 40992

description:
HF1-REV vs HF1
Date:2007/06/21


title: HF0 vs. HF3 40929

description:
HF0 vs HF3
Date:2007/06/20


title: HF0 vs. HF1 40928

description:
HF0 vs HF1
Date:2007/06/20


title: STD vs. HF3 16505

description:
STD vs HF3
Date:2006/10/10

hyb_protocol: CGH-Agilent-4rpm : 750.0 ng at 62 degree_C during 17 hours

extract_protocol: Trizol


title: HF3 vs. HF4 40995

description:
HF3 vs HF4
Date:2007/06/21


title: HF3 vs. STD 16666

description:
HF3 vs STD
Date:2006/10/10


title: STD vs. HF4 16667

description:
STD vs HF4
Date:2006/10/10


title: HF0 vs. HF3 17723

description:
HF0 vs HF3
Date:2006/10/10


title: STD vs. HF0 312408

description:
STD vs HF0
Date:2007/06/29


title: HF4 vs. HF0 17721

description:
HF4 vs HF0
Date:2006/10/10


title: HF0 vs. HF4 17650

description:
HF0 vs HF4
Date:2006/10/10


title: HF3 vs. HF4 17722

description:
HF3 vs HF4
Date:2006/10/10


title: HF0 vs. HF4 312265

description:
HF0 vs HF4
Date:2007/06/29


title: HF0 vs. STD 312410

description:
HF0 vs STD
Date:2007/06/29


title: HF4 vs. STD 17533

description:
HF4 vs STD
Date:2006/10/10


title: HF4 vs. HF3 17537

description:
HF4 vs HF3
Date:2006/10/10


title: HF4 vs. HF0 312409

description:
HF4 vs HF0
Date:2007/06/29


title: HF3 vs. HF0 17649

description:
HF3 vs HF0
Date:2006/10/10


title: HF0 vs. STD 17535

description:
HF0 vs STD
Date:2006/10/10


title: 212409_Control

city: Bethesda

first: Taura

middle: L

last: Barr

state: MD

address: Bldg 10 CRC Room 2-1339

department: Tissue Injury Unit

institute: NINR/NIH

description: Control

hyb_protocol: Standard Illumina hybridizaion protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Robust multiarray analysis normalization was conducted in GeneSpring, resulting in background correction, quantile normalization, and summarization in the log base 2 scale.

source_name: Whole blood RNA

label_protocol: RNA was amplified using the Illumina TotalPrep RNA amplification kit, resulting in biotin labeled cRNA.

extract_protocol: RNA was extracted using the Qiagen Paxgene Blood RNA kit. Hemoglobin reduction was not performed.

tag: gender

value: Female

tag: age

tag: race

value: Caucasian


title: 201203_Control

description: Control


title: 213401_Control

description: Control


title: 213902_Control

description: Control


title: HF1 vs. HF1-REV 309315

description:
HF1 vs HF1-REV
Date:2007/06/21


title: 212405_Control

description: Control


title: 212412_Control

description: Control


title: 213905_Control

description: Control


title: Blood from colon cancer patient HRCRC-104

description: Hybridized to SNP 5.0 array

value: colon cancer

value: CAPE = 35

value: FLOX = 23

value: FLIRI = 35


title: 212407_Control

description: Control


title: 213901_Control

description: Control


title: HF0 vs. STD 309314

description:
HF0 vs STD
Date:2007/06/21


title: Testis vs. Epididymis 345356

description:
Testis vs. Epididymis
Date:2008/09/18

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 17 hours

source_name: epididymis

value: epididymis

source_name: testis

value: testis


title: 212402_Control

description: Control


title: Stromal-vascular fraction of adipose tissue vs. Epididymis 345355

description:
Stromal-vascular fraction of adipose tissue vs. Epididymis
Date:2008/09/18

source_name: Stromal-vascular fraction


title: Epididymis vs. Testis 345548

description:
Epididymis vs. Testis
Date:2008/09/18


title: 212411_Control

description: Control


title: STD vs. HF0 17534

description:
STD vs HF0
Date:2006/10/10


title: 212401_Control

description: Control


title: 212418_Control

description: Control


title: 213906_Control

description: Control

value: Male


title: Stromal-vascular fraction of adipose tissue vs. Testis 345549

description:
Stromal-vascular fraction of adipose tissue vs. Testis
Date:2008/09/18


title: Testis vs. Stromal-vascular fraction of adipose tissue 345544

description:
Testis vs. Stromal-vascular fraction of adipose tissue
Date:2008/09/18


title: Epididymis vs. Stromal-vascular fraction of adipose tissue 345547

description:
Epididymis vs. Stromal-vascular fraction of adipose tissue
Date:2008/09/18


title: 213405_Control

description: Control


title: 213406_Control

description: Control


title: 213302_Control

description: Control


title: 212415_Control

description: Control


title: 212404_Control

description: Control


title: 3100084_Stroke

description: Stroke


title: 3100044_Stroke

description: Stroke


title: 212417_Control

description: Control


title: 212414_Control

description: Control


title: Strongly lung metastatic line 4180

city: Princeton

first: Yibin

last: Kang

state: NJ

address: LTL 254, Washington Road

department: Molecular Biology

institute: Princeton University

description: Strongly lung metastatic line 4180

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Genespring GX 7.3 Expression Analysis using Per Chip (normalized to 50th percentile) and Per Gene (normalized to median) normalization methods.

source_name: Strongly lung metastatic line 4180

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: These sublines and their fusion variants were maintained in DMEM with 10% FBS and antibiotics supplemented with appropriate selective drugs.

extract_protocol: Total RNA was extracted using Qiagen RNAeasy mini kit following manufacturer's instructions.

treatment_protocol: Cells were grown to sub-confluency before harvesting RNA.

tag: cell type

value: breast cancer

tag: parental cell line


title: 3100047_Stroke

description: Stroke


title: 213403_Control

description: Control


title: 3100021_Stroke

description: Stroke


title: Weakly Lung metastatic line SCP26

description: Weakly Lung metastatic line SCP26

source_name: Weakly Lung metastatic line SCP26

tag: cell line


title: 212416_Control

description: Control


title: Strongly lung metastatic line 4173

description: Strongly lung metastatic line 4173

source_name: Strongly lung metastatic line 4173


title: Strongly lung metastatic line 4175

description: Strongly lung metastatic line 4175

source_name: Strongly lung metastatic line 4175


title: Strongly lung metastatic line 4142

description: Strongly lung metastatic line 4142

source_name: Strongly lung metastatic line 4142


title: 3100035_Stroke

description: Stroke


title: Weakly Lung metastatic line SCP6

description: Weakly Lung metastatic line SCP6

source_name: Weakly Lung metastatic line SCP6


title: 3100126_Stroke

description: Stroke


title: 212413_Control

description: Control


title: Weakly Lung metastatic line SCP21

description: Weakly Lung metastatic line SCP21

source_name: Weakly Lung metastatic line SCP21


title: 3100061_Stroke

description: Stroke


title: Strongly Bone metastatic line 2269

description: Strongly Bone metastatic line 2269

source_name: Strongly Bone metastatic line 2269


title: 3100121_Stroke

description: Stroke


title: Strongly Bone metastatic line 2268

description: Strongly Bone metastatic line 2268

source_name: Strongly Bone metastatic line 2268


title: 3100117_Stroke

description: Stroke


title: 3100050_Stroke

description: Stroke


title: 3100197_Stroke

description: Stroke


title: 3100041_Stroke

description: Stroke


title: 3100077_Stroke

description: Stroke


title: Strongly Bone metastatic line 1833

description: Strongly Bone metastatic line 1833

source_name: Strongly Bone metastatic line 1833


title: 3100193_Stroke

description: Stroke


title: Weakly Bone metastatic line 2295

description: Weakly Bone metastatic line 2295

source_name: Weakly Bone metastatic line 2295


title: 3100036_Stroke

description: Stroke


title: hyperploid subline of 4175

description: hyperploid subline of 4175

source_name: hyperploid subline of 4175


title: 3100034_Stroke

description: Stroke


title: modalploid subline of 4175

description: modalploid subline of 4175

source_name: modalploid subline of 4175


title: 3100042_Stroke

description: Stroke

source_name: Whole blood RNA


title: Weakly Bone metastatic line 2296

description: Weakly Bone metastatic line 2296

source_name: Weakly Bone metastatic line 2296


title: Strongly Bone metastatic line 2274

description: Strongly Bone metastatic line 2274

source_name: Strongly Bone metastatic line 2274


title: hyperploid subline of 1833

description: hyperploid subline of 1833

source_name: hyperploid subline of 1833


title: Weakly Bone metastatic line 2293

description: Weakly Bone metastatic line 2293

source_name: Weakly Bone metastatic line 2293


title: 3100137_Stroke

description: Stroke


title: 3100048_Stroke

description: Stroke


title: modalploid subline of 1833

description: modalploid subline of 1833

source_name: modalploid subline of 1833


title: 3100118_Stroke

description: Stroke


title: 3100076_Stroke

description: Stroke


title: 3100023_Stroke

description: Stroke


title: 3100114_Stroke

description: Stroke


title: 3100066_Stroke

description: Stroke


title: Parental MDA-MB-231


title: 3100113_Stroke

description: Stroke


title: 3100157_Stroke

description: Stroke


title: 3100060_Stroke

description: Stroke


title: 3100124_Stroke

description: Stroke


title: 3100058_Stroke

description: Stroke


title: 3100138_Stroke

description: Stroke


title: 3100025_Stroke

description: Stroke


title: 3100039_Stroke

description: Stroke


title: 3100135_Stroke

description: Stroke


title: 3100191_Stroke

description: Stroke


title: 3100112_Stroke

description: Stroke


title: T00306165: cardiomyocytes, 48 hour conditioned

description:
Cardiac media was diluted 50% with conditioned hesc media while FBS and HS percentages were held constant at 5% and 10% respectively.
RNA extracted after 48 hours.

hyb_protocol: GE Healthcare Amersham CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection protocol Detection dye: streptavidin - Alexa Fluor 647

scan_protocol: Scanned using a GenePix 4000B at 600 PMT and CodeLink software (version 5.0).

data_processing:
The threshold was calculated by removing the top 10% and bottom 10% of negative controls and averaging the remaining intensities. The threshold was subtracted from each of the discovery probes. An average was computed for the following positive controls: LEUB, HISB, FIXB (FIXB_PROBE2 was not used on arrays T00306161 and T00306162 because its intensity was greater than 2 standard deviations away from the mean), GND, ENTF, and ARAB. The averages of each of these positive controls was grouped together with its average on all the other arrays in this series. By taking the median of each group, a global median was created which represents the median value for a positive control across all of the arrays. Correction factors for this array were calculated by dividing the average of each positive control by its corresponding global median. It was observed that the arrays behaved differently at high intensity levels compared to low intensity levels. As the positive controls increased in intensity, the correction factors also steadily increased or steadily decreased. Therefore, a correction factor derived from a low intensity positive control was not a good correction for high intensity probes. To accommodate for the effect of intensity, the correction factor for each positive control was graphed versus its intensity and a best-fit regression line was created. The equation of the best-fit line was used to calculate a correction factor for each individual discovery probe based on where it fit into the slope of the correction factors. Negative values were replaced by a placeholder of ".0001".
In summary, the data was normalized by comparing each positive control to its median value across arrays and correcting based on the slope of the positive controls versus intensity. Note that the data was never median normalized or log transformed.

organism: Rattus norvegicus

source_name: cardiomyocytes, 48 hour conditioned

label_protocol: GE Healthcare Amersham CodeLink iExpress Assay Reagent Kit protocol

extract_protocol: Extracted using Invitrogen Trizol LS Reagent and Invitrogen's RNA isolation protocol supplied with the reagent.

tag: Rat neonatal cardiomyocytes harvested from day 1 ventricles (n=24). Cells purified via serial Percoll gradients and plated at 2.5x10^5 cells per 100 mm sq dish.


title: 3100068_Stroke

description: Stroke


title: 3100195_Stroke

description: Stroke


title: T00306164: cardiomyocytes, time zero control

description: No treatment, time zero control

source_name: cardiomyocytes, time zero control


title: T00306162: cardiomyocytes, 24 hour unconditioned

description:
Cardiac media was diluted 50% with unconditioned hesc media while FBS and HS percentages were held constant at 5% and 10% respectively.
RNA extracted after 24 hours.

source_name: cardiomyocytes, 24 hour unconditioned


title: T00306159: cardiomyocytes, time zero control

description: No treatment, time zero control

data_processing:
The threshold was calculated by removing the top 10% and bottom 10% of negative controls and averaging the remaining intensities. The threshold was subtracted from each of the discovery probes. An average was computed for the following positive controls: LEUB, HISB, FIXB, GND, ENTF, and ARAB. The averages of each of these positive controls was grouped together with its average on all the other arrays in this series. By taking the median of each group, a global median was created which represents the median value for a positive control across all of the arrays. Correction factors for this array were calculated by dividing the average of each positive control by its corresponding global median. It was observed that the arrays behaved differently at high intensity levels compared to low intensity levels. As the positive controls increased in intensity, the correction factors also steadily increased or steadily decreased. Therefore, a correction factor derived from a low intensity positive control was not a good correction for high intensity probes. To accommodate for the effect of intensity, the correction factor for each positive control was graphed versus its intensity and a best-fit regression line was created. The equation of the best-fit line was used to calculate a correction factor for each individual discovery probe based on where it fit into the slope of the correction factors. Negative values were replaced by a placeholder of ".0001".
In summary, the data was normalized by comparing each positive control to its median value across arrays and correcting based on the slope of the positive controls versus intensity. Note that the data was never median normalized or log transformed.


title: T00306161: cardiomyocytes, 24 hour unconditioned


title: T00306160: cardiomyocytes, time zero control

description: No treatment, time zero control


title: T00306158: cardiomyocytes, 24 hour conditioned

description:
Cardiac media was diluted 50% with conditioned hesc media while FBS and HS percentages were held constant at 5% and 10% respectively.
RNA extracted after 24 hours.

source_name: cardiomyocytes, 24 hour conditioned


title: 3100083_Stroke

description: Stroke


title: T00219257: cardiomyocytes, 24 hour unconditioned


title: T00219258: cardiomyocytes, time zero control

description: No treatment, time zero control


title: T00306156: cardiomyocytes, 48 hour conditioned


title: T00219256: cardiomyocytes, 48 hour unconditioned

description:
Cardiac media was diluted 50% with unconditioned hesc media while FBS and HS percentages were held constant at 5% and 10% respectively.
RNA extracted after 48 hours.

source_name: cardiomyocytes, 48 hour unconditioned


title: T00306155: cardiomyocytes, 48 hour unconditioned


title: T00306157: cardiomyocytes, 48 hour unconditioned


title: T00219252: cardiomyocytes, 24 hour conditioned


title: G-IV_THP-1+B. pseudomallei 24h+CAZ_Rep3.

status: Public on May 31 2010

city: Augusta

first: Pachiappan

last: Arjunan

state: Georgia

address: 1120 15th ST, Laney walker Blvd,

department: Anatomy, Unit on Retinal Vascular Neurobiology, BMB

institute: NUS, NIH, GRU

description: Total RNA was isolated from THP-1 cells infected with B. pseudomallei (n = 5 flasks for each replicate) and treated with standared antimicrobial drug ceftazidime using RNeasy® mini kit. The target chip hybridization followed successful Genechip Test3 arrays hybridization. All relevant procedures, such as amplification of cDNA, fragmentation of cRNA for hybridization, and concurrent assessment of expression levels of genes were carried out. Briefly, we synthesized double-stranded cDNA from the total RNA isolated from the THP-1 cells infected with with B. pseudomallei, and treated with CAZ. We generated biotin-labeled cRNAs by in-vitro transcription from the ds-cDNA. The cRNAs were fragmented before hybridization, and a hybridization cocktail was prepared and hybridized to the oligonucleotide probes on the HG-U133A GeneChip arrays for 16h incubation at 45°C. Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station. We scanned the GeneChips and processed the signals using Affymetrix genechip scanner and expression analysis algorithm (Affymetrix, Santa Clara, CA).

hyb_protocol: The preparation and processing of labeled, fragmented cRNA and hybridization cocktail for hybridization has been performed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station (Replicate-3).

data_processing: Three chips were used for each experiment (Group) according to MIAME guidelines. Expression values for each gene were calculated using the Affymetrix Microarray suite (MAS v5.0) software. Using the 50th percentile of each chip’s (per chip normalization) intensity range, expression values were normalized across the sample set by scaling the average of the intensities of all genes to constant target intensity of 800 and a comparison of signal intensities using Microsoft® Excel showed results from duplicate chips highly correlated with R values = 0.96. These data were further categorized and analyzed using stringent filter (statistical inclination) in order to identify the target genes. Hence, the resultant data were further put into marketable GeneSpring v7.0 (Silicon Genetics, Redwood City, CA, USA http://www.silicongenetics.com/cgi/SiG.cgi/Products/ GeneSpring?index.smf) for temporal sequence analyses by parametric test based on cross gene error model (PCGEM). Relative expression data for each probe set were generated by normalization over the median of the entire experiment set (per gene normalization).

organism:
Homo sapiens
Burkholderia pseudomallei

source_name: THP-1+ Infected with B. pseudomallei 24h and treated with ceftazidime_Rep3.

label_protocol: cRNA was labeled with Biotin according to the manufacturer’s instructions (Enzo BioArrayTM HighYieldTM RNA Transcript Labeling Kit, Affymetrix, Santa Clara, CA).

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were infected with with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h, and treated with commercial antimicrobial drug ceftazidime (10mg/ml) served as a drug control. (Replicate 3).

extract_protocol: All glasswares used for RNA isolation were treated with diethyl pyrocarbonate (DEPC) to ensure RNase-free environment. They were filled with DEPC-treated water (1.0ml DEPC in 1L of sterile DD-H2O), allowed to stand overnight at 37°C and then autoclaved to eliminate residual DEPC. Total RNA was isolated from THP-1 cells infected with B. pseudomallei (n = 5 flasks for each replicate) and treated with commercial antimicrobial drug ceftazidime using RNeasy® mini kit. The RNA sample was subsequently treated with RNase-free Dnase-I at room temperature for 20min and stored at -80°C until use. The isolated RNA was subjected to several levels of testing before using for microarray hybridization. The purity and quantity of the RNA was determined by A260/A280 ratios and then A260, respectively, using Biophotometer (Eppendorf, CA, USA). RNA samples that had good OD values (1.8–2.0) were further tested on gels for the integrity of both the 28S and 18S ribosomal RNA by denaturing agarose gels and visualized with ethidium bromide under UV light.

treatment_protocol: Group IV :- Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) and treated with commercial antimicrobial drug ceftazidime (10mg/ml) served as a drug control. (Replicate 3).

tag: Human monocytic macrophage (THP-1) cells were infected with Burkholderia pseudomallei and treated with commercial antimicrobial drug ceftazidime (10mg/ml) served as a drug control. (Replicate 3).


title: 3100031_Stroke

description: Stroke


title: T00219253: cardiomyocytes, time zero control

description: No treatment, time zero control


title: T00219254: cardiomyocytes, 48 hour conditioned


title: T00306153: cardiomyocytes, time zero control

description: No treatment, time zero control


title: THP-1+ treated with DbTx_Rep3.

description: Total RNA was isolated from Daboiatoxin treated (n = 5 flasks for each replicate) THP-1 cells using RNeasy® mini kit. The target chip hybridization followed successful Genechip Test3 arrays hybridization. All relevant procedures, such as amplification of cDNA, fragmentation of cRNA for hybridization, and concurrent assessment of expression levels of genes were carried out. Briefly, we synthesized double-stranded cDNA from the total RNA isolated from the THP-1 cells exposed to DbTx. We generated biotin-labeled cRNAs by in-vitro transcription from the ds-cDNA. The cRNAs were fragmented before hybridization, and a hybridization cocktail was prepared and hybridized to the oligonucleotide probes on the HG-U133A GeneChip arrays for 16h incubation at 45°C. Immediately after the hybridization, the hybridized probe arrays underwent an automated washing and staining protocol on an Affymetrix Fluidics Station. We scanned the GeneChips and processed the signals using Affymetrix genechip scanner and expression analysis algorithm (Affymetrix, Santa Clara, CA).

source_name: THP-1+ treated with DbTx_Rep3.

growth_protocol: Human macrophage (THP-1) cells were cultured in 72 cm2 flask in DMEM culture medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The culture medium containing THP-1 cells were exposed to Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom without bacterial infection. (Replicate 3).

extract_protocol: All glasswares used for RNA isolation were treated with diethyl pyrocarbonate (DEPC) to ensure RNase-free environment. They were filled with DEPC-treated water (1.0ml DEPC in 1L of sterile DD-H2O), allowed to stand overnight at 37°C and then autoclaved to eliminate residual DEPC. Total RNA was isolated from THP-1 cells Total RNA was isolated from Daboiatoxin treated (n = 5 flasks for each replicate) THP-1 cells using RNeasy® mini kit. The RNA sample was subsequently treated with RNase-free Dnase-I at room temperature for 20min and stored at -80°C until use. The isolated RNA was subjected to several levels of testing before using for microarray hybridization. The purity and quantity of the RNA was determined by A260/A280 ratios and then A260, respectively, using Biophotometer (Eppendorf, CA, USA). RNA samples that had good OD values (1.8–2.0) were further tested on gels for the integrity of both the 28S and 18S ribosomal RNA by denaturing agarose gels and visualized with ethidium bromide under UV light.

treatment_protocol: Group V:- Human monocytic macrophage (THP-1) cells were exposed to Daboiatoxin (0.5 mM, EC50~1 mM) isolated from Daboia russelli russelli venom without bacterial infection. (Replicate 3).

tag: Human monocytic macrophage (THP-1) cells were exposed to Daboiatoxin without bacterial infection. (Replicate 3)