title: NODULE CONTROL_M5_BEAN

city: Cuernavaca

first: Mario

last: Ramírez

state: Morelos

address: Avenida Universidad S/N

department: Functional Genomics of Eukaryotes

country: Mexico

institute: Centro de Ciencias Genomicas-UNAM

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/µl Salmon Sperm DNA, 0.05% SDS) for 30 minutes at 45 °C. 4 µg of labeled aRNA were fragmented by incubation with 5 µl of Fragmentation Solution (200mM Tris Acetate pH 8.1, 500 mM KOAc, 150 mM MgOAc) for 20 min at 95 °C. Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% Diformamide, 100 ng/µl Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as the following: wash with SSPET wash solution (6X SSPE, 0.05% Tween-20), wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20), wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20), wash with PBST wash solution (2X PBS, 0.1% Tween-20), 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a GenePix 4000B microarray scanner (Axon, Toronto, CA) and the accompanying acquisition software (CombiMatrix Microarray Imager Software). Multiple scanning at different PMT was provided for each hybridization.

data_processing: The raw intensities data were first processed using the CombiMatrix Microarray Imager software. This program allows the visual inspection of the entire microarray slide and is used to check the quality of each spot and, if needed, to perform possible corrections (i.e. dust or scratches on the surface). Intensity data were then exported into the Feature and Probe format of CombiMatrix, where the actual raw intensity per probe and per spot is stored. Data were loaded into R and analyzed using the Limma package (Smyth 2004). The median value of each spot on the array was considered and the probes were filtered to remove quality and factory controls. Within-array probe replicates were defined as technical replicates, by calculating the mean intensity across the different probes. The probe intensity values of each biological condition were then normalized using the quantile function of Limma.

organism: Phaseolus vulgaris

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with Cy5-ULS using the RNA Amplification and Labelling Kit from CombiMatrix (ampULSe Cat. no. GEA-022; Kreatech Biotechnology, Amsterdam, The Netherlands) according to manufacturer's instructions.

growth_protocol: Phaseolus vulgaris cv. Negro Jamapa 81 seeds were surface sterilized in sodium hypochlorite solution (10%) for 10 min and germinated on moist sterile filter paper at 30°C. Three-day-old seedlings were planted in pots with vermiculite and then inoculated with 1 ml bacterial suspension (approximately 10^7 cells) per plant. The inoculum was prepared from an over-night culture of Rhizobium tropici CIAT 899 grown in PY medium at 30°C. Pots were watered 3 days per week with a nitrogen-free nutrient plant solution reported by Summerfield et al. (1977). Nodulated plants were grown in a naturally lighted greenhouse with controlled temperature (26°C - 28°C) for 16 days, when nodules are mature.

extract_protocol: Total RNA was isolated from 18 dpi PQ treated and control bean nodules using Trizol reagent (Life Technologies, Carlsbad, California. USA) according to manufacturer's instructions.

treatment_protocol: For oxidative stress conditions, at 16 days post-inoculation (dpi) plants were watered with 1 mM 1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate, the herbicide Paraquat (PQ), for 48 hours. Mature nodules from stressed PQ  and control plants were harvested at 18 dpi, immediately frozen in liquid nitrogen and stored at –80°C until used.

tag: cultivar

value: Negro Jamapa 81

value: 16 dpi nodules


title: CB4857_infection_3

status: Public on Jun 30 2012

type: RNA

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description: Strain=CB4857;Environment=infection;Replicate=3

hyb_protocol: Agilent one-color hybridization protocol.  To minimize post-amplification biases, we randomized the position and order of hybridizations.

scan_protocol: Scanned at 10% laser power to avoid signal saturation

data_processing: Agilent Feature Extraction software (GE1-v5_95_Feb07) used to calculate fluorescence values which were then log2-transformed and rank-normalized across 120 hybridizations

molecule: polyA RNA

organism: Caenorhabditis elegans

label_protocol: 10 µg aRNA labeled with Cy3 using the Ambion MessageAmpII kit and 1.65µg labeled aRNA used to hybridize with each array

growth_protocol: We used standard methods to culture and handle C. elegans (Brenner, 1974), except we used the sporulation-defective Bacillus subtilis strain RL1275 (spoIIAC::erm in a PY79 background, kind gift from Richard Losick) as worm food, because B. subtilis is substantially less pathogenic to C. elegans than the standard C. elegans food E. coli OP50 at 25°C (Garsin et al., 2003).

extract_protocol: We collected embryos and purified RNA as described (Baugh et al., 2003), except we increased the number of embryos per sample to 50.  In brief, we picked young adults into water, chopped them in half, treated them with alkaline bleach to destroy any RNA and protein not protected by the eggshell, stopped the bleach reaction with bovine serum albumin, collected and washed early embryos in DEPC-treated water using a glass mouth pipette, flash-froze the embryos in liquid nitrogen in low-adhesion 600 μl microcentrifuge tubes, and transferred the tubes to a -80° freezer for storage.  For the microarray experiment, the total time from picking of the first worm to bleaching was not allowed to exceed 15 min.  For all subsequent experiments, the time was not allowed to exceed 8 min.  We added Trizol (phenol/guanidine isothiocyanate, Invitrogen), with added linear polyacrylamide and yeast tRNA as carriers, to the frozen embryos for RNA extraction and isopropanol precipitation.  We used the RNA pellet directly for RT (reverse transcription), starting from a T7-oligo-dT RT primer.  To obtain sufficient RNA for microarray analysis, RNA was amplified by two rounds of in vitro transcription (IVT) using the MessageAmpII kit (Ambion) with the following modifications designed to increase the average lengths of the aRNA populations (Baugh et al. 2001): First-round cDNA construction from total RNA was carried out at 1/5 of the recommended quantities and total volume, while IVT was carried out at 1/2 of the recommended volume.  100ng aRNA from the first round was used as input for the second round of amplification following the manufacturers protocol for amino-allyl modified nucleotides.

treatment_protocol: Before each of the experiments, we cultured the worms for at least three generations at 20°C without allowing the worms to deplete their food.  Other than the 25°C treatments, done in a 25±0.5° incubator, all incubations and procedures involving live worms were done in a temperature controlled room at 20±0.3°C.  To minimize temperature variation during handling, we used large (10 cm diameter) plates, wore insulated gloves while handling plates, and used an external light source for the dissecting microscope.  For the microarray experiment, we used a platinum wire loop to transfer several hundred embryos to fresh plates for each generation.  For the multigenerational follow-up experiments (not included in this accession because they were analyzed by RT-QPCR only), we used a platinum wire pick to transfer 60 L4 larvae to fresh plates for each generation.  The purpose of transferring L4s instead of embryos in the multigenerational experiment was to eliminate males from the cultures, thereby eliminating variation in the frequency of sex-specific imprinting (most C. elegans individuals are hermaphrodites, with a low rate of spontaneous males that increases with temperature).  For the same set of experiments, we used HOBO miniature temperature loggers (Onset) to continuously monitor culture temperatures.  For post-25° steps of all experiments, we interleaved the constant 20° (control) plates with post-25° treatment plates in common stacks whenever possible, so that treatment and control plates experience the same microenvironment on average.  In practice, the treatment plates were slightly staggered in time relative to the corresponding control plates of the same generation, because of time constraints and because development time from zygote to adult is ~17 hours faster at 25° than at 20°.  For the each condition and generation in the microarray experiment, we collected 3 replicates (50 embryos each replicate) of the standard C. elegans laboratory strain N2 and three replicates (50 embryos each replicate) of the strain HC445 (sid-1(qt9) in an N2 background).

tag: strain

tag: developmental stage

value: 4-cell stage

tag: environment

value: infection

tag: replicate


title: RC301_infection_3

description: Strain=RC301;Environment=infection;Replicate=3


title: AB2_Liquid_3

description: Strain=AB2;Environment=Liquid;Replicate=3

value: Liquid


title: CB4856_infection_3

description: Strain=CB4856;Environment=infection;Replicate=3


title: NODULE STRESSED_M6_BEAN

status: Public on Jul 01 2012

molecule: total RNA

source_name: PQ treated_nodule

tag: tissue

tag: treated with

value: 1 mM herbicide Paraquat (PQ) for 48hr


title: AB2_infection_3

description: Strain=AB2;Environment=infection;Replicate=3


title: CB4856_Liquid_3

description: Strain=CB4856;Environment=Liquid;Replicate=3


title: sid-1_Liquid_3

description: Strain=sid-1;Environment=Liquid;Replicate=3


title: N2_infection_3

description: Strain=N2;Environment=infection;Replicate=3


title: N2_High-pH-Salt_3

description: Strain=N2;Environment=High-pH-Salt;Replicate=3

value: High-pH-Salt


title: N2_25C_3


title: CB4857_High-pH-Salt_3

description: Strain=CB4857;Environment=High-pH-Salt;Replicate=3


title: AB2_High-pH-Salt_3

description: Strain=AB2;Environment=High-pH-Salt;Replicate=3


title: sid-1_25C_3

description: Strain=sid-1;Environment=25C;Replicate=3


title: RC301_Liquid_3

description: Strain=RC301;Environment=Liquid;Replicate=3


title: CB4856_High-pH-Salt_3

description: Strain=CB4856;Environment=High-pH-Salt;Replicate=3


title: sid-1_High-pH-Salt_3

description: Strain=sid-1;Environment=High-pH-Salt;Replicate=3


title: N2_Liquid_3

description: Strain=N2;Environment=Liquid;Replicate=3


title: CB4857_25C_3

description: Strain=CB4857;Environment=25C;Replicate=3


title: CB4857_Liquid_3

description: Strain=CB4857;Environment=Liquid;Replicate=3


title: RC301_High-pH-Salt_3

description: Strain=RC301;Environment=High-pH-Salt;Replicate=3


title: Female-Sham-pool1

city: Little rock

first: Kartik

last: Shankar

state: AR

address: 1120 Marshall Street, Slot 512-20B

department: Pharmacology and Toxicology

country: USA

institute: University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center

description:
ratFsham_P1
osteogenic gene expression

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N = 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing:
Cel files were generated using GCOS and utilized for analysis using GeneSpring Gx v 11.0
RMA normalization was utilized to generated values using GeneSpring v 11.0

label: biotin

organism: Rattus norvegicus

source_name: postnatal day 81-rat bone

label_protocol: First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

growth_protocol: Bone quality was compared among casein control diet sham operated, casein diet ovariectomized, long term BB diet ovariectomized and short term BB diet ovariectomized female rats

extract_protocol: Total bone RNA was isolated from the experimental rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion

treatment_protocol: Femur were collected from rats at sacrifice and flash frozen in liquid nitrogen

tag: gender

value: female

tag: diet

value: control (casein)

tag: operation

value: control

tag: age

value: postnatal day 81

value: femur bone


title: RC301_25C_3

description: Strain=RC301;Environment=25C;Replicate=3


title: CB4856_25C_3

description: Strain=CB4856;Environment=25C;Replicate=3


title: aCGH of NKC rep2

type: genomic

city: Montreal

first: Brian

last: Wilhelm

address: 2950 Chemin Polytechnique

country: Canada

institute: University of Montreal

description: Dye Swap of Sample 1

hyb_protocol: Two-color hybridizations were carried out using 6 μg of Cy5-labeled and 6 μg of Cy3-labeled gDNA using the NimbleGen hybridization kit as recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Axon 4000B scanner at 5um resolution as per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.5 CGH data extraction.

molecule: genomic DNA

organism: Mus musculus

label_protocol: Genomic DNA from WT and NKCKD mice were labeled with Cy5- and Cy3-labeled 9mers (Trilink technologies) using 3'-5' exo- Klenow fragment (NEB) and a dye swap was performed.

extract_protocol: Genomic DNA was extracted from cells WT and NKCKD strains using DNAzol according to the manufacturers instructions

tag: genotype/variation

value: lacking the Ly49 gene cluster

source_name: C57BL/6 Genomic DNA

value: wild type


title: aCGH of NKC rep1

description: Dye swap of Sample 2

source_name: B6.NKCKD genomic DNA


title: sid-1_Control_3

description: Strain=sid-1;Environment=Control;Replicate=3

value: Control


title: AB2_25C_3


title: CB4857_Control_3

description: Strain=CB4857;Environment=Control;Replicate=3


title: N2_infection_2

description: Strain=N2;Environment=infection;Replicate=2


title: sid-1_infection_2

description: Strain=sid-1;Environment=infection;Replicate=2


title: CB4856_infection_2

description: Strain=CB4856;Environment=infection;Replicate=2


title: RC301_Control_3

description: Strain=RC301;Environment=Control;Replicate=3


title: CB4856_Control_3

description: Strain=CB4856;Environment=Control;Replicate=3


title: AB2_Control_3

description: Strain=AB2;Environment=Control;Replicate=3


title: CB4857_Liquid_2

description: Strain=CB4857;Environment=Liquid;Replicate=2


title: sid-1_Liquid_2

description: Strain=sid-1;Environment=Liquid;Replicate=2


title: N2_Control_3

description: Strain=N2;Environment=Control;Replicate=3


title: N2_Liquid_2

description: Strain=N2;Environment=Liquid;Replicate=2


title: sid-1_High-pH-Salt_2

description: Strain=sid-1;Environment=High-pH-Salt;Replicate=2


title: CB4857_infection_2

description: Strain=CB4857;Environment=infection;Replicate=2


title: AB2_Liquid_2

description: Strain=AB2;Environment=Liquid;Replicate=2


title: N2_High-pH-Salt_2

description: Strain=N2;Environment=High-pH-Salt;Replicate=2


title: AB2_infection_2

description: Strain=AB2;Environment=infection;Replicate=2


title: CB4856_Liquid_2

description: Strain=CB4856;Environment=Liquid;Replicate=2


title: N2_25C_2


title: RC301_High-pH-Salt_2

description: Strain=RC301;Environment=High-pH-Salt;Replicate=2


title: CB4857_25C_2

description: Strain=CB4857;Environment=25C;Replicate=2


title: AB2_High-pH-Salt_2

description: Strain=AB2;Environment=High-pH-Salt;Replicate=2


title: sid-1_25C_2

description: Strain=sid-1;Environment=25C;Replicate=2


title: CB4857_High-pH-Salt_2

description: Strain=CB4857;Environment=High-pH-Salt;Replicate=2


title: RC301_infection_2

description: Strain=RC301;Environment=infection;Replicate=2


title: RC301_25C_2

description: Strain=RC301;Environment=25C;Replicate=2


title: RC301_Liquid_2

description: Strain=RC301;Environment=Liquid;Replicate=2


title: CB4856_25C_2

description: Strain=CB4856;Environment=25C;Replicate=2


title: CB4856_High-pH-Salt_2

description: Strain=CB4856;Environment=High-pH-Salt;Replicate=2


title: N2_Control_2

description: Strain=N2;Environment=Control;Replicate=2


title: sid-1_Control_2

description: Strain=sid-1;Environment=Control;Replicate=2


title: CB4857_Control_2

description: Strain=CB4857;Environment=Control;Replicate=2


title: RC301_Control_2

description: Strain=RC301;Environment=Control;Replicate=2


title: CB4856_infection_1

description: Strain=CB4856;Environment=infection;Replicate=1


title: sid-1_Liquid_1

description: Strain=sid-1;Environment=Liquid;Replicate=1


title: CB4856_Control_2

description: Strain=CB4856;Environment=Control;Replicate=2


title: AB2_infection_1

description: Strain=AB2;Environment=infection;Replicate=1


title: RC301_infection_1

description: Strain=RC301;Environment=infection;Replicate=1


title: sid-1_High-pH-Salt_1

description: Strain=sid-1;Environment=High-pH-Salt;Replicate=1


title: N2_High-pH-Salt_1

description: Strain=N2;Environment=High-pH-Salt;Replicate=1


title: AB2_Liquid_1

description: Strain=AB2;Environment=Liquid;Replicate=1


title: CB4856_Liquid_1

description: Strain=CB4856;Environment=Liquid;Replicate=1


title: CB4857_infection_1

description: Strain=CB4857;Environment=infection;Replicate=1


title: AB2_Control_2

description: Strain=AB2;Environment=Control;Replicate=2


title: AB2_High-pH-Salt_1

description: Strain=AB2;Environment=High-pH-Salt;Replicate=1


title: N2_Liquid_1

description: Strain=N2;Environment=Liquid;Replicate=1


title: CB4856_High-pH-Salt_1

description: Strain=CB4856;Environment=High-pH-Salt;Replicate=1


title: CB4857_Liquid_1

description: Strain=CB4857;Environment=Liquid;Replicate=1


title: RC301_High-pH-Salt_1

description: Strain=RC301;Environment=High-pH-Salt;Replicate=1


title: CB4857_High-pH-Salt_1

description: Strain=CB4857;Environment=High-pH-Salt;Replicate=1


title: CB4857_25C_1

description: Strain=CB4857;Environment=25C;Replicate=1


title: RC301_25C_1

description: Strain=RC301;Environment=25C;Replicate=1


title: AB2_25C_2


title: sid-1_25C_1

description: Strain=sid-1;Environment=25C;Replicate=1


title: N2_25C_1


title: N2_infection_1

description: Strain=N2;Environment=infection;Replicate=1


title: sid-1_Control_1

description: Strain=sid-1;Environment=Control;Replicate=1


title: Case four: metastatic breast cancer tissue

status: Public on Jun 23 2012

city: Nottingham

first: Sarkawt

last: Khoshnaw

address: Queens Medical Centre

country: United Kingdom

institute: University of Nottingham

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3018-4]

hyb_protocol: Cyanine-3-labelled miRNA samples were hybridised to human miRNA microarrays (Release 16.0, 8x60K) (Agilent Technologies, Santa Clara, USA) at 55°C for 20 hrs. Microarray slides were washed with increasing stringency (Gene Expression Wash Buffers, Agilent Technologies, Santa Clara), and subsequently dried with acetonitrile (Sigma-Aldrich, St. Louis, USA).

scan_protocol: Fluorescent signal intensities were detected on an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, USA) using the Scan Control A.8.4.1 Software (Agilent Technologies, Santa Clara, USA).

data_processing: Fluorescent signal intensities were extracted from the images with the Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). The raw signal values were 'normalized to the 90th percentile' when importing the FE files into GeneSpring (the analysis software). Only the top 20% of probes on the array typically had any detectable signal so shifting to the 90th percentile meant the median line was around the centre of this expressed set.

organism: Homo sapiens

source_name: Mastectomy

label_protocol: MiRNAs extracted from laser microdissected tissue components were profiled using Agilent microRNA microarray profiling system (Agilent Technologies, Santa Clara, USA). Total RNA samples were spiked using the MicroRNA Spike-In Kit (Agilent Technologies, Santa Clara, USA) to evaluate efficiencies of labelling and hybridisation. Total RNA was treated with Calf Intestinal Alkaline Phosphatase (CIP), and then 100 ng of total RNA was used per sample to initiate a labelling reaction. Ligation master mix for T4 RNA ligase, which includes Cyanine 3-Cytidine biphosphate (Cyanine 3-pCp) (Complete miRNA Labelling and Hyb Kit, Agilent Technologies, Santa Clara, USA) was used to label the dephosphorylated RNA.

extract_protocol: Twenty μm thick FFPE sections were cut and mounted on PALM Membrane Slides. Under direct microscopic visualization, tissues of interest were micro-dissected using PALM non-contact Laser catapulsion instrument (P.A.L.M. Microlaser Technologies, Carl Zeiss Ltd). Total RNA, including miRNAs, was extracted with the TRIzol reagent (Invitrogen, supplied by Fisher Scientific UK Ltd) according to the manufacturer’s instructions. Total RNA was quantified with Quant-iT RiboGreen RNA Quantitation Kit (Fisher Scientific UK Ltd), which is an accurate method of measuring total RNA with a detection limit of 0.001-1ng/µl. RNA purity and RNA integrity number (RIN) were determined on an Agilent 2100 Bioanalyzer and RNA 6000 NanoLabChip Kits (both Agilent Technologies, Santa Clara, USA).

treatment_protocol: Mastectomised breast and the axillary lymph nodes kept in formalin

value: 28 years

tag: tissue origin

value: breast

value: metastatic breast cancer tissue


title: sid-1_infection_1

description: Strain=sid-1;Environment=infection;Replicate=1


title: CB4857_Control_1

description: Strain=CB4857;Environment=Control;Replicate=1


title: N2_Control_1

description: Strain=N2;Environment=Control;Replicate=1


title: CB4856_25C_1

description: Strain=CB4856;Environment=25C;Replicate=1


title: Case four: invasive breast cancer tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3018-3]

value: invasive breast cancer tissue


title: Case four: ductal carcinoma in situ

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3018-2]

value: ductal carcinoma in situ


title: AB2_25C_1

value: 4-cell stage


title: Case four: normal breast tissue

description:
miRNAs expression profiling using Human miRNA Microarrays Release 16.0 (Agilent Technologies)
[3018-1]

value: normal breast tissue


title: RC301_Liquid_1

description: Strain=RC301;Environment=Liquid;Replicate=1

value: Liquid


title: CB4856_Control_1

description: Strain=CB4856;Environment=Control;Replicate=1


title: RC301_Control_1

description: Strain=RC301;Environment=Control;Replicate=1


title: liver-HCV-Non Tumor-rep7

status: Public on Jun 15 2012

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

description: 270_ 28N

hyb_protocol: 750ng of each aRNA in water (10ul) was suspended in Illumina “HYB” buffer (20ul) and heated to 65C for five minutes, then allowed to cool to room temperature.  The samples were applied to HumanHT12v3 Expression Beadchips and hybridized at 58C for 16-20 hours at high humidity.  Arrays were washed according to Illumina standard protocol.  Immobilized, biotinylated aRNAs were then detected by staining with cy3 Steptavidin (1ug cy3-SA per 1 ml of Illumina “Block E1”) for 10 minutes at room temperature.  Arrays were washed and dried according to Illumina standard protocol.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader.  Laser power and PMT voltage were kept constant for Cy3 scans.  Images were quantitated by Illumina Beadscan, v3.  Quantitated data was imported into Beadstudio software.  On-slide spot replicates were averaged by Beadstudio and individual spot data was reported

data_processing: The data were normalized using quantile normalization implemented in Illumina Genome studio version 1.7.0.

source_name: liver-HCV-Non Tumor

label_protocol: RNA samples were labeled with biotin according to Manufacturer's instructions.

growth_protocol: The study was approved by the Institutional Review Board at Washington University in St. Louis and all patients were enrolled after informed consent.

extract_protocol: Liver biopsy that were snap frozen obtained from HCV or control normal liver, were used to isolate RNA using Trizol reagent (Invitrogen, Carlsbad, CA) as per manufacturer’s protocol.

value: liver

tag: tissue type

value: Non Tumor


title: liver-Tumor-rep3

description: 244_ 36T

source_name: liver-Tumor

value: Tumor


title: liver-HCV-Non Tumor-rep6

description: 269_ 30N


title: liver-HCV-Non Tumor-rep5

description: 265_ 27N


title: liver-Tumor-rep6

description: 262_ 38


title: liver-Tumor-rep4

description: 246_ 41T


title: liver-HCV-Non Tumor-rep8

description: 271_ 26N


title: liver-HCV-Non Tumor-rep4

description: 245_ 41N


title: AB2_Control_1

description: Strain=AB2;Environment=Control;Replicate=1


title: liver-Normal-PRP-rep1

description: 230_ 61PRP

source_name: liver-Normal-PRP

value: Normal

tag: status

value: Post reperfusion


title: liver-HCV-Non Tumor-rep2

description: 236_ 51E


title: liver-Tumor-rep5

description: 260_ 40


title: liver-Tumor-rep2

description: 213_ 46T


title: liver-HCV-rep2

description: 221_ 34

source_name: liver-HCV

value: HCV


title: liver-Normal-rep2

description: 224_ 61D

source_name: liver-Normal


title: liver-HCV-rep3

description: 235_ 52E


title: liver-HCV-rep1

description: 217_ 50E


title: liver-Normal-rep3

description: 225_ 51D


title: liver-HCV-rep4

description: 237_ 49E


title: liver-HCV-Non Tumor-rep1

description: 212_ 46E


title: Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 6

status: Public on May 02 2012

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 6 of 6.

hyb_protocol: Hybridization and fluidics were performed according to standard Affymetrix protocols (http://www.affymetrix.com).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus according to standard Affymetrix protocols.

data_processing: The data were analyzed with GCOS 1.4 and EC 1.1 using Affymetrix default settings except the trimmed mean target intensity of each array was arbitrarily set to 1250.

label_protocol: Affymetrix GeneChip targets were made by amplification of 50 ng RNA using the WT-Ovation RNA Amplification System (Nugen Inc., San Carlos, CA).

growth_protocol: Bone marrow-derived mast cells (BMMCs) were developed from bone marrow obtained from the femurs of C57BL/6 mice (The Jackson Laboratory, Bar Harbor, ME) as described (Kuehn, H. S., M. A. Beaven, H. T. Ma, M. S. Kim, D. D. Metcalfe, and A. M. Gilfillan. 2008. Synergistic activation of phospholipases Cγ and Cβ: a novel mechanism for PI3K-independent enhancement of FcεRI-induced mast cell mediator release. Cell Signal 20:625-636 (PMID 18207701)).

extract_protocol: RNAs were extracted using an RNeasy 96 kit (Qiagen, Valencia, CA) with each sample treated with 27 units DNase I during the extraction process.

treatment_protocol: Essentially, the cells were cultured for 4-6 weeks in media containing mouse recombinant IL-3 (30 ng/ml) (Peprotech, Rocky Hill, NJ) and mouse recombinant SCF (unless otherwise indicated: 100 ng/ml) (Peprotech). The cells were maintained at 37 ˚C in a humidified incubator gassed with 95% air and 5% CO2. The purity of the cultures, as assessed by toluidine blue staining and FceRIa and KIT expression, was >99%.

tag: cell type

value: bone marrow-derived mast cells

tag: treatment

value: interleukin 3 and stem cell factor


title: liver-Normal-rep1

description: 223_ 44D


title: Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 4

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 4 of 6.


title: Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 2

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 2 of 6.


title: Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 5

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 5 of 6.


title: Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 3

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 3 of 6.


title: Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 1

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 1 of 6.


title: Mouse bone marrow-derived mast cells treated with IL3, rep 4

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 4 of 6.

treatment_protocol: Essentially, the cells were cultured for 4-6 weeks in media containing mouse recombinant IL-3 (30 ng/ml) (Peprotech, Rocky Hill, NJ). The cells were maintained at 37 ˚C in a humidified incubator gassed with 95% air and 5% CO2. The purity of the cultures, as assessed by toluidine blue staining and FceRIa and KIT expression, was >99%.

value: interleukin 3


title: Mouse bone marrow-derived mast cells treated with IL3, rep 6

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 6 of 6.


title: Mouse bone marrow-derived mast cells treated with IL3, rep 3

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 3 of 6.


title: Mouse bone marrow-derived mast cells treated with IL3, rep 2

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 2 of 6.


title: liver-HCV-Non Tumor-rep3

description: 243_ 36N


title: liver-Tumor-rep1

description: 211_ 60T


title: Mouse bone marrow-derived mast cells treated with IL3, rep 5

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 5 of 6.


title: Middle temporal area (MT)_V5_L2-6: control CR5C1.08.01_2

status: Public on Mar 21 2012

city: Seattle

first: Susan

last: Sunkin

address: 551 N. 34th Street

institute: Allen Institute for Brain Science

description:
Gene expression data from rhesus MT.
@52031700789764081009405808017338

hyb_protocol: Following fragmentation, 10 ug of cDNA was hybridized for 18 hr at 45C on the GeneChip Rhesus Macaque Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were normalized using Matlab2007b. Each batch was normalized within itself by RMA. Batch effects were subsequently removed by normalizing each probe based on common whole brain control samples across batches. Data is reported as Log10 normalized intensity.

organism: Macaca mulatta

source_name: middle temporal area (MT)

label_protocol: Biotinylated cDNA was prepared using 5ng total RNA input and 2 cycles of the GeneChip HT One-Cylce cDNA Synthesis Kit from Affymetrix.

extract_protocol: RNA was isolated from each brain region following the manufacturer's directions for the RNeasy Micro kit. Whole rhesus brain RNA pool obtained from Biochain.

tag: sample type

value: control

value: middle temporal area (MT)


title: Hippocampus CA3: control CR5C1.08.01_5

description:
Gene expression data from rhesus hippocampus.
@52031700647950061408403392032258

source_name: hippocampus

value: hippocampus


title: Hippocampus CA3: control CR5C1.08.01_9

description:
Gene expression data from rhesus hippocampus.
@52031700789764081009405808017332


title: Middle temporal area (MT)_V5_L2-6: control CR5C1.08.01_3

description:
Gene expression data from rhesus MT.
@52031700789764081009405808017321


title: Hippocampus CA3: control CR5C1.08.01_4

description:
Gene expression data from rhesus hippocampus.
@52031700647949061408403392032190


title: Hippocampus CA3: control CR5C1.08.01_6

description:
Gene expression data from rhesus hippocampus.
@52031700647950061408403392032282


title: Middle temporal area (MT)_V5_L2-6: control CR5C1.08.01_1

description:
Gene expression data from rhesus MT.
@52031700789764081009405808017337


title: Hippocampus CA3: control CR5C1.08.01_8

description:
Gene expression data from rhesus hippocampus.
@52031700789764081009405808017313


title: Hippocampus CA3: control CR5C1.08.01_3

description:
Gene expression data from rhesus hippocampus.
@52031700647949061408403392032184


title: Hippocampus CA3: control CR5C1.08.01_7

description:
Gene expression data from rhesus hippocampus.
@52031700789765081009405808017369


title: Hippocampus CA3: control CR5C1.08.01_2

description:
Gene expression data from rhesus hippocampus.
@52031700647949061408403392032222


title: E14 - nudelko/+ 1

status: Public on Jan 26 2012

city: San Diego

first: Tiziano

last: Pramparo

state: CA

address: 3611 Valley Centre Drive

department: R&D

institute: Travere

description: embryo at E14, biological rep1

hyb_protocol: Fragmented cRNA was  hybridized in the presence of BSA to an Affymetrix GeneChip™ following manufacture instructions. Volume for fragmented cRNA samples was 40 µl.

scan_protocol: GeneChip® Scanner 3000 with 1 number of scans per array with 2x image, pixel value 3 um and wavelenght 570 nm

data_processing: Microarray data was pre-processed via the Robust Multichip Average (RMA) method, as implemented in the Bioconductor suite of programs (http://www.bioconductor.org/) implemented in the R statistical programming language. Analysis of differential expression was performed using bi-weight analysis.

source_name: mutant Ndel ko/+

label_protocol: manufacture suggested biotin-labeled IVT reaction. 10 µg of total RNA was used in a maximum volume of 10 µl

extract_protocol: Trizol reagent (Invitrogen)

value: brain

tag: genotype

value: mutant Ndel ko/+


title: E14 - nudelcko/ko 1

description: embryo at E14, biological rep1

source_name: mutant Ndel ko/cko

value: mutant Ndel ko/cko


title: Hippocampus CA3: control CR5C1.08.01_1

description:
Gene expression data from rhesus hippocampus.
@52031700647949061408403392032198


title: E14 - nudelko/+ 3

description: embryo at E14, biological rep3


title: Hodgkin lymphoma cell line L-540

status: Public on Dec 11 2010

city: Vancouver

first: Christian

last: Steidl

state: BC

address: 675 West 10th Avenue

department: Pathology

institute: BC Cancer Agency

description: Gene expression data from Hodgkin lymphoma cell line

hyb_protocol: Following fragmentation, cRNA were hybridized O/N at 45C on Affymetrix GeneChip HG 2.0 Plus Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed using DCHIP, http://biosun1.harvard.edu/complab/dchip/

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (2-cycle amplification)

extract_protocol: Qiagen Allprep extraction columns

tag: cell line


title: Cervical tumor biopsy, P-054

status: Public on Jul 19 2011

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

description:
P-054
Basic cohort

hyb_protocol: The samples were hybridized to the arrays at 58oC overnight, using the standard Illumina hybridization protocol.

scan_protocol: Scanning was performed with an Illumina BeadArray reader, using the standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization in J-Express.

source_name: Cervical tumor, 2B

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

growth_protocol: 1-4 tumor samples were collected from each patient at the time of diagnosis.

extract_protocol: RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. RNA from different biopsies of the same tumor was pooled. Quality control was performed with the Agilent Bioanalyzer.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80oC until used for analysis. Biopsies with more than 50% tumor cells in HE stained sections from the central part of the specimen were used further.

tag: cohort (gse36562 study)

value: Validation cohort

tag: hypoxia score

value: High

value: cervical tumor

tag: figo stage

tag: histology

value: Squamous cell carcinoma

tag: cohort

value: basic cohort

tag: cohort (gse38964 study)

value: Integrative cohort

tag: 3p status

value: Loss


title: Hodgkin lymphoma cell line KM-H2


title: Microdissected germinal center, replicate 3

description: Gene expression data from microdissected germinal centers (reactive lymph node tissue)

source_name: Biopsy 3

tag: tissue

value: Reactive lymph node


title: Hodgkin lymphoma cell line L-1236


title: Microdissected germinal center, replicate 5

source_name: Biopsy 5


title: E14 - nudelko/+ 2

description: embryo at E14, biological rep2

tag: age


title: Hodgkin lymphoma cell line HDLM-2


title: Microdissected germinal center, replicate 2

source_name: Biopsy 2


title: Hodgkin lymphoma cell line L-428


title: Cervical tumor biopsy, P-025

description:
Basic cohort
P-025

value: Low

tag: lymph node status (gse38433 study)

value: No loss


title: Microdissected germinal center, replicate 4

source_name: Biopsy 4


title: Microdissected germinal center, replicate 1

source_name: Biopsy 1


title: Mouse bone marrow-derived mast cells treated with IL3, rep 1

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 1 of 6.

tag: strain

value: bone marrow-derived mast cells

value: interleukin 3


title: SP res2-HA ChIP-chip sample

status: Public on Nov 26 2010

city: Singapore

first: Majid

last: Eshaghi

state: Singapore

address: Biopolis

department: Bilogical Investigation

country: Singapore

institute: Genome Institute of Singapore

description: Schizosaccharomyces pombe res1-HA cells Chip DNA vs Schizosaccharomyces pombe res2_HA WCE DNA.

hyb_protocol: Samples were mixed with DIG Easy Hyb buffer (Roche) and Herring Sperm DNA (Invitrogen) before applying to MAUI mixer-slide assembly.  The slides were hybridized overnight for 16 hours at 42C under MAUI system (BioMicro). Hybridized slides were washed consecutively in 2xSSC/0.1% SDS for 1 min, 1xSSC for 4 min, 0.2xSSC for 4 min, and 0.05xSSC for 1 min, and then spin-dried before scanning.

scan_protocol: Microarray slides were scanned using the Axon genepix 4000B scanner at the resolution of 5 mirocon/ pixel at both red and green channels.  The data were acquired using the GAL file and normalized with the NimbleGen Scan software (NimbleGen Inc.).

data_processing: Analyses of ChIP-chip microarray data included identification of significantly enriched regions, prediction of occupancy patterns, and assignment to genomic features were done as describled in materials and metholds.

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe res2-HA cells were cross-linked with formaldehyde and subjected to ChIP-chip experiment .

label_protocol: Chip genomic DNA was random-priming labeled with amino-allyl-dUTP (aa-dUTP) using the BioPrime DNA Labeling kit (Invitrogen Corporation, Carlsbad, CA) according the manufacture's instruction.  Labeled DNA was extracted with phenol/chloroform/isoamyl alcohol and precipitated with ethanol or siopropanol. The labeled DNA was then coupled with cyanine dyes Cy5 (Amersham, Buckinghamshire, UK)

growth_protocol: Yeast cells were cultured at 30 degree centigrade.

extract_protocol: Chip genomic DNA was extracted as describled in materials and metholds.

tag: antibody

value: anti-HA

source_name: Reference DNA was obtained from whole cell extract (WCE).

label_protocol: WCE DNA was random-priming labeled with amino-allyl-dUTP (aa-dUTP) using the BioPrime DNA Labeling kit (Invitrogen Corporation, Carlsbad, CA) according the manufacture's instruction.  Labeled DNA was extracted with phenol/chloroform/isoamyl alcohol and precipitated with ethanol or siopropanol. The labeled DNA was then coupled with cyanine dyes Cy3 (Amersham, Buckinghamshire, UK)

extract_protocol: WCE DNA of the cells were extracted as describled in materials and metholds.

value: whole cell extract (WCE)


title: HF-23896-(1), Affymetrix HG-U133 plus 2.0 array

status: Public on May 27 2010

city: South San Francisco

first: Peter

last: Haverty

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: 10 ug of labeled cRNA was fragmented and hybridized to the arrays following manufacturer's protocol (Affymterix).

scan_protocol: Affymetrix user manual (GeneChip scanner 3000)

data_processing: Raw data  were processed with the MAS5.0 method to obtain normalized probe set summaries. Values for each sample were scaled to mean, trimmed 2%, of 500.

label_protocol: 3 ug of total RNA was converted to double-stranded cDNA using Invitrogen's SuperScript Choice kit. cDNA was purified using Affymterix Sample Cleanup Module kit and used to generate biotin labeled cRNA with Enzo in vitro transcription kit. The labeled cRNA was purified using Affymetrix Sample Cleanup Module kit.

extract_protocol: Qiagen AllPrep extraction kit was used according to the manufacturer's instructions

tag: organ

value: Lung Cancer


title: muscle_normal_16446

status: Public on Jan 19 2010

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

institute: University of Stirling

description: Total RNA was prepared for hybridization using the protocol published by Affymetix

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: All array data were normalized using RMA and the Microarray Suite version 5.0 (MAS 5.0) algorithm to a global scaling intensity of 100. Data were filtered using present/absent calls. Probes called absent by MAS 5.0 across all arrays were discarded.

source_name: Skeletal muscle, vastus lateralis

label_protocol: Standard Affymetrix protocol

extract_protocol: Muscle was homogenized in Trizol with Polytron motor driven homogenizer and RNA extraction carried out using Trizol protocol (Invitrogen). Hybridization, washing, staining and scanning of the arrays were performed according to manufacturer's instructions (Affymetrix).

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: SP cdc10-HA treated with phenanthroline 15 min sample

description: Schizosaccharomyces pombe Cdc10-HA cells Chip DNA treated with phenanthroline for 15 min vs Schizosaccharomyces pombe cdc10_HA WCE DNA treated with phenanthroline for 15 min.

source_name: Schizosaccharomyces pombe cdc10-HA cells treated with phenanthroline for 15 min and were cross-linked with formaldehyde and subjected to ChIP-chip experiment .

tag: strain

tag: antibody

tag: sample type


title: muscle_normal_16191

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: HF-23897-(1), Affymetrix HG-U133 plus 2.0 array

tag: organ

value: Adjacent Normal


title: muscle_glucoseIntolerant_16437

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_diabetic_16425

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_16164

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: hip

tag: waist

tag: bpsyst

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_16410

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_16431

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: hip

tag: waist

tag: bpsyst

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_glucoseIntolerant_16197

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_16401

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: hip

tag: waist

tag: bpsyst

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_16188

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_glucoseIntolerant_16443

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: hip

tag: waist

tag: bpsyst

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: SP res1-HA cdc10-v50 ChIP-chip sample

description: Schizosaccharomyces pombe res1-HA cdc10-v50 cells Chip DNA vs Schizosaccharomyces pombe res1_HA cdc10-v50 WCE DNA.

source_name: Schizosaccharomyces pombe res1-HA cdc10-v50 cells grown at 36°C for 4 hr were cross-linked with formaldehyde and subjected to ChIP-chip experiment .

growth_protocol: Yeast cells were cultured at 36 degree C for 4 hr.

tag: strain

value: res1-HA cdc10-v50

tag: antibody

tag: sample type


title: SP rep2-HA ChIP-chip sample

description: Schizosaccharomyces pombe rep2-HA cells Chip DNA vs Schizosaccharomyces pombe rep2_HA WCE DNA.

source_name: Schizosaccharomyces pombe res1-HA cells were cross-linked with formaldehyde and subjected to ChIP-chip experiment .


title: muscle_diabetic_16413

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_16149

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_diabetic_16173

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: SP cdc10-HA treated with phenanthroline 60 min sample

description: Schizosaccharomyces pombe Cdc10-HA cells Chip DNA treated with phenanthroline for 60 min vs Schizosaccharomyces pombe cdc10_HA WCE DNA treated with phenanthroline for 60 min.

source_name: Schizosaccharomyces pombe cdc10-HA cells treated with phenanthroline for 60 min and were cross-linked with formaldehyde and subjected to ChIP-chip experiment .

tag: strain

tag: antibody

tag: sample type


title: SP cdc10-HA ChIP-chip sample

description: Schizosaccharomyces pombe Cdc10-HA cells Chip DNA vs Schizosaccharomyces pombe cdc10_HA WCE DNA.

source_name: Schizosaccharomyces pombe cdc10-HA cells were cross-linked with formaldehyde and subjected to ChIP-chip experiment .


title: SP res1-HA ChIP-chip sample

description: Schizosaccharomyces pombe res1-HA cells Chip DNA vs Schizosaccharomyces pombe res1_HA WCE DNA.


title: FnrL_rep 3

status: Public on Jul 01 2010

city: Madison

first: Yann

middle: S

last: Dufour

state: WI

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin - Madison

description: ChIP-chip FnrL in wild-type cells

hyb_protocol: 4 ug of labelled DNA were hybridized on 385K NimbleGen custom arrays according to NimbleGen's protocol.

scan_protocol: Arrays were scanned on an Axon 4000B scanner according to the manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. The signal from Beta' ChIP was subtracted from the signals from FnrL and Sigma70 ChIP using loess normalization to remove background signal.

organism: Cereibacter sphaeroides 2.4.1

source_name: FnrL ChIP DNA

label_protocol: Before labelling, the ChIP DNA was amplified using ligation mediated PCR. 1 ug of DNA was labelled using the NimbleGen Dual-color DNA labelling Kit (05223547001) according to the manufacturer's protocol.

growth_protocol: cells were cultured in minimal succinate based medium under anaerobic photosynthetic conditions until mid-exponential growth phase

extract_protocol: cells were fixed with 1% formaldehyde in culture medium for 5 minutes at 30°C followed by quenching with 0.125 M clycine for 30 minutes on ice. The cells were washed twice with ice cold PBS, frozen in dry/ethanol bath and stored at -80°C. Cells were resuspended in 500uL IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritinX-100), and sonicated (50% output, level 6) for 20 seconds 8 times to shear the DNA to fragments of 1 kbp in average. 50 units of micrococcal DNase and 0.5ug of RNaseA were added to the lysate and incubated for 1 hour at 4°C to reduce fragment size to 500 bp in avergage and degrade RNA. To stop the nucleases EDTA was added to 10mM final concentration. The lysate was cenrtrifuged to remove cell debris and 100 uL was saved for Input DNA. The lysate was was incubated with polyclonal antibodies against FnrL at 4°C over night. Then, ProteinA coated sepharose beads were added to the lysate, which was incubated for another 3 hours to capture antibodies. Beads were washed once with LiCl buffer (125 mM LiCL, 50 mM Tris pH 8, 1 % TritonX-100), twice with 600 mM NaCl Tris buffer, twice with 300mM NaCl Tris buffer and twive with TE buffer (10 mM Tris ph 8, 1 mM EDTA). Beads were ressupended in 200 uL Elution buffer (50 mM Tris pH 8, 10 nM EDTA, 1% SDS) and incubated at 65°C for 15 hours to reverse cross linking. DNA was cleaned using QIAGen DNA purification kit.

value: Wild-type

value: FnrL

source_name: Input DNA

extract_protocol: cells were fixed with 1% formaldehyde in culture medium for 5 minutes at 30°C followed by quenching with 0.125 M clycine for 30 minutes on ice. The cells were washed twice with ice cold PBS, frozen in dry/ethanol bath and stored at -80°C. Cells were resuspended in 500uL IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritinX-100), and sonicated (50% output, level 6) for 20 seconds 8 times to shear the DNA to fragments of 1 kbp in average. 50 units of micrococcal DNase and 0.5ug of RNaseA were added to the lysate and incubated for 1 hour at 4°C to reduce fragment size to 500 bp in avergage and degrade RNA. To stop the nucleases EDTA was added to 10mM final concentration. The lysate was cenrtrifuged to remove cell debris and 100 uL was saved for Input DNA and incubated at 65°C for 15 hours to reverse cross linking. DNA was cleaned using QIAGen DNA purification kit.


title: FnrL_rep 2

description: ChIP-chip FnrL in wild-type cells


title: FnrL_rep 1

description: ChIP-chip FnrL in wild-type cells


title: CGH YJS329_vs_BYZ1

status: Public on Sep 15 2011

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

hyb_protocol: Competitively hybed ~10ug channel 1 and 2 DNA on NimbleGen 385k whole genome arrays using Maui SL mixers in Maui hybridization chamber. Washed as per NimbleGen hybridization protocol.

scan_protocol: Axon GenePix 4000B microarray scanner

data_processing: Raw data were extracted as pair files by NimbleScan software. Log2-ratio data were calculated and normalized by spatial correction and qspline fit normalization.

organism: Saccharomyces cerevisiae

label_protocol: NimbleGen amplification and labeling

growth_protocol: Growth in YPD medium (1g/L yeast extract, 2g/L peptone, 2g/L glucose,  pH of 5.5).

extract_protocol: Total genomic DNA from yeast cells was isolated with the OMEGA Yeast DNA kit.

tag: application

value: bioethanol strain

value: BYZ1 (MATa/MATα his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 lys2Δ0/+ met15Δ0/+ ura3Δ0/ura3Δ0)

value: laboratory strain (S288c background)


title: muscle_diabetic_16107

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_glucoseIntolerant_16140

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_16116

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpdiast

tag: heartrate

tag: bpancle

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_15697

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_15661

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpdiast

tag: heartrate

tag: bpancle

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_diabetic_16122

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_15667

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpdiast

tag: heartrate

tag: bpancle

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_glucoseIntolerant_15682

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_glucoseIntolerant_15670

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpdiast

tag: heartrate

tag: bpancle

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_15685

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_15676

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpdiast

tag: heartrate

tag: bpancle

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_diabetic_15646

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_15655

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpdiast

tag: heartrate

tag: bpancle

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_diabetic_15640

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_glucoseIntolerant_15637

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpdiast

tag: heartrate

tag: bpancle

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_15619

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_15588

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpdiast

tag: heartrate

tag: bpancle

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_diabetic_15628

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_15625

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpdiast

tag: heartrate

tag: bpancle

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_diabetic_15576

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_15594

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpdiast

tag: heartrate

tag: bpancle

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: adenocarcinoma, biological replicate 2

status: Public on Feb 17 2011

city: Manchester

first: Hui Sun

last: Leong

address: Wilmslow Road

department: The University of Manchester

institute: Cancer Research UK Manchester Institute

description:
V524
0909_CaW(2)85_nuExH_FFPE_V524.CEL

hyb_protocol: RNA was quantified using a Bioanalyser (Agilent Technologies) and 100 ng amplified using NuGEN WT-Ovation FFPE v2 kit. The WT-Ovation Exon Module V1.0 was used to generate ST-cDNA and 4 µg was hybridised to Affymetrix Human Exon 1.0 ST arrays.

scan_protocol: Affymetrix GeneChip 3000 running GCOS software.

data_processing:
Background adjustment, quantile normalisation and summarisation of probe-level intensity were performed with the Robust Multi-array Average (RMA) algorithm.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: not applicable

source_name: cervix

label_protocol: The RNA was amplified using the WT-Ovation Pico RNA Amplification System, converted using the WT-Ovation Exon Module, and fragmented and labelled using the NuGEN FL-Ovation cDNA Biotin Module v2.

growth_protocol: not applicable

extract_protocol: 3 x 20uM sections of FFPE material was used for all samples. Total RNA was recovered using the Recoverall (Ambion kit) as per manufactures instructions.

treatment_protocol: not applicable

tag: disease state

value: adenocarcinoma

tag: age of ffpe block (years)

tag: p63 staining status


title: muscle_diabetic_16101

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_15582

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_diabetic_15570

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_15564

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_glucoseIntolerant_15552

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_glucoseIntolerant_15558

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_glucoseIntolerant_15537

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_glucoseIntolerant_15522

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_15534

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_15516

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_diabetic_15549

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_15504

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_15501

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_15498

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_diabetic_15510

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_15494

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_glucoseIntolerant_15496

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_17173

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_glucoseIntolerant_17182

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_15497

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_17191

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_glucoseIntolerant_17188

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_15652

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: Exon arrays of Roadmap cell types; IMR90 Cell Line; DS13229-exon

status: Public on Oct 06 2010

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3478
sample alias: IMR90
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1632

hyb_protocol: Hybridizations were carried out according the manufacturer (Affymetrix) protocol

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

source_name: IMR90 Cell Line; DS13229-exon

label_protocol: A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.

growth_protocol: Followed vendor recommendations for growth protocol/media

extract_protocol: At cell harvest, a subset of cells was stored at -20 C in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).

tag: disease

value: ATCC

value: Cell Line

tag: line

tag: lineage

value: Fetal lung fibroblast

tag: passage

tag: medium

value: Eagle's Minimum Essential Medium, Catalog No. 30-2003.

tag: Sex

value: Female

tag: batch


title: muscle_glucoseIntolerant_17164

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_glucoseIntolerant_15493

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_17134

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: evf

tag: baso

tag: eosino

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_glucoseIntolerant_17152

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_17146

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: evf

tag: baso

tag: eosino

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_17170

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_diabetic_17110

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: evf

tag: baso

tag: eosino

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_17167

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_17131

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: evf

tag: baso

tag: eosino

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_glucoseIntolerant_17013

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: Exon arrays of Roadmap cell types; IMR90 Cell Line; DS11759-exon

status: Public on May 05 2010

description:
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2588
sample alias: IMR90
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1632

source_name: IMR90 Cell Line; DS11759-exon

tag: disease

tag: line

tag: lineage

tag: passage

tag: medium

tag: Sex

tag: batch


title: muscle_normal_17010

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: evf

tag: baso

tag: eosino

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh


title: muscle_normal_17025

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: weight

tag: hip

tag: waist

tag: bpsyst

tag: bpdiast

tag: heartrate

tag: bpancle

tag: lymfo

tag: mono

tag: neutro

tag: leuko

tag: fibrinogen

tag: crp

tag: orosomucoid

tag: myoglobin

tag: basp


title: muscle_normal_17007

tag: dmdebut

tag: diabetesdisposition

tag: euglycemia

tag: igt

tag: dmverified

tag: glycemiagroup

tag: obesity

tag: hypertension

tag: dyslipidemia

tag: age

tag: bmi

tag: whr

tag: dietonly

tag: sulfonyl

tag: metformin

tag: tzd

tag: statin

tag: fibrat

tag: asa

tag: smokercurrent

tag: smokerex

tag: smokerstopyear

tag: examination

tag: born

tag: gender

tag: height

tag: evf

tag: baso

tag: eosino

tag: ck

tag: ldh

tag: asat

tag: bilirubiner

tag: cholesteroler

tag: hdl

tag: ldl

tag: tag

tag: creatininium

tag: natrium

tag: kalium

tag: calcium

tag: tsh