title: human_drug_treated_2

status: Public on Feb 23 2010

type: RNA

city: Szeged

first: Agnes

last: Zvara

address: Temesvari krt 62

country: Hungary

institute: Biological Research Center

hyb_protocol: Agilent hybridization protocol for DNA microarrays. 65 degree, 14 hours.

scan_protocol: Using the Agilent Scanner XDR function. 10 % and 100 % laser power and 10u resolution.

data_processing: Data processing was carried out by Agilent Feature Extraction software. Lowess normalization.

molecule: total RNA

organism: Homo sapiens

source_name: K562 cell line, drug-treated, 4 hours

label_protocol: Amino Allyl MessageAmp II aRNA Amplification Kit by Ambion. According the manufacturer's instructions.

extract_protocol: RNA isolation protocol by Bioneer Company, DNAse treated

tag: cell line

tag: cell type

value: leukaemia

source_name: K562 cell line, untreated, 4 hours


title: human_drug_treated_1


title: human_drug_treated_4


title: Liver_stage_infected_hepatocyte_40hr_post_infection_rep4

status: Public on Feb 24 2010

city: Seattle

last: Phan

state: WA

address: 307 Westlake Av N

country: USA

institute: SBRI

description: PyGFP 40-4: Liver stage (LS) infected hepatocytes isolated from PyGFP-infected BALB/c mice at 40hr post-infection

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction. To assess the differential expression between different samples, the processed expression data were analyzed together by using linear model methods . Each of the three samples, LS24, LS40 and mock was included as a coefficient in the linear model. After fitting the linear model to the expression data, all pair-wise comparisons between three groups were done in the contrast step by specifying the corresponding contrasts. Differential expression was assessed using the moderated t-statistics. To control the false discovery rate, p-values corresponding to the t-statistics were adjusted for multiple testing by using the method of Benjaminini et al .

organism: Mus musculus

source_name: Plasmodium yoelii + Mus musculus

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Female Swiss Webster and BALB/c mice (6-8 weeks old) were purchased from Harlan Company (Indianapolis, USA) and kept in a temperature- and humidity-controlled environment at the SBRI/Children’s Hospital animal care facility under a 12 hr light/dark cycle. Animal handling was conducted according to the Institutional Animal Care and Use Committee approved protocols.  PyGFP  was routinely cycled between Anopheles stephensi mosquitoes and Swiss Webster mice (Harlan Labs). Infected mosquitoes were maintained at 24 ºC and 70% humidity on sugar and water. HepG2:CD81 (a gift from Dominique Mazier;  were propagated in Dulbecco’s modified Eagle medium: Nutrient mix F12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS), 2% penicillin-streptomycin (5000 U/ml), and 1% amphotericin B (250 U/ml).

extract_protocol: Total RNA from each sample was extracted using Trizol (Invitrogen) and DNase treated using Turbo-DNAfree (Ambion).Total RNA was then subjected to two rounds of linear amplification using the Amino Allyl Message Amp II aRNA Amplification Kit (Ambion) according to manufaturer’s directions. The quality of total and amplified RNAs were examined with the Agilent 2100 BioanalyzerTM (Agilent Technologies) and the quantity of the RNA samples was assessed using a Nanodrop ND-1000 spectrophotometer  prior to microarray hybridization. For each stage of the parasite analyzed, 2-5 independent biological replicates were obtained for a total of 22 individual RNA samples.

treatment_protocol: Liver stage (LS) infected hepatocytes were isolated from PyGFP-infected BALB/c mice by a two-step collagenase perfusion technique as described . LS-infected hepatocytes were isolated at two time points post-infection (pi): 24 hr pi (LS24) and 40 hr pi (LS40). As control, hepatocytes from mock-infected mice were also isolated following the same procedure. Flow cytometric analyses and cell sorting of PyGFP-infected hepatocytes were carried out with a Cytopeia Influx Cell Sorter using the Spigot Operating Software Version 5.0.3.1 (Cytopeia).

tag: strain

value: M.musculus Swiss Webster and BALB/c

tag: pygfp

value: P. yoelii yoelii line that is stably transfected with the green fluorescent protein (gfp) gene;


title: Hepatocyte_24hr_mock_sample

description: 24 hrs mock sample: hepatocytes from mock-infected mice

source_name: Mus musculus


title: Liver_stage_infected_hepatocyte_40hr_post_infection_rep1

description: PyGFP 40-1: Liver stage (LS) infected hepatocytes isolated from PyGFP*-infected BALB/c mice at 40hr post-infection


title: human_drug_treated_3


title: Empty vector control (RNAi 1B)_3of3

status: Public on Feb 22 2010

city: Washington

first: Jaime

last: Guidry Auvil

state: DC

address: 3970 Reservoir Road, NW

department: Lombardi Comprehensive Cancer Center

institute: Georgetown University Medical Center

description:
MDA-MB-231 breast cancer cells stably expressing empty vector control siRNA (RNAi 1B)
This study involved seven arrays (3 control, 4 treated) to assess genetic differences in breast cancer cells when cadherin-11 was stably depleted.  Cadherin-11 expression is associated with tumor progression and metastasis in various cancers, including basal-like breast carcinoma and advanced prostate cancer, and invasive cell lines, yet is absent in normal epithelium.  Cadherin-11 attenuation in aggressive breast and prostate cancer cells results in marked decreases in proliferation, migration, and invasion.  Cadherin-11 depletion in MDA-231 cells prevents tumor growth in mice and alters gene expression and survival outcome associated with poor prognosis malignancies, as observed through publically available data mining.  This study was aimed at uncovering possible mechanisms associated with these facts.

hyb_protocol: Fragmented cRNA was analyzed for quality and given to the Microarray Shared Resources Core at Georgetown University Medical Center for hybridization to Affymetrix U133A gene chips (please contact for further information).

scan_protocol: Performed by Microarray Shared Resources Core at Georgetown University Medical Center (please contact for further information).

data_processing:
Seven U133A Affymtrix GeneChip arrays were run in this study. Three of these were hybridized with RNA prior to treatment, while the remaining four were hybridized with treated RNA (gene knockout). Our data analysis began with preprocessing of the probe-level Affymetrix data (.cel files). To accomplish this, we applied low-level analysis methods that have been recently optimized to perform better than those provided by the Affymetrix’s software, MicroArray Suite (MAS 5.0). Note that Affymetrix data preprocessing involves three major steps: i) background adjustment to minimize the effect of non-specific binding and optical noise, ii) normalization to ensure that the measurements from different arrays are comparable; and iii) summarization to obtain an expression value for a probeset by combining multiple probe intensities. Recent studies have shown that the performance of MAS 5.0 in accomplishing the above three preprocessing steps is suboptimal and new approaches have been proposed (Bolstad, 2004).
For background adjustment, Irizarry et al. (2003) proposed a robust multi-array analysis (RMA) method that employs the perfect match probe data only. RMA estimates background based on a convolution model that is motivated by the distribution of probe intensities (Bolstad et al., 2003). It models the observed intensity as the sum of a signal and a background component, S = X + Y, where X and Y denote the signal and the background, respectively. The model assumes that X and Y are independent with X following an exponential distribution and Y a normal distribution truncated at 0, i.e. Y ≥ 0. The corrected probe intensities is estimated as E(X | S = s).
Normalization methods such as quantile and cyclic loess use information from across all arrays to produce the normalization. For example, quantile normalization uses this approach to give the same distribution to each array. These methods have been shown to outsmart the baseline methods such as MAS 5.0’s scaling method that select one array to represent the typical array and all other arrays are scaled to have the same mean intensity as this array.
Several methods of summarization procedures have been used including single-chip methods (e.g. averages and robust averages) and multi-chip models such as the model-based expression index (MBEI) (Li and Wong, 2001), Tukey's median polish, and the robust multi-array average (Irrizary et al., 2003).
	In our low-level analysis, we used RMA for background adjustment, quantile method for normalization, and a robust multi-array average for summarization. These methods have provided better performance than MAS 5.0 and MBEI in detecting known levels of differential expression using spike-in Affymetrix data (Irizarry et al., 2003; Bolstad, 2004). They are implemented in several statistical tools including Bioconductor and BRB-ArrayTools (NCI, Bethesda, MD).
We analyzed the preprocessed data to identify those that were differentially expressed between the untreated and treated groups. The random variance model implemented in BRB-ArrayTools was used for this analysis. The random-variance t-test is an improvement over the standard separate t-test as it permits sharing information among genes about within-class variation without assuming that all genes have the same variance (Wright and Simon, 2003). Probesets were considered statistically significant if their p-value was less than 0.001. A stringent significance threshold was used to limit the number of false positive findings. With this threshold, 28 probesets were found statistically significant (p<0.001). A less stringent significance threshold of p<0.01 produced 236 differentially expressed probesets.
	Furthermore, we performed statistical analysis to determine which gene ontology (GO) categories were differentially expressed between the untreated and treated groups. This was performed using a functional class scoring analysis as described by Pavlidis et al. (2004). For each gene in a GO class, the p value for comparing treated versus untreated groups samples was computed. The set of p values for a class was summarized by two summary statistics: (i) The LS summary is the average log p values for the genes in that class and (ii) the KS summary is the Kolmogorov-Smirnov statistic computed on the p values for the genes in that class. The statistical significance of the GO class containing n genes represented on the array was evaluated by computing the empirical distribution of the above two summary statistics in random samples of n genes. We considered a GO category significantly differentially regulated if either significance level was less than 0.005. We considered all GO categories with between 5 and 100 genes represented on the array. Some of the categories were overlapping. 92 GO categories are significant at the 0.005 level of the LS permutation test or KS permutation test. Functional class scoring is a more powerful method of identifying differentially expressed gene classes than the more common over-representation analysis or annotation of gene lists based on individually analyzed genes. The functional class scoring analysis for Gene Ontology classes was performed using BRB-ArrayTools.

label: Biotin

source_name: MDA-MB-231 breast cancer cells

label_protocol: Enzo BioArray High Yield RNA Transcript Labeling Kit (Affymetrix) was used for generating labeled cRNA.  Briefly, template cDNA (assessed for quality and quantitated) was mixed very carefully with kit reagents to include ddH2O, HY buffer, Biotin-labeled ribonucleotides, DTT, RNase inhibitor mix, and T7 RNA polymerase.  The mixed contents were incubated in 37 degree C water bath for 4-5 hours with contents mixed gently every 30-45 minutes.  cRNA was cleaned-up and fragmented according to protocol using the GeneChip Sample Cleanup Module.

growth_protocol: Cells were maintained in DMEM containing 5% fetal bovine serum and 1mg/ml hygromycin for stable selection, and grown in a humid 5% CO2 incubator at 37 degrees C.

extract_protocol: Trizol/RNeasy hybrid protocol from Affymetrix was used to extract total RNA from these samples.  Briefly, cells were washed with PBS, resuspended in 1ml of Trizol for 5 minutes at RT, then scraped into a 1.5 ml Eppendorf tube.  200ul of chloroform was added to each sample, shaken vigorously for 15 seconds, allowed to sit for 2-3 minutes prior to spinning at 12,000xg for 15 minutes at 4 degrees C.  Aqueous phase was very carefully removed so as not to disturb any of the aqueous/organic interface and placed into a fresh tube.  An equal amount of cold 70% EtOH was added and mixed with aqueous solution.  Sample was loaded into RNeasy column (Qiagen Mini Kit) and processed according to their protocol (washes, then spins, with RWI and RPE buffers, prior to elution of RNA using RNase-free H2O).

treatment_protocol: RNA interference: siRNA (either an empty vector control or a construct targeting the intracellular domain of the cadherin-11 wild type isoform) is stably expressed in MDA-MB-231 breast cancer cells.

value: MDA-MB-231 breast cancer cells

tag: protocol

value: control

tag: other


title: Testis_Rep2

status: Public on Feb 20 2010

city: College Station

first: Clayton

middle: M

last: Small

state: TX

address: 3258 TAMU

department: Biology

institute: Texas A&M University

description: Upon euthanasia the entire reproductive tract from each individual was removed under a dissecting microscope (320X) with sterilized fine-tipped forceps, placed in 200 ul Trizol, and snap-frozen in a dry ice-ethanol bath.  At this time the remainder of the body was placed in 4000 ul Trizol, and similarly snap-frozen.  All downstream procedures were performed according to standardized manufacturer protocols.

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing:
Data were analyzed 4 different ways:
VALUE [GCOS]: Expression values were computed using the MAS5 algorithm in GCOS version 1.2, under suggested settings.  All probesets were scaled using a TGT value of 500, and no normalization was applied (i.e., the normalization factor was 1.0).
VALUE2 [GC-RMA]: Expression values were computed using the GC-RMA model-based algorithm in GeneSpring GX 7.3.1 (Agilent Technologies).  Default normalization is performed as follows: the raw intensity value for each probe set on a chip is divided by the overall median intensity value for that chip.  This “prenormalized” value is then divided by the median “prenormalized” value for that specific probe set across all 12 chips in the experiment.
VALUE3 [PM-Only]: All 12 chips were analyzed simultaneously in dCHIP, which uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM-Only procedure under default parameters.
VALUE4 [PM-MM]: All 12 chips were analyzed simultaneously in dCHIP, which uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM-MM procedure under default parameters.

label: biotin

organism: Danio rerio

source_name: Testes

label_protocol: Standard Affymetrix

growth_protocol:
Standard rearing protocols were used, as described in Westerfield, 2000:
Westerfield, M. (2000). The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio). 4th ed., Univ. of Oregon Press, Eugene.

extract_protocol: Standard Trizol (Invitrogen) extraction.

treatment_protocol: Reproductive males and females (3 each) were paired on day 1, and spawning was confirmed on day 2 by the presence of eggs.  Males and females were subsequently separated and housed for five days.  On day 7 individuals were sacrificed and dissections were performed.

value: AB (wild type)

tag: gender

value: Male

tag: age

value: 4-12 months


title: Empty vector control (RNAi 1B)_2of3

description: This study involved seven arrays (3 control, 4 treated) to assess genetic differences in breast cancer cells when cadherin-11 was stably depleted.  Cadherin-11 expression is associated with tumor progression and metastasis in various cancers, including basal-like breast carcinoma and advanced prostate cancer, and invasive cell lines, yet is absent in normal epithelium.  Cadherin-11 attenuation in aggressive breast and prostate cancer cells results in marked decreases in proliferation, migration, and invasion.  Cadherin-11 depletion in MDA-231 cells prevents tumor growth in mice and alters gene expression and survival outcome associated with poor prognosis malignancies, as observed through publically available data mining.  This study was aimed at uncovering possible mechanisms associated with these facts.


title: Cadherin-11 siRNA (RNAi 4A)_2of2

description:
Cadherin-11 wt pooled stable knockdown cells (RNAi 4A)
This study involved seven arrays (3 control, 4 treated) to assess genetic differences in breast cancer cells when cadherin-11 was stably depleted.  Cadherin-11 expression is associated with tumor progression and metastasis in various cancers, including basal-like breast carcinoma and advanced prostate cancer, and invasive cell lines, yet is absent in normal epithelium.  Cadherin-11 attenuation in aggressive breast and prostate cancer cells results in marked decreases in proliferation, migration, and invasion.  Cadherin-11 depletion in MDA-231 cells prevents tumor growth in mice and alters gene expression and survival outcome associated with poor prognosis malignancies, as observed through publically available data mining.  This study was aimed at uncovering possible mechanisms associated with these facts.

value: cadherin-11 knockdown


title: Hepatocyte_40hr_mock_sample

description: 40 hrs mock sample: hepatocytes from mock-infected mice


title: Liver_stage_infected_hepatocyte_24hr_post_infection_rep1

description: PyGFP 24-1: Liver stage (LS) infected hepatocytes isolated from PyGFP-infected BALB/c mice at 24hr post-infection


title: Cadherin-11 siRNA (RNAi 4A)_1of2

description:
Depletion of Cadherin-11 in MDA-MB-231 breast cancer cells
This study involved seven arrays (3 control, 4 treated) to assess genetic differences in breast cancer cells when cadherin-11 was stably depleted.  Cadherin-11 expression is associated with tumor progression and metastasis in various cancers, including basal-like breast carcinoma and advanced prostate cancer, and invasive cell lines, yet is absent in normal epithelium.  Cadherin-11 attenuation in aggressive breast and prostate cancer cells results in marked decreases in proliferation, migration, and invasion.  Cadherin-11 depletion in MDA-231 cells prevents tumor growth in mice and alters gene expression and survival outcome associated with poor prognosis malignancies, as observed through publically available data mining.  This study was aimed at uncovering possible mechanisms associated with these facts.


title: Cadherin-11 siRNA (RNAi 6A)_2of2


title: Testis_Rep3


title: Liver_stage_infected_hepatocyte_24hr_post_infection_rep2

description: PyGFP 24-2: Liver stage (LS) infected hepatocytes isolated from PyGFP-infected BALB/c mice at 24hr post-infection


title: Cadherin-11 siRNA (RNAi 6A)_1of2


title: Empty vector control (RNAi 1B)_1of3


title: MaleBody_Rep2

source_name: Male Body (minus testes)


title: Testis_Rep1


title: MaleBody_Rep3


title: Ovary_Rep1

source_name: Ovaries

value: Female


title: Ovary_Rep2


title: FemaleBody_Rep2

source_name: Female Body (minus ovaries)


title: MaleBody_Rep1


title: FemaleBody_Rep3


title: Ovary_Rep3


title: FemaleBody_Rep1


title: Wild-type Mouse Embryonic Heart (E12.5), sample 1

status: Public on Feb 18 2010

city: Hanover

first: Sergei

middle: G

last: Tevosian

state: NH

address: 7400 Hinman Box

department: Genetics

institute: Dartmouth Medical School

description: E12.5 cardiac RNA served as a control to the experimental mutant sample (Fog2 null).

hyb_protocol: Biotinylated cRNA products were hybridized to Affymetrix GeneChip mouse arrays for 16 h at 40oC in a Gene Chip Hybridization oven 640 using the manufacturer's hybridization buffer (Affymetrix).

scan_protocol: After hybridization, the arrays were washed and stained using the Fluidics Station 450 (Affymetrix). Chips were scanned with the 7G Affymetrix Gene Scanner (Affymetrix) according to manufacturer's recommendation.

source_name: mouse embryonic heart, wild-type

label_protocol: Synthesized cRNA were labeled during transcription (Megascript system; Ambion) with biotin-11-cytidine triphosphate and biotin-16-uridine triphosphate (Enzo Diagnostics).

extract_protocol: Total RNA isolated from the 10 E12.5 Embryonic Hearts using RNeasy Mini kit (Qiagen). Total RNA quantity was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc.)

treatment_protocol: Tissue was isolated from embryos in PBS

tag: genotype

value: wild-type

tag: tissue

value: heart (both atria and ventricles)

tag: developmental stage

value: embryo

tag: day


title: Fog2 (Zfpm2) null Mouse Embryonic Heart (E12.5), sample 1

description: E12.5 cardiac RNA from the experimental mutant sample Fog2 (Zfpm2) null.

source_name: mouse embryonic heart, Fog2 (Zfpm2) null

value: Fog2 (Zfpm2) null


title: GATA4ki Mouse Embryonic Heart (E12.5), sample 3

description: E12.5 cardiac RNA from the experimental mutant sample (Gata4ki/ki). The GATA4ki mutation specifically cripples the interaction between the GATA4 protein and FOG molecules.

source_name: mouse embryonic heart, GATA4ki/ki mutant

extract_protocol: Total RNA isolated from the 8 E12.5 Embryonic Hearts using RNeasy Mini kit (Qiagen). Total RNA quantity was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc.)

value: GATA4ki mutation


title: CIS 11

status: Public on Feb 17 2010

city: Ramat Gan

first: Michael

last: Gurevich

address: Tel Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

description: working set58

hyb_protocol: cDNA was synthesized, labeled, hybridized to HG-U133A-2 array containing 22,215 gene-transcripts according to Affymetrix (Inc, Santa Clara, CA) protocol

scan_protocol: Hewlett Packard, GeneArray-TM scanner G2500A

data_processing: Data analysis was performed by Partek Genomics Solution software (www.partek.com ). Expression values were computed from raw CEL files by applying the Robust Multi-Chip Average (RMA) background correction algorithm. The RMA correction included: 1) values background correction; 2) quantile normalization; 3) log2 transformation; 4) median polish summarization. In order to avoid the noise caused by variable set effects we normalized each set to pre-saved distribution pattern of a well balanced set used as a reference distribution.

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

extract_protocol: Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA)

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were separated on ficoll-hypaque gradient

tag: disease state

value: clinically isolated syndrome

value: PBMC

value: 31 years

value: F


title: Wild-type Mouse Embryonic Heart (E12.5), sample 2

description: E12.5 cardiac RNA served as a control.


title: CIS 10

description: working set58

value: 34 years


title: Wild-type Mouse Embryonic Heart (E12.5), sample 3

description: E12.5 cardiac RNA served as a control to the experimental mutant sample (Gata4ki/ki). The GATA4ki mutation specifically cripples the interaction between the GATA4 protein and FOG molecules.


title: Fog2 (Zfpm2) null Mouse Embryonic Heart (E12.5), sample 2


title: CIS 7

description: working set58

value: 38 years


title: 90d Yellow 3

city: Vermillion

first: Kathleen

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

description: IACUC approval was obtained for all animal treatments.

data_processing: global median normalization, CodeLink Expression Analysis 4.1.0.4163

source_name: ovary

extract_protocol: The ovaries were collected into RNAlater (Ambion) and frozen. The RNAlater was blotted and the ovaries were homogenized in 1 ml TRI reagent (MRC).  Bromochloropropane and sodium acetate were added to the homogenate and the sample was centrifuged to separate the phases.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity of the total RNA was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

value: ovary

value: female

value: 90 days

value: C56BL/6J Ay/a

tag: treatment 1

value: Antide on days 1 and 4

tag: dose

value: 10 microg/g

tag: treatment 2

value: equine chorionic gonadotropin

value: 1 IU/5g body weight

tag: tissue collection

value: day 7


title: Cont-CIS 3

description: working set58

value: healthy

value: 39 years

value: M


title: 90d Black 2

value: C56BL/6J a/a


title: 180d Black 3

value: 180 days


title: 90d Yellow 1


title: CIS 1

description: working set34

value: clinically isolated syndrome

value: PBMC


title: Cont-CIS 4

description: working set58

value: 32 years

value: F


title: CIS 12

description: working set58

value: 31 years


title: 90d Black 1

value: ovary

value: female

value: 90 days


title: CIS 9

description: working set58


title: 180d Yellow 3

value: C56BL/6J Ay/a

value: Antide on days 1 and 4

value: 10 microg/g


title: 180d Black 2

value: equine chorionic gonadotropin

value: 1 IU/5g body weight

value: day 7


title: 90d Yellow 2


title: CIS 13

description: working set58

value: 46 years


title: CIS 8

description: working set58

value: 30 years


title: CIS 3

description: working set34

value: 28 years


title: 90d Black 3

value: C56BL/6J a/a


title: 180d Yellow 1

value: 180 days


title: MSf 7

description: working set74

value: multiple sclerosis free

value: PBMC

value: 20 years


title: CIS 6

description: working set58

value: clinically isolated syndrome

value: 35 years

value: M


title: 180d Black 1

value: ovary

value: female


title: 180d Yellow 2

value: C56BL/6J Ay/a

value: Antide on days 1 and 4

value: 10 microg/g


title: CIS 5

description: working set34

value: 27 years

value: F


title: CIS 4

description: working set34

value: 29 years


title: CIS 2

description: working set34

value: 25 years


title: Cont-CIS 2

description: working set34

value: healthy


title: MSf 10

description: working set74


title: MSf 2

description: working set76


title: MSf 9

description: working set74


title: MSf 6

description: working set74


title: MS2b 2

description: working set76

value: prior to onset of multiple sclerosis


title: MM_CL-Vel_8V3_A

status: Public on Feb 15 2010

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: 9 Cell lines with 2 conditions (incubated (xVx) or not (xCx) with bortezomib and dexamethasone)

hyb_protocol: Labelled cDNAs were then hybridized in 0.3 ml hybridization mix in scintillation vials for 48 h at 68° C. After hybridization filters were washed twice in 0.1x SSC, 0.1% SDS at 68° C for 90 min.

scan_protocol: DNA microarrays were scanned at 25-µm resolution using a Fuji BAS 5000 image plate system (Raytest, Paris, France). The hybridization signals were quantified using ArrayGauge software v.1.3 (Fuji, Ltd, Tokyo, Japan).

data_processing: For each membrane, the data were normalized by the global intensity hybridization. A background value was calculated from negative controls ± 6 SD and subtracted to each value. After expression data correction for the amount of PCR product spotted onto the membrane, only features detected in at least 5% of the cell lines were retained for subsequent analysis. Data were finally log2 and ln-transformed [step 1: log2 transformed; step 2: ln((value from step 1) x 1000) transformed].

source_name: Human myeloma bone marrow cell lines

label_protocol: Between 0.4 and one µg of total RNA was used as template to generate cDNA bearing T7 promoter, then antisense RNA (aRNA) was generated by in vitro transcription using MEGAscript technology according to the Ambion protocol (Ambion Inc., Austin TX). An aliquot of 2µg of labelled aRNA was then primed with random hexaprimers and reverse transcribed with a mix of cold dNTPs and [alpha-33P]dCTP. Unincorporated nucleotides were removed by purification on a Sephadex G-50 column.

extract_protocol: Total RNA from human myeloma cell lines was extracted using the guanidinium thiocyanate–phenol method. The RNA integrity was randomly verified by using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: Human myeloma bone marrow cell lines. Cell line and Code

value: JJN3 = Vel_1x; L363 = Vel_2x; LP1 = Vel_3x; MDN = Vel_4x; NCI = Vel_5x; RPMI = Vel_6x; SBN = Vel_7x; U266 = Vel_8x; XG1 = Vel_9x.


title: MSf 11

description: working set74

value: multiple sclerosis free

tag: cell type

value: PBMC

value: 18 years


title: MM_CL-Vel_9C3_A


title: MSf 4

description: working set74


title: MSf 8

description: working set74

value: 20 years


title: Differentiated HES3 18P Human Embryonic Stem Cells

type: SAGE

anchor: NlaIII

city: Singapore

first: Zhenyang

last: Lai

address: Science Drive 4

department: Department of Biologcial Sciences

country: Singapore

institute: National University of Singapore

description: HES3 cell line was grown to 18 passages (P18) on MEFs, after which no sub-culturing was performed. The medium was changed daily for 25 days and the differentiated cell population was harvested at the end of the culture period by micro-dissection. HES3 is a proprietary human ES cell line of ES Cell International Pte Ltd. Singapore.

source_name: HES3 Human Embryonic Stem Cells, Differentiated

extract_protocol: Cells were harvested at the end of culture period and RNA was isolated using Trizol reagent according to manufacturer’s protocol (Invitrogen) followed by DNase I treatment

tag: Tissue of Origin

value: Blastocyst inner cell mass

tag: Cell Line NIH Code

value: ES03; Provider’s Code:HES-3

tag: Gender

value: Female

tag: Karotype


title: Cont-CIS 1

description: working set34

tag: gender

value: M


title: MSf 3

description: working set76

tag: age


title: MS2b 8

description: working set74


title: MS2b 9

description: working set74


title: MSf 5

description: working set74


title: MS2b 6

description: working set74


title: MM_CL-Vel_8V1_A


title: MS2b 4

description: working set76


title: MS2b 5

description: working set76


title: Partially Differentiated HES3 24P Human Embryonic Stem Cells

description: HES3 (XX) human embryonic stem cells grown on mouse embryonic fibroblast feeder layers. Colonies which had started differentiation, as suggested by the morphological changes towards the centre and periphery of the colonies were used. Entire HES3 colonies (24P) which had started differentiation were harvested by micro-dissection and used for library construction. HES3 is a proprietary human ES cell line of ES Cell International Pte Ltd. Singapore.

source_name: embryonice stem cell HES3, partially differentiated

extract_protocol: Cells were harvested at the end of culture period and RNA was isolated using Trizol reagent according to manufacturer’s protocol (Invitrogen) followed by DNase I treatment.


title: MS2b 3

description: working set76


title: MS2b 7

description: working set74


title: MSf 1

description: working set76


title: MM_CL-Vel_8C2_A


title: MS2b 1

description: working set76


title: MM_CL-Vel_9V1_A


title: MM_CL-Vel_9C2_A


title: MM_CL-Vel_9V2_A


title: MM_CL-Vel_7V3_A


title: MM_CL-Vel_9V3_A


title: MM_CL-Vel_8C3_A


title: MM_CL-Vel_8V2_A


title: MM_CL-Vel_9C1_A


title: MM_CL-Vel_8C1_A


title: MM_CL-Vel_7C2_A


title: MM_CL-Vel_6C2_A


title: MM_CL-Vel_6V3_A


title: MM_CL-Vel_6C1_A


title: MM_CL-Vel_7C3_A


title: MM_CL-Vel_7V2_A


title: MM_CL-Vel_7V1_A


title: MM_CL-Vel_6V2_A


title: MM_CL-Vel_5V1_A


title: MM_CL-Vel_7C1_A


title: MM_CL-Vel_6C3_A


title: MM_CL-Vel_5V2_A


title: MM_CL-Vel_6V1_A


title: MM_CL-Vel_5V3_A


title: MM_CL-Vel_4V3_A


title: MM_CL-Vel_5C2_A


title: MM_CL-Vel_5C3_A


title: MM_CL-Vel_4C3_A


title: MM_CL-Vel_4V2_A


title: MM_CL-Vel_5C1_A


title: MM_CL-Vel_4V1_A


title: MM_CL-Vel_4C2_A


title: MM_CL-Vel_3C3_A


title: MM_CL-Vel_4C1_A


title: MM_CL-Vel_3V4_A


title: MM_CL-Vel_3V3_A


title: MM_CL-Vel_3C1_A


title: MM_CL-Vel_3V2_A


title: MM_CL-Vel_2V1_A


title: MM_CL-Vel_2C3_A


title: MM_CL-Vel_3C2_A


title: MM_CL-Vel_2V3_A


title: MM_CL-Vel_2C1_A


title: MM_CL-Vel_2V2_A


title: OSTEOSARCOMA_0019_A

description: Twenty patients treated for an osteosarcoma at the La Timone hospital (Marseille, France) between 1993 and 2004. All patients received high-dose Methotrexate in neoadjuvant setting.

hyb_protocol: Labeled cDNAs were then hybridized onto stripped microarrays in 0.3 ml of hybridization mix (5x SSC, 0.5% SDS, 5x Denhardt's) in scintillation vials for 36 h at 68°C. After hybridization filters were washed twice in 0.1x SSC, 0.1% SDS at 68°C for 3 hr.

data_processing: Data were background noise subtracted (negative controls ± 6 SD), then normalized by original global intensity of hybridization. After expression data correction for the amount of PCR product spotted onto the membrane (testing probe data), data were finally log2-transformed. Only genes well measured for 70% of patients were retained.

source_name: Osteosarcoma tissue, patient 0019_A

extract_protocol: Total RNA extraction was performed using the acid guanidinium isothiocyanate/phenol/chloroform procedure, and analyzed on both nanodrop spectrophotometer and Agilent 2100 Bioanalyser RNA LabChip kit (Chomczynski 1987). Only samples with 28S/18S ratio of >1.5 and no evidence of ribosomal degradation were included. Before use, RNA samples were treated with 10U ribonuclease-free deoxyribonuclease at 37°C for 15 mn.

tag: Osteosarcoma tissue


title: OSTEOSARCOMA_0017_A

source_name: Osteosarcoma tissue, patient 0017_A


title: OSTEOSARCOMA_0013_A

source_name: Osteosarcoma tissue, patient 0013_A


title: OSTEOSARCOMA_0014_A

source_name: Osteosarcoma tissue, patient 0014_A


title: OSTEOSARCOMA_0010_A

source_name: Osteosarcoma tissue, patient 0010_A


title: OSTEOSARCOMA_0015_A

source_name: Osteosarcoma tissue, patient 0015_A


title: OSTEOSARCOMA_0011_A

source_name: Osteosarcoma tissue, patient 0011_A


title: OSTEOSARCOMA_0018_A

source_name: Osteosarcoma tissue, patient 0018_A


title: OSTEOSARCOMA_0016_A

source_name: Osteosarcoma tissue, patient 0016_A


title: MM_CL-Vel_2C2_A


title: OSTEOSARCOMA_0012_A

source_name: Osteosarcoma tissue, patient 0012_A


title: OSTEOSARCOMA_0020_A

source_name: Osteosarcoma tissue, patient 0020_A


title: OSTEOSARCOMA_0008_A

source_name: Osteosarcoma tissue, patient 0008_A


title: OSTEOSARCOMA_0009_A

source_name: Osteosarcoma tissue, patient 0009_A


title: OSTEOSARCOMA_0003_A

source_name: Osteosarcoma tissue, patient 0003_A


title: MM_CL-Vel_1V3_A

source_name: Human myeloma bone marrow cell lines


title: MM_CL-Vel_1V1_A


title: MM_CL-Vel_1C3_A


title: OSTEOSARCOMA_0002_A

source_name: Osteosarcoma tissue, patient 0002_A


title: OSTEOSARCOMA_0007_A

source_name: Osteosarcoma tissue, patient 0007_A


title: OSTEOSARCOMA_0006_A

source_name: Osteosarcoma tissue, patient 0006_A


title: MM_CL-Vel_1C2_A


title: MM_CL-Vel_1V2_A


title: OSTEOSARCOMA_0001_A

source_name: Osteosarcoma tissue, patient 0001_A


title: MM_CL-Vel_1C1_A


title: MM_CL-Vel_9C1_B


title: MM_CL-Vel_9C3_B


title: MM_CL-Vel_8V1_B


title: OSTEOSARCOMA_0004_A

source_name: Osteosarcoma tissue, patient 0004_A


title: OSTEOSARCOMA_0005_A

source_name: Osteosarcoma tissue, patient 0005_A


title: MM_CL-Vel_9V1_B


title: MM_CL-Vel_8C3_B


title: MM_CL-Vel_9V3_B


title: MM_CL-Vel_9V2_B


title: MM_CL-Vel_9C2_B


title: MM_CL-Vel_7V3_B


title: MM_CL-Vel_8V2_B


title: MM_CL-Vel_8V3_B


title: MM_CL-Vel_7V2_B


title: MM_CL-Vel_8C1_B


title: MM_CL-Vel_8C2_B


title: MM_CL-Vel_7C2_B


title: MM_CL-Vel_6V1_B


title: MM_CL-Vel_7C1_B


title: MM_CL-Vel_7V1_B


title: MM_CL-Vel_7C3_B


title: MM_CL-Vel_6C2_B


title: MM_CL-Vel_6V3_B


title: MM_CL-Vel_6C3_B


title: MM_CL-Vel_6C1_B


title: MM_CL-Vel_5V3_B


title: MM_CL-Vel_6V2_B


title: MM_CL-Vel_5V1_B


title: MM_CL-Vel_5V2_B


title: MM_CL-Vel_5C3_B


title: MM_CL-Vel_4C3_B


title: MM_CL-Vel_4V3_B


title: MM_CL-Vel_5C1_B


title: MM_CL-Vel_5C2_B


title: MM_CL-Vel_4V2_B


title: MM_CL-Vel_4C2_B


title: MM_CL-Vel_4V1_B


title: MM_CL-Vel_3V3_B


title: MM_CL-Vel_3V4_B


title: MM_CL-Vel_4C1_B


title: MM_CL-Vel_3C3_B


title: MM_CL-Vel_3V1_B


title: MM_CL-Vel_2C3_B


title: MM_CL-Vel_3C2_B


title: MM_CL-Vel_3C1_B


title: MM_CL-Vel_2C2_B


title: MM_CL-Vel_1V2_B


title: MM_CL-Vel_1V3_B


title: MM_CL-Vel_2C1_B


title: MM_CL-Vel_1C1_B


title: MM_CL-Vel_2V3_B


title: MM_CL-Vel_2V2_B


title: MM_CL-Vel_2V1_B


title: MM_CL-Vel_1C3_B


title: MM_CL-Vel_1C2_B


title: MM_CL-Vel_1V1_B


title: Glioblastoma  6

status: Public on Feb 13 2010

type: genomic

city: Heidelberg

first: Aurelie

last: Ernst

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

description: NCH 475 tumor

hyb_protocol: Hybridization was carried out in a GeneTAC Hybridization Station (Genomic Solutions, Oberhaching, Germany) for 36 hr at 37°C.

scan_protocol: We scanned hybridized microarrays at a 5-mm resolution and variable PMT voltage to obtain maximal signal intensities with <0.1% probe saturation,a count ratio of 0.8–1.2 (Cy3/Cy5), and maximal congruence of histogram curves, using a Gene-Pix 4000B microarray scanner (Axon Instruments)

data_processing: Data were filtered according to signal/background ratio (>3.0), mean/median spot intensity (<0.3), and replicate standard deviation (<0.25) and normalized by print-tip loess. To identify regions of similar genomic status within the array-CGH data, we applied the segmentation software GLAD. Imbalances with log2 ratios of less than -1.0 were scored as putative homozygous deletions, because this threshold corresponds to an average copy number of less than 1, suggesting the presence of at least one subpopulation of cells with homozygous deletions. Gains with log2 ratios higher than 1.0 were scored as amplifications.

molecule: genomic DNA

source_name: reference DNA from healthy donors

label_protocol: Tumor DNA or DNA from culture and reference  DNA from healthy donors were differentially labeled with Cy3-/ Cy5-conjugated dCTP by use of a BioPrime DNA Labeling Kit (Invitrogen, Karlsruhe, Germany).

extract_protocol: Extraction of high molecular weight DNA was performed via caesium chloride ultracentrifugation

value: normal reference

source_name: glioblastoma

value: glioblastoma


title: Glioblastoma  7

description: NCH 482 tumor


title: Glioblastoma spheroid culture 15

growth_protocol: Glioblastoma tissues were enzymatically dissociated and resuspended in stem-cell medium  made of DMEM/F-12 medium containing 20% BIT serum-free supplement, basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) at 20ng/ml each (all Provitro, Berlin, Germany)

treatment_protocol: No treatment

source_name: glioblastoma spheroid culture


title: Glioblastoma spheroid culture 18


title: Glioblastoma  1

description: NCH 421K tumor


title: Glioblastoma spheroid culture 16


title: Glioblastoma  2

description: NCH 441 tumor


title: Glioblastoma  4

description: NCH 465 tumor


title: Glioblastoma  5

description: NCH 468 tumor


title: Glioblastoma spheroid culture 19


title: MDCK-Late Passage-biological replicate2

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

hyb_protocol: Fifteen micrograms of cRNA was fragmented for hybridization to Affymetrix Canine Genome 2.0 Array GeneChips (Santa Clara, CA), which contains approximately 18,000 C. familiaris mRNA/EST-based transcripts and over 20,000 non-redundant predicted genes. Hybridization was done overnight at 45°C for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed with the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4_450 protocol

scan_protocol: Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.

data_processing: Expression intensity values were extracted from the raw image files using the Robust Multi-Array Average algorithm with the Affymetrix Expression ConsoleTM. Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set

organism: Canis lupus familiaris

source_name: Total RNA from late passage MDCK were plated on tissue culture flasks and allowed to polarize for four days

label_protocol: Complementary DNA and complemetary RNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in-vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: MDCK cells were obtained from the ATCC at passage number 55 (CCL-34) and were subcultured in MEM (ATCC) supplemented with 10% fetal bovine serum (Sigma) and an antibiotic/antimycotic (Invitrogen). Cells were cultured for 4-7 days before being re-seeded at 4-12 x 103 cells/cm2 in T25 culture flasks. Cells were maintained in humidified incubator at 37oC and 5% CO2 and were fed three times per week.

extract_protocol: Total RNA was isolated from biological triplicates of early and late passage MDCK from T25 flasks using a Ribopure kit (Ambion, Austin, TX). Acquired RNA was precipitated with EtOH and subsequently purified employing columns, procedures and reagents from an RNEasy kit (Qiagen, Germantown, MD) and resuspended in RNAse-free H2O provided.

treatment_protocol: Early and late passage MDCK from T25 flasks that had been seeded with 8 x 105 cells and allowed to become confluent and polarize over 4 days in culture cells

tag: species

value: Canine

tag: organ

value: Kidney

tag: cell line

value: Madin Darby Canine Kidney


title: MDCK-Early Passage-biological replicate3

source_name: Total RNA from early passage MDCK were plated on tissue culture flasks and allowed to polarize for four days

growth_protocol: MDCK cells were obtained from the ATCC at passage number 55 (CCL-34) and were subcultured in MEM (ATCC) supplemented with 10% fetal bovine serum (Sigma) and an antibiotic/antimycotic (Invitrogen).  Cells were cultured for 4-7 days before being re-seeded at 4-12 x 103 cells/cm2 in T25 culture flasks.  Cells were maintained in humidified incubator at 37oC and 5% CO2 and were fed three times per week.

extract_protocol: Total RNA was isolated from biological triplicates of early and late passage MDCK from T25 flasks using a Ribopure kit (Ambion, Austin, TX).  Acquired RNA was precipitated with EtOH and subsequently purified employing columns, procedures and reagents from an RNEasy kit (Qiagen, Germantown, MD) and resuspended in RNAse-free H2O provided.

treatment_protocol: Early and late passage MDCK from T25 flasks that had been seeded with 8 x 105  cells and allowed to become confluent and polarize over 4 days in culture cells


title: Glioblastoma spheroid culture 17


title: MDCK-Late Passage-biological replicate3


title: Glioblastoma  3

description: NCH 453 tumor


title: MDCK-Late Passage-biological replicate1


title: Glioblastoma spheroid culture 13


title: Glioblastoma spheroid culture 8


title: Glioblastoma spheroid culture 10


title: MDCK-Early Passage-biological replicate2


title: Glioblastoma spheroid culture 12


title: Glioblastoma spheroid culture 20


title: Glioblastoma spheroid culture 11


title: Glioblastoma spheroid culture 9


title: Glioblastoma spheroid culture 7


title: MDCK-Early Passage-biological replicate1


title: Glioblastoma spheroid culture 6


title: Glioblastoma spheroid culture 14


title: Glioblastoma spheroid culture 4


title: Glioblastoma spheroid culture 1 single sphere 2

description: NCH440 Spheroid 2


title: Glioblastoma spheroid culture 3


title: Glioblastoma spheroid culture 2 single sphere 1

description: NCH441 Spheroid 1


title: Glioblastoma spheroid culture 1 single sphere 3

description: NCH440 Spheroid 3


title: Glioblastoma spheroid culture 2


title: ProE Adult bone marrow, biological replicate 3

city: Toronto

first: Sasan

last: Zandi

state: Ontario

address: 101 college St

country: Canada

institute: UHN

description: Gene expression data from bone marrow of adult mice

hyb_protocol: RNA hybridized to MOE430_2. Chips according to manufacturer manual

scan_protocol: GeneChips were scanned using the GeneChipTM Scanner 3000

data_processing: Probe level expression values and normalization were calculated using RMAExpress and further analysis was done using dChip

source_name: ProE Mouse bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2000 cell

extract_protocol: total RNA extraction was performed with QIAGENE microRNeasy kit according to the manufacturer's instructions.

tag: strain


title: STHSC Adult bone marrow, biological replicate 1

source_name: STHSC Mouse bone marrow


title: ProB Adult bone marrow, biological replicate 2

source_name: ProB Mouse bone marrow


title: ProB Adult bone marrow, biological replicate 1


title: PreCFUE Adult bone marrow, biological replicate 1

source_name: PreCFUE Mouse bone marrow


title: Glioblastoma spheroid culture 1


title: STHSC Adult bone marrow, biological replicate 2


title: Glioblastoma cell line 8

growth_protocol: DMEM containing 10% serum

source_name: Glioblastoma cell line

value: female


title: PreCFUE Adult bone marrow, biological replicate 3


title: Glioblastoma spheroid culture 5


title: Glioblastoma spheroid culture 1 single sphere 1

description: NCH440 Spheroid 1


title: MkP Adult bone marrow, biological replicate 3

source_name: MkP Mouse bone marrow


title: PreB Adult bone marrow, biological replicate 4

source_name: PreB Mouse bone marrow


title: ProE Adult bone marrow, biological replicate 1


title: PreCFUE Adult bone marrow, biological replicate 2


title: ProE Adult bone marrow, biological replicate 2


title: PreB Adult bone marrow, biological replicate 1


title: Glioblastoma cell line 6

value: male


title: PreB Adult bone marrow, biological replicate 3


title: NKmature Adult bone marrow, biological replicate 2

source_name: NKmature Mouse bone marrow


title: MkP Adult bone marrow, biological replicate 2


title: NKmature Adult bone marrow, biological replicate 1


title: MkP Adult bone marrow, biological replicate 1


title: PreB Adult bone marrow, biological replicate 2


title: MkE Adult bone marrow, biological replicate 3

source_name: MkE Mouse bone marrow


title: Glioblastoma cell line 7


title: Serum grown culture 13 passage 25

description: NCH 468 adh p25

hyb_protocol: Hybridization was carried out in a GeneTAC Hybridization Station (Genomic Solutions, Oberhaching, Germany) for 36 hr at 378C.

data_processing: Data were filtered according to signal/background ratio (>3.0), mean/median spot intensity (<0.3), and replicate standard deviation (<0.25) and normalized by print-tip loess. To identify regions of similar genomic status within the array-CGH data, we applied the segmentation software GLAD. Imbalances with log2 ratios of less than -1.0 were scored as putative homozygous deletions, because this threshold corresponds to an average copy number of less than 1, suggesting the presence of at least one subpopulation of cells with homozygous deletions. Gains with log2 ratios higher than 1.0 were scored as amplifications. Chromosomal mapping information was based on Ensembl (v49) and position of candidate genes was verified using Ensembl v52. All data are available at the NCBI Gene Expression Omnibus database.

label_protocol: Cell-line DNA and reference  DNA from healthy donors were differentially labeled with Cy3-/ Cy5-conjugated dCTP by use of a BioPrime DNA Labeling Kit (Invitrogen, Karlsruhe, Germany).

growth_protocol: Glioblastoma tissues were enzymatically dissociated and resuspended in in DMEM containing 10% serum

source_name: glioblastoma adherent culture


title: Glioblastoma cell line 5


title: MkE Adult bone marrow, biological replicate 2


title: LMPP Adult bone marrow, biological replicate 5

source_name: LMPP Mouse bone marrow


title: Serum grown culture 12 passage 32

description: NCH 465 adh p32


title: Glioblastoma cell line 4


title: Glioblastoma cell line 3


title: LMPP Adult bone marrow, biological replicate 1


title: MkE Adult bone marrow, biological replicate 1


title: LMPP Adult bone marrow, biological replicate 2


title: MkE Adult bone marrow, biological replicate 4


title: Serum grown culture 13 passage 6

description: NCH 468 adh p6


title: LTHSC Adult bone marrow, biological replicate 1

source_name: LTHSC Mouse bone marrow


title: Glioblastoma cell line 2

source_name: reference DNA from healthy donors


title: LMPP Adult bone marrow, biological replicate 3


title: Serum grown culture 13 passage 15

description: NCH 468 adh p15


title: Serum grown culture 13 passage 4

description: NCH 468 adh p4


title: Glioblastoma cell line 1


title: Serum grown culture 13 passage 1

description: NCH 468 adh p1


title: LMPP Adult bone marrow, biological replicate 4


title: LTHSC Adult bone marrow, biological replicate 2


title: GMP Adult bone marrow, biological replicate 3

source_name: GMP Mouse bone marrow


title: Serum grown culture 10 passage 6

description: NCH 479 adh p6


title: Serum grown culture 9 passage 5

description: NCH 483 adh p5


title: Serum grown culture 11 passage 5

description: NCH 482 adh p5


title: Serum grown culture 12 passage 4

description: NCH 465 adh p4


title: Serum grown culture 6 passage 13

description: NCH 460 adh p13


title: Serum grown culture 5 passage 39

description: NCH 440 adh p39


title: Serum grown culture 7 passage 6

description: NCH 471 adh p6


title: Serum grown culture 8 passage 4

description: NCH 498 adh p4


title: IgM+SP Adult bone marrow, biological replicate 2

source_name: IgM+SP Mouse bone marrow


title: GMP Adult bone marrow, biological replicate 1


title: IgM+SP Adult bone marrow, biological replicate 1


title: Serum grown culture 5 passage 8

description: NCH 440 adh p8


title: GMP Adult bone marrow, biological replicate 2


title: GM Adult bone marrow, biological replicate 2

source_name: GM Mouse bone marrow


title: ETP Adult bone marrow, biological replicate 1

source_name: ETP Mouse bone marrow


title: Serum grown culture 12 passage 7

description: NCH 465 adh p7


title: ETP Adult bone marrow, biological replicate 2


title: Serum grown culture 5 passage 4

description: NCH 440 adh p4


title: GBM Spheroid culture 10

description: NCH441 Sph

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

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

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

source_name: primary glioblastoma

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

growth_protocol: Glioblastoma samples were enzymatically dissociated and resuspended in stem-cell medium made of DMEM/F-12 medium containing 20% BIT serum-free supplement, basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) at 20ng/ml each (all Provitro, Berlin, Germany)

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

tag: tissue

value: brain

tag: class

value: WHO IV


title: Reference normal brain 1

description: normal brain pool

source_name: non-neoplastic human brain tissue samples of 5 individuals (age range: 26–82)

value: non-neoplastic

value: normal


title: Reference normal brain 2

description: normal brain

source_name: non-neoplastic human brain tissue sample of 1 individual


title: ETP Adult bone marrow, biological replicate 3


title: GBM Spheroid culture 8

description: NCH481 Sph


title: GBM Spheroid culture 9

description: NCH498 Sph


title: GM Adult bone marrow, biological replicate 1


title: GBM Spheroid culture 7

description: NCH499 Sph


title: GBM Spheroid culture 5

description: NCH537 Sph


title: GBM Spheroid culture 6

description: NCH511 Sph


title: CLP Adult bone marrow, biological replicate 2

source_name: CLP Mouse bone marrow


title: Serum grown culture 4 passage 8

description: NCH 337 adh p8


title: Serum grown culture 5 passage 12

description: NCH 440 adh p12


title: Serum grown culture 3 passage 5

description: NCH 453 adh p5


title: Serum grown culture 2 passage 5

description: NCH 441 adh p5


title: Serum grown culture 2 passage 17

description: NCH 441 adh p17


title: Serum grown culture 1 passage 5

description: NCH 421K adh p5


title: GBM Spheroid culture 4

description: NCH475 Sph


title: GBM Spheroid culture 3

description: NCH525 Sph


title: CD4 Adult bone marrow, biological replicate 2

source_name: CD4 Mouse bone marrow


title: CLP Adult bone marrow, biological replicate 1


title: CFUE Adult bone marrow, biological replicate 2

source_name: CFUE Mouse bone marrow


title: CFUE Adult bone marrow, biological replicate 3


title: CD4 Adult bone marrow, biological replicate 1


title: CFUE Adult bone marrow, biological replicate 1


title: GBM Spheroid culture 2

description: NCH551b Sph

source_name: secondary glioblastoma


title: GBM Spheroid culture 1

description: NCH421k Sph


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11227. OD600: 0.465

status: Public on Feb 11 2010

first: Dan

last: Tenenbaum

institute: Institute for Systems Biology

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 0.465 in the presence of 20µg/ml uracil versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 2004 Jun;14(6):1025-35

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding.  see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details

label: Alexa 546

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:0.465 in the presence of 20µg/ml uracil, time:1200 min.

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 0.465 in the presence of 20µg/ml uracil.

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

label: Alexa 647

source_name: Halobacterium NRC-1 grown in standard growth media

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 reference sample.

value: Halobacterium NRC-1


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11232. OD600: 0.832

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 0.832 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:0.832 in the presence of 20µg/ml uracil, time:2280 min.

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 2004 Jun;14(6):1025-35

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 0.832 in the presence of 20µg/ml uracil.


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11233. OD600: 0.975

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 0.975 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:0.975 in the presence of 20µg/ml uracil, time:2760 min.

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 0.975 in the presence of 20µg/ml uracil.


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11234. OD600: 0.975

value: Halobacterium NRC-1 pyrF knockout strain


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11229. OD600: 0.755

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 0.755 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:0.755 in the presence of 20µg/ml uracil, time:1860 min.

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 0.755 in the presence of 20µg/ml uracil.


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11244. OD600: 0.830

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 0.830 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:0.830 in the presence of 20µg/ml uracil, time:2280 min.

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 0.830 in the presence of 20µg/ml uracil.


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11246. OD600: 0.970

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 0.970 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:0.970 in the presence of 20µg/ml uracil, time:2760 min.

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 0.970 in the presence of 20µg/ml uracil.


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11245. OD600: 0.970


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11226. OD600: 0.197

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 0.197 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:0.197 in the presence of 20µg/ml uracil, time:0690 min.

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 0.197 in the presence of 20µg/ml uracil.


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11240. OD600: 0.467

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 0.467 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:0.467 in the presence of 20µg/ml uracil, time:1200 min.

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 0.467 in the presence of 20µg/ml uracil.


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11231. OD600: 0.832


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11235. OD600: 1.136

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 1.136 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:1.136 in the presence of 20µg/ml uracil, time:3120 min.

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 1.136 in the presence of 20µg/ml uracil.


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11236. OD600: 1.136


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11248. OD600: 1.147

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 1.147 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:1.147 in the presence of 20µg/ml uracil, time:3120 min.

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 1.147 in the presence of 20µg/ml uracil.


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11228. OD600: 0.465


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11247. OD600: 1.147


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11249. OD600: 0.830


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11242. OD600: 0.756

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 0.756 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:0.756 in the presence of 20µg/ml uracil, time:1860 min.

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 0.756 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11267. OD600: 1.039

description: Halobacterium grown in standard media with added uracil to an OD600 1.039 in the presence of 20µg/ml uracil versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res .2004 Jun;14(6):1025-35

source_name: Halobacterium NRC-1, OD:1.039 in the presence of 20µg/ml uracil, time:2760 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 1.039 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11265. OD600: 0.876

description: Halobacterium grown in standard media with added uracil to an OD600 0.876 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:0.876 in the presence of 20µg/ml uracil, time:2280 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 0.876 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11266. OD600: 1.039


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11243. OD600: 0.756


title: Halobacterium growth with added uracil. Array 11264. OD600: 0.876


title: Halobacterium growth with added uracil. Array 11269. OD600: 1.341

description: Halobacterium grown in standard media with added uracil to an OD600 1.341 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:1.341 in the presence of 20µg/ml uracil, time:3120 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 1.341 in the presence of 20µg/ml uracil.


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11230. OD600: 0.755


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11241. OD600: 0.467


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11238. OD600: 0.200

description: Halobacterium pyrF knockout strain grown in standard media with added uracil to an OD600 0.200 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1 pyrF knockout strain, OD:0.200 in the presence of 20µg/ml uracil, time:0690 min.

growth_protocol: Halobacterium pyrF knockout strain grown in standard growth media with 20µg/ml uracil to an OD600 of 0.200 in the presence of 20µg/ml uracil.


title: Halobacterium pyrF knockout strain growth with added uracil. Array 11239. OD600: 0.200


title: Halobacterium growth with added uracil. Array 11268. OD600: 1.341


title: Halobacterium growth with added uracil. Array 11263. OD600: 0.882

description: Halobacterium grown in standard media with added uracil to an OD600 0.882 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:0.882 in the presence of 20µg/ml uracil, time:1860 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 0.882 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11262. OD600: 0.882


title: Halobacterium growth with added uracil. Array 11259. OD600: 0.440

description: Halobacterium grown in standard media with added uracil to an OD600 0.440 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:0.440 in the presence of 20µg/ml uracil, time:0890 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 0.440 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11256. OD600: 0.200

description: Halobacterium grown in standard media with added uracil to an OD600 0.200 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:0.200 in the presence of 20µg/ml uracil, time:0540 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 0.200 in the presence of 20µg/ml uracil.

source_name: Halobacterium NRC-1 grown in standard growth media

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 reference sample.


title: Halobacterium growth with added uracil. Array 11261. OD600: 0.785

description: Halobacterium grown in standard media with added uracil to an OD600 0.785 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:0.785 in the presence of 20µg/ml uracil, time:1260 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 0.785 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11285. OD600: 1.133

description: Halobacterium grown in standard media with added uracil to an OD600 1.133 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:1.133 in the presence of 20µg/ml uracil, time:2760 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 1.133 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11257. OD600: 0.200


title: Halobacterium growth with added uracil. Array 11283. OD600: 1.133


title: Halobacterium growth with added uracil. Array 11258. OD600: 0.440


title: Halobacterium growth with added uracil. Array 11277. OD600: 0.912

description: Halobacterium grown in standard media with added uracil to an OD600 0.912 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:0.912 in the presence of 20µg/ml uracil, time:1860 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 0.912 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11260. OD600: 0.785


title: Halobacterium growth with added uracil. Array 11279. OD600: 0.881

description: Halobacterium grown in standard media with added uracil to an OD600 0.881 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:0.881 in the presence of 20µg/ml uracil, time:2280 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 0.881 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11271. OD600: 0.205

description: Halobacterium grown in standard media with added uracil to an OD600 0.205 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:0.205 in the presence of 20µg/ml uracil, time:0540 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 0.205 in the presence of 20µg/ml uracil.


title: Halobacterium growth. Array 11323. OD600: 1.086

description: Halobacterium grown in standard media to an OD600 1.086 versus standard reference.

source_name: Halobacterium NRC-1, OD:1.086, time:3120 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 1.086.

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with AgilentBioanalyzer to verify integrity, and in the spectrophotometer for quantification.


title: Halobacterium growth with added uracil. Array 11273. OD600: 0.420

description: Halobacterium grown in standard media with added uracil to an OD600 0.420 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:0.420 in the presence of 20µg/ml uracil, time:0890 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 0.420 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11287. OD600: 1.296

description: Halobacterium grown in standard media with added uracil to an OD600 1.296 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:1.296 in the presence of 20µg/ml uracil, time:3120 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 1.296 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11275. OD600: 0.812

description: Halobacterium grown in standard media with added uracil to an OD600 0.812 in the presence of 20µg/ml uracil versus standard reference.

source_name: Halobacterium NRC-1, OD:0.812 in the presence of 20µg/ml uracil, time:1260 min.

growth_protocol: Halobacterium grown in standard growth media with 20µg/ml uracil to an OD600 of 0.812 in the presence of 20µg/ml uracil.


title: Halobacterium growth with added uracil. Array 11278. OD600: 0.881


title: Halobacterium growth with added uracil. Array 11274. OD600: 0.812


title: Halobacterium growth with added uracil. Array 11272. OD600: 0.420


title: Halobacterium growth with added uracil. Array 11276. OD600: 0.912


title: Halobacterium growth. Array 11320. OD600: 0.913

description: Halobacterium grown in standard media to an OD600 0.913 versus standard reference.

source_name: Halobacterium NRC-1, OD:0.913, time:2760 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 0.913.


title: Halobacterium growth with added uracil. Array 11270. OD600: 0.205


title: Halobacterium growth. Array 11322. OD600: 1.086


title: Halobacterium growth. Array 11321. OD600: 0.913


title: Halobacterium growth. Array 11319. OD600: 0.764

description: Halobacterium grown in standard media to an OD600 0.764 versus standard reference.

source_name: Halobacterium NRC-1, OD:0.764, time:2280 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 0.764.


title: Halobacterium growth. Array 11318. OD600: 0.764


title: Halobacterium growth. Array 11309. OD600: 0.733

description: Halobacterium grown in standard media to an OD600 0.733 versus standard reference.

source_name: Halobacterium NRC-1, OD:0.733, time:1860 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 0.733.


title: Halobacterium growth. Array 11308. OD600: 0.733


title: Halobacterium growth. Array 11304. OD600: 0.468

description: Halobacterium grown in standard media to an OD600 0.468 versus standard reference.

source_name: Halobacterium NRC-1, OD:0.468, time:0890 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 0.468.


title: Halobacterium growth. Array 11069. OD600: 0.830

description: Halobacterium grown in standard media to an OD600 0.830 versus standard reference.

source_name: Halobacterium NRC-1, OD:0.830, time:1260 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 0.830.


title: Halobacterium growth. Array 11307. OD600: 0.830


title: Halobacterium growth. Array 11298. OD600: 0.913


title: Halobacterium growth. Array 11303. OD600: 0.220

description: Halobacterium grown in standard media to an OD600 0.220 versus standard reference.

source_name: Halobacterium NRC-1, OD:0.220, time:0540 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 0.220.


title: Halobacterium growth. Array 11305. OD600: 0.468


title: Halobacterium growth. Array 11299. OD600: 0.913


title: Halobacterium growth. Array 11302. OD600: 0.220


title: Halobacterium growth. Array 11300. OD600: 1.023

description: Halobacterium grown in standard media to an OD600 1.023 versus standard reference.

source_name: Halobacterium NRC-1, OD:1.023, time:3120 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 1.023.


title: Halobacterium growth. Array 11296. OD600: 0.781

description: Halobacterium grown in standard media to an OD600 0.781 versus standard reference.

source_name: Halobacterium NRC-1, OD:0.781, time:2280 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 0.781.

source_name: Halobacterium NRC-1 grown in standard growth media

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 reference sample.


title: Halobacterium growth with added uracil. Array 11286. OD600: 1.296


title: Halobacterium growth. Array 11295. OD600: 0.758

description: Halobacterium grown in standard media to an OD600 0.758 versus standard reference.

source_name: Halobacterium NRC-1, OD:0.758, time:1860 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 0.758.


title: Halobacterium growth. Array 11301. OD600: 1.023


title: Halobacterium growth. Array 11297. OD600: 0.781


title: Halobacterium growth. Array 11291. OD600: 0.496

description: Halobacterium grown in standard media to an OD600 0.496 versus standard reference.

source_name: Halobacterium NRC-1, OD:0.496, time:0890 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 0.496.


title: Halobacterium growth. Array 11292. OD600: 0.807

description: Halobacterium grown in standard media to an OD600 0.807 versus standard reference.

source_name: Halobacterium NRC-1, OD:0.807, time:1260 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 0.807.


title: Halobacterium growth. Array 11293. OD600: 0.807


title: Halobacterium growth. Array 11294. OD600: 0.758


title: Halobacterium growth. Array 11290. OD600: 0.496


title: Halobacterium growth. Array 11289. OD600: 0.225

description: Halobacterium grown in standard media to an OD600 0.225 versus standard reference.

source_name: Halobacterium NRC-1, OD:0.225, time:0540 min.

growth_protocol: Halobacterium grown in standard growth media to an OD600 of 0.225.


title: Patient 65 diet period 1

first: Jennifer

last: Goldsby

address: 112 Cater-Mattil

department: Nutrition and Food Sciences

hyb_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf except for using Alexa Fluor 647 instead of Cy5.

scan_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/application_notes/63005079.pdf

data_processing: Median normalized values derived from CodeLink Expression Analysis Version 6.0

molecule: polyA RNA

source_name: stool RNA American control diet

label_protocol: Ambion MessageAmp II aRNA Amplification and Biotin Enhanced kits:  Manual Labelled cRNA Target preparation following manufacturer's instructions http://www.ambion.com/techlib/prot/fm_1751.pdf and http://www.ambion.com/techlib/prot/fm_1791.pdf

extract_protocol: PolyA RNA was extracted from stool samples following the protocol published in Biomarkers, 2003, Jan-Feb;8(1):51-61.

tag: sex

tag: insulin resistance

value: positive

tag: polyps

value: negative

tag: sample

value: stool


title: Patient 54 baseline 2

source_name: stool RNA baseline


title: Halobacterium growth. Array 11288. OD600: 0.225


title: Patient 65 diet period 2

source_name: stool RNA legume diet


title: Patient 49 baseline 1


title: Patient 54 diet period 1


title: Patient 65 baseline 2


title: Patient 47 baseline 1


title: Patient 47 diet period 1


title: Patient 49 diet period 2


title: Patient 27 diet period 1


title: Patient 44 diet period 1


title: Patient 33 baseline 1


title: Patient 65 baseline 1


title: Patient 33 diet period 2


title: Patient 54 baseline 1


title: Patient 47 diet period 2


title: Patient 33 diet period 1


title: Patient 49 diet period 1


title: Patient 44 diet period 2


title: Patient 27 diet period 2


title: Patient 27 baseline 2


title: Patient 26 diet period 2


title: Patient 27 baseline 1


title: Patient 47 baseline 2


title: Patient 26 baseline 2


title: Patient 26 diet period 1


title: Patient 24 diet period 1


title: Patient 44 baseline 1


title: Patient 26 baseline 1


title: Patient 24 diet period 2


title: Patient 24 baseline 1


title: Patient 19 baseline 1


title: Patient 19 baseline 2


title: Patient 18 baseline 2


title: Patient 18 baseline 1


title: Patient 14 baseline 2


title: Patient 14 diet period 1


title: Patient 18 diet period 1


title: Patient 19 diet period 2


title: Patient 19 diet period 1


title: Patient 14 baseline 1


title: Patient 11 diet period 2


title: Patient 18 diet period 2


title: Patient 10 diet period 2


title: Patient 11 baseline 1


title: Patient 9 diet period 2


title: Patient 13 diet period 1


title: Patient 13 diet period 2


title: Patient 10 diet period 1


title: Patient 13 baseline 1


title: Patient 9 baseline 1


title: Patient 11 baseline 2


title: Patient 11 diet period 1


title: Patient 10 baseline 1


title: Patient 14 diet period 2


title: Patient 9 diet period 1


title: Patient 8 diet period 2


title: Patient 8 baseline 2


title: Patient 9 baseline 2


title: Patient 8 baseline 1


title: Patient 6 baseline 2


title: Patient 5 baseline 2


title: Patient 5 baseline 1


title: Patient 6 baseline 1


title: Patient 4 baseline 2


title: Patient 8 diet period 1


title: Patient 5 diet period 2


title: Patient 6 diet period 1


title: Patient 5 diet period 1


title: Patient 6 diet period 2


title: Patient 3 diet period 1


title: Patient 3 baseline 1


title: Patient 4 diet period 1


title: Patient 1 diet period 1


title: Patient 2 diet period 1


title: Patient 2 diet period 2


title: Patient 3 baseline 2


title: Patient 2 baseline 1


title: Patient 4 baseline 1


title: Patient 3 diet period 2


title: Patient 1 baseline 1


title: Patient 4 diet period 2


title: Patient 1 baseline 2


title: Patient 2 baseline 2


title: Patient 1 diet period 2


title: fetal colon adult  wt vs. Spdef ko 2 dyeswap

status: Public on Feb 10 2010

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using Feature Extraction (V.9.5.3, Agilent Technologies). All data analyses were performed using ArrayAssist (5.5.1, Stratagene) and Microsoft Excel (Microsoft Corporation). Raw signal intensities were corrected by subtracting local background. Negative values were changed into a positive value close to zero (standard deviation of the local background) in order to allow calculation of ratios between intensities for features only present in one sample (wt or Spdef-/-). Data were filtered if both (wt or Spdef-/-) intensities were changed or if both intensities were less than two times the background signal and normalized with a LOESS algorithm.

source_name: fetal colon wt

label_protocol: 500 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

extract_protocol: Total RNA was isolated from dissected whole small intestines or colons using TRIzol Reagent (Invitrogen, Carlsbad, CA). Pooled total RNA from 2-3 littermates were utilized for each experiment.

treatment_protocol: Tissue from wildtype and Spdef knockout mice were used for the study

value: colon

tag: developmental stage

value: fetal

tag: genotype

value: wildtype mouse

source_name: fetal colon Spdef ko

value: Spdef ko mouse


title: Expression profiling of P. stutzeri A1501 treated with 20mM ammonia shock for 10 min-2

type: mixed

city: Beijing

first: yongliang

last: yan

address: zhongguancun south 12th

country: China

institute: CAAS

hyb_protocol: Labeled cDNA/DNA was purified using QIAquick columns and mixed with 50× Denharts; 20× SSC; yeast tRNA 24 μg; 1 mM HEPES, 10% SDS, the mixture was heated at 100 °C for 2 min and cooled to room temperature and applied to the array slides under glass coverslips. Hybridization was performed at 65°C overnight in a Micro hybridization incubator (Robbins Scientific; Sunnyvale, CA).

scan_protocol: GenePix 6.0 software (Axon Instruments, Inc.) was used for image analysis and data visualization.

data_processing:
First, the signals were normalized using with the GenePix 6.0 software and then with a locally weighted scatterplot smoothing regression (LOWESS) algorithm in the MIDAS software package.
Genes were considered to be differentially expressed if (i) average expression changed by at least 2-fold in three independent experiments performed with triplicate RNA samples or (ii) the change in gene expression was in the same direction (“increased” or “decreased”) in three experiments.

organism: Stutzerimonas stutzeri A1501

source_name: Genomic DNA of P. stutzeri A1501

label_protocol: The genomic DNA were then fluorescently labeled using BioPrime DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. The genomic DNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy3-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.

extract_protocol: The genomic DNA was extracted as the Protocol from the TIANamp Bacteria DNA kit from TIANGEN BIOTECH (BEIJING) CO., LTD

source_name: The cDNA of P. stutzeri A1501 - treated

label_protocol: The cDNA were then fluorescently labeled using BioPrime DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. The cDNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy5-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.

extract_protocol: The total RNA was extracted as the Protocol from the SV Total RNA Isolation System (Promega)

treatment_protocol: The bacterium was treated with 0.1 mM ammonia and 0.5% Oxygen tension until the nitrogenase activity was detectable. Then the cells were sudden shifted from the nitrogen fixation conditions to the ammonia repression conditions by addition of 20 mM ammonia for 10min. Subsequently, the bacterium was collected and began the RNA extraction process.


title: Expression profiling of P. stutzeri A1501 treated with 20mM ammonia shock for 10 min-3


title: Expression profiling of P. stutzeri A1501 treated with 20mM ammonia shock for 10 min-1


title: fetal colon adult  wt vs. Spdef ko 1 dyeswap


title: adult colon wt vs. Spdef ko 3 dyeswap

source_name: adult colon wt

value: adult

source_name: adult colon Spdef ko


title: fetal colon adult  wt vs. Spdef ko 2


title: adult colon wt vs. Spdef ko 3


title: fetal smal intestine wt vs. Spdef ko 3 dyeswap

source_name: fetal small intestine wt

value: small intestine

source_name: fetal small intestine Spdef ko


title: fetal smal intestine wt vs. Spdef ko 2 dyeswap


title: adult colon wt vs. Spdef ko 1


title: fetal colon adult wt vs. Spdef ko 1


title: fetal smal intestine wt vs. Spdef ko 3


title: Arabidopsis_seedlings_Col_BR_DL_rep_2

city: Shang Hai

first: Li

last: Song

address: FengLin Road

institute: SIPPE

description: wild type grown in dark treated with BR then 2 hours light response

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Affy GeneChip Scanner 3000.

data_processing: The data normalized using MAS5.0 methods were analyzed parallel in order to improve the stability of Statistical Analysis (Smyth, 2004). Genes with absent for the detection value in the baseline data and decrease (or increase) for the change value were excluded from the list, only those regulated in both repeats were selected for further analysis. And linear statistical model in Limma package (Smyth et al., 2005) from Bioconductor was used to identify significant differently expressed genes between two groups.

organism: Arabidopsis thaliana

source_name: seedlings

label_protocol: Standard Affymetrix Protocol

extract_protocol: Triazol

tag: treatment


title: adult smal intestine wt vs. Spdef ko 2

source_name: adult small intestine Spdef ko

source_name: adult small intestine wt


title: Arabidopsis_seedlings_Col_BL_rep_2

description: wild type grown in dark treated with BR

value: grown in dark treated with BR


title: Arabidopsis_seedlings_Col_DL_rep_2

description: wild type grown in dark then 2 hours light response


title: adult smal intestine wt vs. Spdef ko 2 dyeswap


title: Arabidopsis_seedlings_Col_BR_DL_rep_1

value: grown in dark treated with BR then 2 hours light response


title: adult colon wt vs. Spdef ko 1 dyeswap


title: Arabidopsis_seedlings_Col_rep_2

description: wild type grown in dark

value: grown in dark


title: Arabidopsis_seedling_Col_rep_1

description: wild type grown in dark

source_name: Col seedling

value: 7 days


title: Arabidopsis_seedlings_Col_DL_rep_1

value: grown in dark then 2 hours light response


title: adult colon wt vs. Spdef ko 2


title: adult colon wt vs. Spdef ko 2 dyeswap


title: fetal smal intestine wt vs. Spdef ko 1 dyeswap


title: fetal smal intestine wt vs. Spdef ko 2


title: Arabidopsis_seedlings_Col_BL_rep_1

description: wild type grown in dark treated with BR


title: fetal smal intestine wt vs. Spdef ko 1


title: Patient 24 baseline 2

value: male


title: adult smal intestine wt vs. Spdef ko 1


title: hippocampus_31_7H

status: Public on Feb 09 2010

city: Sao Paulo

first: Oswaldo

middle: Keith

last: Okamoto

state: SP

address: R. Botucatu, 862.

department: Neurology

country: Brazil

institute: UNIFESP

hyb_protocol: As described in the manufacturer's protocol.

scan_protocol: Fluorescence was measured using an Axon GenePix 4000B Scanner (Axon Instruments Inc, Sunnyvale, CA).

data_processing: Data were normalized with the CodeLink Software v.2.3 (GE Healthcare, Piscataway, NJ).

label: Cyanine-5 dye

organism: Rattus norvegicus

source_name: pilocarpine, 7 days post-SE

extract_protocol: Manufacturer’s protocol

value: brain

value: hippocampus


title: adult smal intestine wt vs. Spdef ko 1 dyeswap


title: hippocampus_26_CONTR

source_name: saline-treated, 3 day control

label_protocol: As described in the manufacturer's protocol.


title: hippocampus_35_7H


title: hippocampus_42_CR

source_name: pilocarpine, immediate


title: hippocampus_43_CR


title: hippocampus_33_7H


title: hippocampus_13_3H

source_name: pilocarpine, 3 days post-SE


title: hippocampus_44_CR


title: hippocampus_12_3H


title: hippocampus_34_7H


title: hippocampus_15_3H


title: hippocampus_47_CONTR

source_name: saline-treated, immediate control


title: hippocampus_45_CR


title: hippocampus_32_7H


title: hippocampus_41_CR


title: Pancreatic islets_DCD_8

city: Madison

first: Jamie

last: Sperger

state: WI

address: 1111 Highland Ave.  RM 5168

department: Department of Surgery

institute: University of Wisconsin - Madison

description: Biological replicate 8 of 9.

hyb_protocol: After purification, 1.65 ug of cRNA was fragmented and hybridized to the array for 17 hr. at 65 C.  Microarray slides were hybridized overnight, then washed.

scan_protocol: Microarray slides were scanned with Agilent G2565CA Microarray Scanner. Images were analyzed with Feature Extraction 9.5.3 or Feature Extraction 10.1 (Agilent Technologies, CA).

data_processing: Data was processed using the Genesifter software package.  Data were normalized using median normalization.  Pairwise analysis (t-test with cutoff of 0.05 and fold change cutoff of 2) were done to determine list of differentially expressed genes.

source_name: Pancreatic islets, DCD

label_protocol: Approximately 500 ng of total RNA was amplified and labeled with Cy3 using the Quick Amp Labeling Kit, One Color (Agilent Technologies, CA). This labeling reaction produces 0.25 – 2.0 µg of Cy3-labeled cRNA (anti-sense), by first Converting mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT and then amplifying the sample using T7 RNA Polymerase in the presence of Cy3-CTP.

growth_protocol: Pancreatic islets were isolated from DCD or DBD donors.

extract_protocol: Islets (2000 – 4000 IEQ) were pelleted by centrifugation, washed in PBS, resuspended in 1 mL Trizol (Invitrogen, Carlsbad, CA) and RNA purified following manufacturer’s instructions.   RNA was further purified using the Qiagen RNeasy Kit (Qiagen, Germantown, MD) including the on-column DNase digestion step.  The concentration of the samples was determined using the NanoDrop® ND-1000 UV-Vis Spectrophotometer. RNA samples were analyzed by the FGC using an Agilent 2100 Bioanalyzer Lab-On-A-Chip Agilent 6000 Series II chip to determine the integrity of the samples. The RNA was of high quality and all samples passed our QC cutoff.

treatment_protocol: Islets were isolated using a modification of the automated Ricordi method. In brief, Collagenase NB1, Neutral Protease (Serva Electrophoresis, Heidelberg, Germany) and DNase (RocheApplied-Sciences, Inc., Indianapolis, IN) in Hanks’ balanced salt solution were infused manually into the main pancreatic duct. The Ricordi chamber was shaken manually and islets purified by centrifugation on a continuous biocoll gradient (Biochrom AG, Berlin, Germany) in a COBE 2991 cell processor (Lakewood, CO).  For islet equivalent (IEQ) determination, islet samples were stained with dithizone (Sigma-Aldrich) and sized using an eyepiece reticle and inverted microscope.  The calculation of purity was based on the ratio of dithizone positive (islets) compared to dithizone negative (acinar) elements.  Islets were cultured in M1A Media (Mediatech, Herndon, VA) supplemented with reduced glutathione (Sigma-Aldrich) at 25oC in a 5% CO2/95% air incubator.

tag: donation time

value: after cardiac death

value: pancreatic islets

tag: cold ischemia time

value: 607 min

tag: bmi


title: Pancreatic islets_DBD_10

description: Biological replicate 10 of 10.

source_name: Pancreatic islets, DBD

value: after brain death

value: 578 min

tag: gender

value: female

tag: age


title: Pancreatic islets_DCD_9

description: Biological replicate 9 of 9.

value: 600 min


title: Pancreatic islets_DBD_7

description: Biological replicate 7 of 10.

value: 551 min


title: hippocampus_36_CONTR

source_name: saline-treated, 7 day control


title: Pancreatic islets_DBD_9

description: Biological replicate 9 of 10.

value: 660 min


title: Pancreatic islets_DBD_6

description: Biological replicate 6 of 10.

value: 528 min


title: Pancreatic islets_DCD_5

description: Biological replicate 5 of 9.

value: 298 min


title: hippocampus_14_3H


title: Pancreatic islets_DCD_7

description: Biological replicate 7 of 9.

value: 623 min


title: Pancreatic islets_DBD_8

description: Biological replicate 8 of 10.

value: 586 min


title: hippocampus_11_3H


title: Pancreatic islets_DCD_6

description: Biological replicate 6 of 9.

value: 362 min


title: Pancreatic islets_DBD_5

description: Biological replicate 5 of 10.

value: 634 min

value: male


title: Pancreatic islets_DCD_3

description: Biological replicate 3 of 9.

data_processing: Data was processed using the Genesifter software package.  Data were normalized using median normalization.  Pairwise analysis (t-test with cutoff of 0.05 and fold change cutoff of 2) were done to determine the list of differentially expressed genes.

value: 424 min


title: Pancreatic islets_DBD_2

description: Biological replicate 2 of 10.

value: 150 min


title: Pancreatic islets_DCD_2

description: Biological replicate 2 of 9.

value: after cardiac death

value: pancreatic islets

value: 192 min


title: Pancreatic islets_DCD_1

description: Biological replicate 1 of 9.

value: 360 min


title: Pancreatic islets_DBD_1

description: Biological replicate 1 of 10.

value: after brain death

value: 415 min


title: Pancreatic islets_DCD_4

description: Biological replicate 4 of 9.

value: 328 min

value: female


title: cell line: U266 - ch128.1Av - 24h - rep2

city: Los Angeles

first: Manuel

last: Penichet

state: CA

institute: University of California, Los Angeles

description:
Time course experiment
Replicate 2/2
U266AT24R2

hyb_protocol: Illumina HumanRef-8 V2 BeadChips were hybridized, washed, stained and scanned according to Illumina’s protocol using the updated wash procedure

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

data_processing: Data was extracted with Illumina BeadStudio software.

source_name: cell line: U266 (tolerant) - ch128.1Av - 24h - rep2

label_protocol: Illumina protocol

growth_protocol: Cells were grown in 24-well plates under tissue culture conditions (37ºC and 5%CO2)

extract_protocol: RNA isolation as previously described (Pattenden et al., EMBO (2002) 21: 1978). Targets were prepared from 200 ng total RNA using Illumina. TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791).

treatment_protocol:
Treatment with ch128.1Av
2x10e5 IM-9 and cell line: U266 (tolerant) were incubated in 24-well plates under tissue culture conditions (37ºC and 5%CO2) with 10 nM ch128.1Av or buffer for 1h, 3h, 9h, and 24h

value: U266 (tolerant)


title: cell line: U266 - ch128.1Av - 24h - rep1

description:
Time course experiment
Replicate 1/2
U266AT24R1

source_name: cell line: U266 (tolerant) - ch128.1Av - 24h - rep1


title: cell line: U266 - ch128.1Av - 3h - rep2

description:
Time course experiment
Replicate 2/2
U266AT3R2

source_name: cell line: U266 (tolerant) - ch128.1Av - 3h - rep2


title: cell line: U266 - Control - 3h - rep1

description:
Time course experiment
Replicate 1/2
U266CT3R1

source_name: cell line: U266 (tolerant) - Control - 3h - rep1

treatment_protocol:
No treatment
2x10e5 IM-9 and cell line: U266 (tolerant) were incubated in 24-well plates under tissue culture conditions (37ºC and 5%CO2) with 10 nM ch128.1Av or buffer for 1h, 3h, 9h, and 24h


title: cell line: U266 - ch128.1Av - 1h - rep3

description:
Time course experiment
Replicate 3/3
U266AT1R3

source_name: cell line: U266 (tolerant) - ch128.1Av - 1h - rep3


title: cell line: U266 - ch128.1Av - 1h - rep1

description:
Time course experiment
Replicate 1/3
U266AT1R1

source_name: cell line: U266 (tolerant) - ch128.1Av - 1h - rep1


title: cell line: U266 - Control - 1h - rep2

description:
Time course experiment
Replicate 2/2
U266CT1R2

source_name: cell line: U266 (tolerant) - Control - 1h - rep2


title: cell line: U266 - ch128.1Av - 9h - rep3

description:
Time course experiment
Replicate 3/3
U266AT9R3

source_name: cell line: U266 (tolerant) - ch128.1Av - 9h - rep3