title: MEF Med23-/- (KO) cells 20% serum stimulated Set 2

treatment_protocol: Starved 16 h in 0.5% FBS DMEM and then stimulated with 20% FBS for 30 minutes, then total RNA harvested (see below). Second replicate.


title: Halobacterium salinarum at OD=0.58, t=1200 min., Array 07303

status: Public on Apr 14 2009

type: RNA

city: Seattle

first: Dan

last: Tenenbaum

state: WA

country: USA

institute: Institute for Systems Biology

description: Cells incubated under entrainment conditions

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. The arrays are 75th percentile normalized between channels on each array. Taking ratios to the common reference RNA serves as a means of normalization to compare across arrays.

molecule: total RNA

organism: Halobacterium salinarum

source_name: Halobacterium salinarum

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

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.

tag: od

tag: time

source_name: Halobacterium standard reference sample

tag: sample

value: standard Halobacterium standard reference sample

tag: media

value: CM


title: Rat SSC GDNF 4hr Replacement Rep1

city: Philadelphia

first: Jonathan

middle: A

last: Schmidt

state: PA

address: 3850 Baltimore Avenue

institute: University of Pennsylvania

description: Rat SSC GDNF 4hr Replacement Rep1

hyb_protocol: The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays.  Each sample (n=15) was hybridized to its own array.  Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.

scan_protocol: The average signal from two sequential scans was calculated for each microarray.  For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes.  The default values were provided by Affymetrix and were applied to all analysis parameters.  For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed.  The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector.  Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features.  The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.

data_processing: For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm.  The newly generated probeset signal values were exported into GeneSpring (Agilent).  Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis.  The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed.  In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets).  This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation.  To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets).  Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).

label: biotin

organism: Rattus norvegicus

source_name: Rat SSC GDNF 4hr Replacement

label_protocol: 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter.  Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF.  After 1 month of culture, which included self-renewal expansion, treatments were applied.

extract_protocol: Trizol + RNeasy Column

treatment_protocol: Cultured rat SSCs were subjected to 1 of 5 treatments.  Each treatment was replicated 3 times with independent cultures.  Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.

tag: cell type

value: Cultured spermatogonial stem cells


title: Halobacterium salinarum at OD=0.58, t=1200 min., Array 07370

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


title: Halobacterium salinarum at OD=0.64, t=720 min., Array 07301


title: MEF wt cells 20% serum stimulated Set 2

city: Berkeley

first: Michael

middle: Andrew

last: Balamotis

state: CA

address: 1 Cycotron Rd. Bld. 84

department: Life Sciences

institute: Lawrence Berkeley National Lab

hyb_protocol: UCLA Microarray Core

scan_protocol: UCLA Microarray Core

organism: Mus musculus

source_name: Mouse embryonic fibroblasts (E11) passaged through crisis, cultured

label_protocol: UCLA Microarray Core

extract_protocol: Trizol and Qiagen column purification

tag: strain

value: WT


title: Rat SSC GDNF 8hr Replacement Rep1

description: Rat SSC GDNF 8hr Replacement Rep1

source_name: Rat SSC GDNF 8hr Replacement


title: MEF wt cells 20% serum stimulated Set 1

treatment_protocol: Starved 16 h in 0.5% FBS DMEM and then stimulated with 20% FBS for 30 minutes, then total RNA harvested (see below). First replicate.


title: Rat SSC GDNF 2hr Replacement Rep3

description: Rat SSC GDNF 2hr Replacement Rep3

source_name: Rat SSC GDNF 2hr Replacement


title: MEF Med23-/- (KO) cells serum starved 16 h Set 2

source_name: Mouse Med23 -/- embryonic fibroblasts (E11) passaged through crisis, cultured

extract_protocol: Trizol and Qiagen RNeasy column purification.

treatment_protocol: Starved 16 h in 0.5% FBS DMEM and then total RNA harvested (see below). Second replicate.


title: Rat SSC GDNF 2hr Replacement Rep2

description: Rat SSC GDNF 2hr Replacement Rep2


title: Halobacterium salinarum at OD=0.69, t=480 min., Array 07300


title: Halobacterium salinarum at OD=0.64, t=720 min., Array 07263


title: MEF wt cells serum starved 16 h Set 2


title: Halobacterium salinarum at OD=0.61, t=960 min., Array 07264


title: MEF Med23-/- (KO) cells serum starved 16 h Set 1

treatment_protocol: Starved 16 h in 0.5% FBS DMEM and then total RNA harvested (see below). First replicate.


title: Halobacterium salinarum at OD=0.66, t=240 min., Array 07299


title: Rat SSC GDNF Control Rep2

description: Rat SSC GDNF Control Rep2

source_name: Rat SSC + GDNF


title: Rat SSC GDNF Withdrawal Rep1

description: Rat SSC GDNF Withdrawal Rep1

source_name: Rat SSC GDNF Withdrawal


title: MEF wt cells serum starved 16 h Set 1


title: Halobacterium salinarum at OD=0.63, t=0 min., Array 07366

value: 0 min.


title: Rat SSC GDNF 2hr Replacement Rep1

description: Rat SSC GDNF 2hr Replacement Rep1


title: Control_rep13

status: Public on Apr 13 2009

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

description:
control_13
Gene expression data from Control_rep13

hyb_protocol: per Affymetrix

scan_protocol: per Affymetrix

data_processing: Preprocessing of Affymetrix array data was performed in the R/Bioconductor package Affy. The raw Affymetrix Perfect Match probes were normalized by the robust multichip analysis method combined with median polish. The marginal data distributions were adjusted through quantile normalization. The resulting normalized values were imported into JMP Genomics software version 3.2, where they were then log transformed.

organism: Homo sapiens

source_name: PBMC

label_protocol: per Affymetrix

extract_protocol: Trizol reagent (Invitrogen) then RNEasy minicolumn (Qiagen)

treatment_protocol: Blood was collected in BD CPT tubes, PBMC isolated after density gradient centrifugation

tag: disease state

value: control

tag: symptom

value: PBMC


title: Halobacterium salinarum at OD=0.66, t=240 min., Array 07261


title: Halobacterium salinarum at OD=0.63, t=0 min., Array 07298


title: Halobacterium salinarum at OD=0.69, t=480 min., Array 07262


title: Rat SSC GDNF Control Rep3

description: Rat SSC GDNF Control Rep3


title: Control_rep7

description:
control_7
Gene expression data from Control_rep7


title: Rat SSC GDNF Withdrawal Rep3

description: Rat SSC GDNF Withdrawal Rep3


title: Control_rep10

description:
control_10
Gene expression data from Control_rep10


title: Control_rep12

description:
control_12
Gene expression data from Control_rep12


title: Control_rep5

description:
control_5
Gene expression data from Control_rep5


title: Control_rep6

description:
control_6
Gene expression data from Control_rep6


title: Control_rep9

description:
control_9
Gene expression data from Control_rep9


title: JIA_CR_rep6

description:
patient_CR_6
Gene expression data from JIA_CR_rep6

value: polyarticular JIA

value: CR


title: Control_rep8

description:
control_8
Gene expression data from Control_rep8


title: Control_rep2

description:
control_2
Gene expression data from Control_rep2


title: JIA_CR_rep5

description:
patient_CR_5
Gene expression data from JIA_CR_rep5


title: JIA_CR_rep3

description:
patient_CR_3
Gene expression data from JIA_CR_rep3


title: Control_rep4

description:
control_4
Gene expression data from Control_rep4


title: JIA_CR_rep4

description:
patient_CR_4
Gene expression data from JIA_CR_rep4


title: Rat SSC GDNF Control Rep1

description: Rat SSC GDNF Control Rep1


title: Control_rep3

description:
control_3
Gene expression data from Control_rep3


title: Control_rep1

description:
control_1
Gene expression data from Control_rep1


title: Control_rep11

description:
control_11
Gene expression data from Control_rep11


title: JIA_CR_rep2

description:
patient_CR_2
Gene expression data from JIA_CR_rep2


title: JIA_CRM_rep9

description:
patient_CRM_9
Gene expression data from JIA_CRM_rep9

value: CRM


title: JIA_CRM_rep8

description:
patient_CRM_8
Gene expression data from JIA_CRM_rep8


title: JIA_CRM_rep6

description:
patient_CRM_6
Gene expression data from JIA_CRM_rep6


title: JIA_CRM_rep5

description:
patient_CRM_5
Gene expression data from JIA_CRM_rep5


title: JIA_CRM_rep7

description:
patient_CRM_7
Gene expression data from JIA_CRM_rep7


title: JIA_CRM_rep3

description:
patient_CRM_3
Gene expression data from JIA_CRM_rep3


title: JIA_CRM_rep1

description:
patient_CRM_1
Gene expression data from JIA_CRM_rep1


title: Rat SSC GDNF Withdrawal Rep2

description: Rat SSC GDNF Withdrawal Rep2


title: JIA_CRM_rep2

description:
patient_CRM_2
Gene expression data from JIA_CRM_rep2


title: JIA_Active_rep9

description:
patient_active_9
Gene expression data from JIA_Active_rep9

value: active


title: JIA_Active_rep8

description:
patient_active_8
Gene expression data from JIA_Active_rep8


title: JIA_CRM_rep4

description:
patient_CRM_4
Gene expression data from JIA_CRM_rep4


title: JIA_Active_rep4

description:
patient_active_4
Gene expression data from JIA_Active_rep4


title: JIA_Active_rep13

description:
patient_active_13
Gene expression data from JIA_Active_rep13


title: JIA_Active_rep5

description:
patient_active_5
Gene expression data from JIA_Active_rep5


title: JIA_Active_rep7

description:
patient_active_7
Gene expression data from JIA_Active_rep7


title: JIA_Active_rep12

description:
patient_active_12
Gene expression data from JIA_Active_rep12


status: Public on Apr 12 2009

type: genomic

city: Baltimore

first: George

middle: S.

last: Bova

state: MD

address: 600 N. Wolfe St

department: Pathology

institute: Johns Hopkins University

description: Spinal Cord Compressing Met 391T 11 yrs before death_BT_16090

hyb_protocol: Samples hybridized to the Affy6 chip for 18 hrs. We washed and stained the arrays using an Affymetrix fluidics Station 450 and scanned the arrays using a GeneChip Scanner 3000 7G (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: The Affymetrix GeneChip® Operating Software (GCOS) was used to collect and extract feature data from Affymetrix GeneChip® Scanners.

data_processing:
Allele-specific genomic analysis was performed using the Partek Genomic Suite (PGS) verion 6.4 allele-specific analysis algorithm, which takes advantage of genotype information and allele-specific intensities from paired samples to estimate DNA copy number for each heterozygous SNP. Allele-specific analysis can also help determine the effect of normal DNA contamination from nonmalignant cells in the tumor samples through comparison of allele ratios inside and outside regions of apparent hemizygous deletion. Please note that the currently released PGS allele-specific copy number algorithm for single sample analysis assigns one allele "Max" status and colors its data red, and assigns the other allele "Min" status and colors its data blue based on the estimated copy number for the different alleles (max=red, min=blue). This labeling is meant to convey the structure of contiguous regions with differing allele prevalence, but by itself does not imply haplotype phase across regions of similar allele prevalence. Each allele specific display in Figures 2-4 is thus independently displayed and categorization of changes into omniclonal/subclonal/indeterminate groups are based on visual interpretation of overall pattern. Examples of homozygous deletion displayed in Figure 4 were identified by examination of the allele-specific copy number data using a combination of relative and absolute copy number (both alleles generally well below 0.5 copy number) and genomic length of affected segment containing more than approximately 20 probes (each dot in Figure 4 represents data from 10 probes). We applied three different methods to jointly assess the statistical significance of observed "clonality", namely, unsupervised cluster-subject matching, supervised sample classification, and Fisher"s distance statistics. Based on a large number of random permutations, we generated the empirical distribution of the "summary statistics" under the null hypothesis that the observed "clonality" is a by-chance event. Accordingly, we used three summary statistics criteria to measure the degree of clonality, namely, cluster-subject matching error, predictive classification error, and Fisher's distance. Specifically, in the unsupervised cluster-subject matching experiment, we used the matching error between subject ID assignments and Affymetrix 6 data clusters (obtained via unsupervised hierarchical clustering) as the summary statistics. The underling null hypothesis is that the subject IDs are randomly assigned to tissue samples independent of samples" genomic signatures. We performed a large number of random permutations to assess the statistical significance of the observed label assignment. We exhaustively search among different number of clusters, to find the minimum number of "unmatched" samples as the error rate of mismatching. We obtained the observed error of hierarchical clustering as 0/58, which means 0 samples are mismatched in total 58 samples. The histogram of the error rates obtained by 10,000 permutations is shown in Supplementary Figure 5. Error rate by permutation ranges from 34/58 to 44/58. The P value associated with the observed error rate of 0/58 is below , upon which we can safely reject the null hypothesis and support the claim of "clonality".

Please refere to GSE14996_Methods.doc on Series record for the figures.

molecule: genomic DNA

label_protocol: 250 ng of genomic DNA were digested with either Nsp I or Sty I and then ligated to adapters that recognize cohesive four-basepair (bp) overhangs. A generic primer that recognizes the adapter sequence was used to amplify adapter ligated DNA fragments with PCR conditions optimized to preferentially amplify fragments in the 200 to 1,100 bp size range in a GeneAmp PCR System 9700 (Applied Biosystems, Foster City, CA). After purification with magnetic beads from Agencourt (Beverly, MA), the PCR product was fragmented using DNase I and a sample of the fragmented product was visualized on a 4% TBE agarose gel to confirm that the average size was smaller than 180 bp. The fragmented DNA was then labeled with biotin.

growth_protocol: Samples isolated and frozen rapidly during research autopsy

extract_protocol: Standard DNA isolation methods

value: metastatic prostate cancer

tag: sample identifier (case number and anatomic site designation for metastatic samples)

tag: case number

tag: anatomic location category subdural (met=1, liver met=2, adrenal met=3, pericardial met=4, lymph node met=5, bone met=6, ca found in prostate at autopsy=7, other=8)

tag: omb race/ethnicity

value: White, Nonhispanic

value: pool of noncancerous samples, control


title: Liver Met 3

description: Liver Met 3_BT_16111

source_name: Liver Met 3


title: JIA_Active_rep3

description:
patient_active_3
Gene expression data from JIA_Active_rep3


title: JIA_Active_rep6

description:
patient_active_6
Gene expression data from JIA_Active_rep6


title: Liver Met 12

description: Liver Met 12_BT_16110

source_name: Liver Met 12


title: JIA_Active_rep14

description:
patient_active_14
Gene expression data from JIA_Active_rep14


title: JIA_Active_rep1

description:
patient_active_1
Gene expression data from JIA_Active_rep1


title: JIA_CR_rep1

description:
patient_CR_1
Gene expression data from JIA_CR_rep1


title: JIA_Active_rep11

description:
patient_active_11
Gene expression data from JIA_Active_rep11


title: A33 T12-1 Vertebral Met

description: A33 T12-1 Vertebral Met_BT_16031

source_name: A33 T12-1 Vertebral Met


title: JIA_Active_rep2

description:
patient_active_2
Gene expression data from JIA_Active_rep2


title: A33 L Axillary LN Met

description: A33 L Axillary LN Met_BT_16010

source_name: A33 L Axillary LN Met


title: A31 R Rib 7 Met

description: A31 R Rib 7 Met_BT_16025

source_name: A31 R Rib 7 Met


title: A32 R Rib 8 Met 1-11

description: A32 R Rib 8 Met 1-11_BT_16034

source_name: A32 R Rib 8 Met 1-11


title: Liver Met 1

description: Liver Met 1_BT_16109

source_name: Liver Met 1


title: A33 R Rib 7 Met

description: A33 R Rib 7 Met_BT_16030

source_name: A33 R Rib 7 Met


title: A33 L Adrenal Met

description: A33 L Adrenal Met_BT_16035

source_name: A33 L Adrenal Met


title: A31 R Subdural Met

description: A31 R Subdural Met_BT_16086

source_name: A31 R Subdural Met


title: A32 Prostate 10-1-3 CA

description: A32 Prostate 10-1-3 CA_BT_16026

source_name: A32 Prostate 10-1-3 CA


title: A31 L Adrenal Met

description: A31 L Adrenal Met_BT_16085

source_name: A31 L Adrenal Met


title: A28 Anterior Mediastinal LN Met A8

description: A28 Anterior Mediastinal LN Met A8_BT_16079

source_name: A28 Anterior Mediastinal LN Met A8


title: A32 L Cervical LN Met 1-2

description: A32 L Cervical LN Met 1-2_BT_16027

source_name: A32 L Cervical LN Met 1-2


title: A33 Paratracheal LN Met

description: A33 Paratracheal LN Met_BT_16029

source_name: A33 Paratracheal LN Met


title: A31 R Ing LN Met

description: A31 R Ing LN Met_BT_16024

source_name: A31 R Ing LN Met


title: A30 R Humerus Marrow Met 3

description: A30 R Humerus Marrow Met 3_BT_16017

source_name: A30 R Humerus Marrow Met 3


title: A28 R Lower Lung Met A2

description: A28 R Lower Lung Met A2_BT_16021

source_name: A28 R Lower Lung Met A2


title: A30 R Femur Marrow Met 1

description: A30 R Femur Marrow Met 1_BT_16016

source_name: A30 R Femur Marrow Met 1


title: A28 L Superficial Ing LN Met A1

description: A28 L Superficial Ing LN Met A1_BT_16022

source_name: A28 L Superficial Ing LN Met A1


title: A32 R Humerus Met 1-12

description: A32 R Humerus Met 1-12_BT_16028

source_name: A32 R Humerus Met 1-12


title: A32 L Subclavicular LN Met 1-5

description: A32 L Subclavicular LN Met 1-5_BT_16033

source_name: A32 L Subclavicular LN Met 1-5


title: A30 L Liver Single.Met 1-7

description: A30 L Liver Single.Met 1-7_BT_16082

source_name: A30 L Liver Single.Met 1-7


title: A31 Prostate 1-1-2 CA

description: A31 Prostate 1-1-2 CA_BT_16023

source_name: A31 Prostate 1-1-2 CA


title: A24 R Axillary LN Met

description: A24 R Axillary LN Met_BT_16008

source_name: A24 R Axillary LN Met


title: A28 Posterior Bladder Polypoid Met A1

description: A28 Posterior Bladder Polypoid Met A1_BT_16020

source_name: A28 Posterior Bladder Polypoid Met A1


title: A24 Xiphoid Met

description: A24 Xiphoid Met_BT_16032

source_name: A24 Xiphoid Met


title: A24 R Diaphragmatic Met

description: A24 R Diaphragmatic Met_BT_16075

source_name: A24 R Diaphragmatic Met


title: A30 L Liver Single Met 2-5

description: A30 L Liver Single Met 2-5_BT_16083

source_name: A30 L Liver Single Met 2-5


title: A24 R Rib7 Met

description: A24 R Rib7 Met_BT_16013

source_name: A24 R Rib7 Met


title: A21 L Adrenal Met

description: A21 L Adrenal Met_BT_15996

source_name: A21 L Adrenal Met


title: JIA_Active_rep10

description:
patient_active_10
Gene expression data from JIA_Active_rep10

source_name: PBMC


title: A33 L Subdural Met

description: A33 L Subdural Met_BT_16036

source_name: A33 L Subdural Met


title: A21 R Rib Nodular Met

description: A21 R Rib Nodular Met_BT_15997

source_name: A21 R Rib Nodular Met


title: A22 L Pelvic LN7  Met

description: A22 L Pelvic LN7  Met_BT_16003

source_name: A22 L Pelvic LN7  Met

value: White, Hispanic


title: A21 Single Liver Met #5

description: A21 Single Liver Met #5_BT_15999

source_name: A21 Single Liver Met #5


title: A22 L Humerus Bone Marrow Met

description: A22 L Humerus Bone Marrow Met_BT_16002

source_name: A22 L Humerus Bone Marrow Met


title: A22 Apical Prostate CA

description: A22 Apical Prostate CA_BT_16072

source_name: A22 Apical Prostate CA


title: A22 L Adrenal  Met

description: A22 L Adrenal  Met_BT_16071

source_name: A22 L Adrenal  Met


title: Spleen NL_BT_16108

description: Spleen NL_BT_16108

source_name: Spleen NL

tag: tissue

value: Spleen NL


title: Blood 391B NL_BT_16091

description: Blood 391B NL_BT_16091

source_name: Blood 391B NL

value: Blood 391B NL


title: Liver NL_BT_16089

description: Liver NL_BT_16089

source_name: Liver NL

value: Liver NL


title: Spleen NL_BT_16037

description: Spleen NL_BT_16037


title: BLASTOMERE-EMBRYO_2-cell_g (CGH)

status: Public on Apr 26 2009

city: Leuven

first: Thierry

last: Voet

address: Herestraat 49

department: Department of Human Genetics

country: Belgium

institute: KULeuven

hyb_protocol: 1.75 µg of test and reference DNA were mixed with 50 µg of human Cot-1 DNA (Invitrogen) and precipitated by adding 2.5 volumes of 96% ethanol and 0.1 volume of sodium acetate (3M, pH5.2). The DNA pellet was resuspended in 15 µl hybridization buffer (50% formamide, 10% dextran sulfate, 0.1% Tween-20, 2xSSC and 10 mM Tris–HCl, pH 7.5) containing 200 µg yeast tRNA, denatured at 98°C for 15 minutes and hybridized to a BAC array (spotted area of 18 x 18 mm) over one night in a humid chamber at 37°C. This area was preblocked for 1 hour at 37°C with 16.6 µg human Cot-1 DNA and 0.1 mg salmon testes DNA (Sigma Aldrich) dissolved in 20 µl hybridization buffer. Arrays were washed in 1xPBS (pH8.0)/0,05% Tween20 for 10 minutes at room temperature, 2xSSC (pH7.0)/50% formamide for 30 minutes at 42°C, 1xPBS (pH8.0)/0,05% Tween20 for 10 minutes at room temperature and subsequently dried

scan_protocol: Slides were scanned at 532 and 635 nm using a GenePix 4000B scanner (Axon Instruments Inc., Foster City, CA). The scans were processed with GenePix Pro 6.0 software.

data_processing: Only spots with signal intensities at least 2-fold above the autosomal median background intensity were included in the analysis. Since all clones were present in duplicate, two log2-ratios of Cy5/Cy3-intensities were calculated per clone. Unmapped (n=150) and polymorphic clones (n=68) were masked out. As a preprocessing step, the ratios were loess normalised using the R package snapCGH;

source_name: blastomere

label_protocol: Test and reference DNA were labeled for 2h by random primer labeling (BioPrime aCGH Genomic Labeling System; Invitrogen; Carlsbad, CA) using respectively Cy5- and Cy3-dCTPs (GE Healthcare). Labeled DNA was purified with the BioPrime Purification Module (Invitrogen; Carlsbad, CA).

extract_protocol: Single cells were transferred to a 200 µl PCR tube containing 1.5 µl alkaline lysis buffer (ALB; 200 mM KOH and 50 mM DTT) by mouth controlled pipetting using 75 µm stripper tips (MidAtlantic Diagnostics, Mount Laurel, USA). An aliquot from the last washing droplet was taken as a negative control per cell line. The samples were stored at -20°C for at least 30 min and were further incubated for 10 min at 65°C prior to the multiple displacement amplification (MDA) reaction. Single cell DNA was amplified following an MDA-approach with Genomi Phi V2 (GE Healthcare, Piscataway, NJ). The MDA products were purified and resuspended in 50 µl of elution buffer (High Pure PCR Product Purification Kit, Roche, Basel, Switzerland). All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies, Rockland, DE). SC-amplifications yielding less than 2 µg DNA were not further used.

treatment_protocol: Embryos were incubated briefly in Acid Tyrod (AT; pH 2.4 Sigma-Aldrich, St Louis, MO) to remove the zona pellucida (ZP) by mouth controlled pipetting using Flexipet micromanipulation pipettes (130 µm, Cook, IVF Queensland, Australia). They were then transferred to Ca2+/Mg2+ free medium (PGD biopsy Medium, GlobalLife) and 0.01% (w/v) phenol red supplemented with 4 mg/ml BSA (Sigma-Aldrich, St Louis, MO) (dissociation medium) and gently pipetted to disaggregate the individual blastomeres. Single blastomeres were washed three times in the dissociation medium.

tag: single cell from a 3-day-old human IVF embryo

tag: IVF protocol

value: controlled ovarian hyperstimulation was performed using a “long protocol” as follows.  In the previous cycle an oral contraceptive pill was given for 25 days (Cilest®, Janssen-Cilag), followed by pituitary downregulation with bucerelin acetate (Suprefact®, Hoechst, Frankfurt, Germany; 600 µg daily) from day 21 onwards. Human menopausal gonadotropins or human recombinant gonadotrophins  (Humegon® or Puregon, Organon, Oss, The Netherlands; Gonal F, Merck Serono, Geneva, Switzerland) were started on the second day after the subsequent menstruation while ovulation was induced with 10000 IU HCG (Pregnyl®, Organon, Oss, The Netherlands) when at least 3 follicles with a diameter of at least 17 mm were observed at gynecological ultrasound. Ultrasound guided oocyte aspiration was performed 36 hours later. Luteal supplementation was given by vaginal progesterone (600 mg/day, Utrogestan®, Piette International, Drogenbos, Belgium). Subsequently, oocytes were fertilized using conventional IVF (n=8) or ICSI (n=1) with ejaculated sperm. Embryos were cultured in Global Medium (GlobalLife) and the morphology was daily assessed. Only genetically normal embryos of good morphology (with compaction or blastocyst formation) were transferred on day 4 or 5. Supernumerary genetically normal embryos of good morphology were frozen at day 4 or 5. Day 3 (evening) or day 4 (morning) embryos diagnosed with a microdeletion or with a normal sex but not suitable for transfer due to a familial genetic reason were used for this study if fulfilling all inclusion criteria (see patient info).

tag: Patient info

value: Couples entering the IVF-PGD-program for sex selection due to X-linked disorders or BRCA mutations or for familial microdeletion syndromes were asked to participate. Inclusion criteria were:(1) written informed consent from each couple, (2) maternal and paternal age ≤ 35 years, (3) normal karyotype for both partners, (4) a maternal body mass index of 18-30 kg/m², (5) initial normal semen parameters according to WHO regulation, (6) good quality embryos:2-5 blastomeres on day 2, 6-10 blastomeres on day 3, <20% fragmentation, equal sized blastomeres, (7) no recurrent miscarriages. The study was approved by the Ethical Committee of the University Hospital (registration number NCT00614367).

source_name: Blood

tag: karyotype


title: Liver NL_BT_16088

description: Liver NL_BT_16088


title: A17 R Femur marrow Met

description: A17 R Femur marrow Met_BT_15983

source_name: A17 R Femur marrow Met


title: A19 Paraaortic LN Met

description: A19 Paraaortic LN Met_BT_16066

source_name: A19 Paraaortic LN Met


title: A17 Abd Paraaortic LN Met

description: A17 Abd Paraaortic LN Met_BT_16060

source_name: A17 Abd Paraaortic LN Met


title: A17 L Axillary LN #2 Met

description: A17 L Axillary LN #2 Met_BT_15986

source_name: A17 L Axillary LN #2 Met


title: A21 Single Liver Met #4

description: A21 Single Liver Met #4_BT_16068

source_name: A21 Single Liver Met #4


title: Spleen NL_BT_16087

description: Spleen NL_BT_16087


title: A19 Subdural Met

description: A19 Subdural Met_BT_16065

source_name: A19 Subdural Met


title: A19 Sternum Soft Met

description: A19 Sternum Soft Met_BT_15994

source_name: A19 Sternum Soft Met


title: A17 R Supraclavicular LN Met

description: A17 R Supraclavicular LN Met_BT_16061

source_name: A17 R Supraclavicular LN Met


title: Spleen NL_BT_16084

description: Spleen NL_BT_16084


title: A12 Mediastinal LN Met

description: A12 Mediastinal LN Met_BT_16053

source_name: A12 Mediastinal LN Met

value: African American, Nonhispanic


title: Saccharopolyspora rif6 RNA at 72h biological rep.B

city: Segrate - Milan

first: Giorgio

last: Corti

address: via Fratelli Cervi 93

department: Institute of Biomedical Technologies

country: Italy

institute: National Research Council

description: Gene expression data from Saccharopolyspora erythraea rif6 after 72h of growth

hyb_protocol: The labeled cDNAs were then hybridised for 16h at 50°C on individual GeneChips

scan_protocol: GeneChips were washed and stained with streptavidin-conjugated phycoerythrin by using the Fluidic Station FS450 (Affymetrix) following the ProkGE-WS2v3_450 Protocol. Fluorescent images of the microarrays were acquired using a GeneChip Scanner 3000 (Affymetrix).

data_processing: Raw data quality was assessed considering MAS5.0 control parameters after a global scaling at a target intensity of 100. Quality and control parameters as well as boxplot of raw intensities indicated the overall high quality of the data set and the absence of any outlying sample. Probe level data was converted to expression values using both Robust Multi-array Average procedure  and MAS5.0 algorithms. In the former case, PM values have been background adjusted, normalized using invariant set normalization, and log transformed. In the latter case, intensity levels have been normalized using the Global Scaling option to target value (i.e., TGT=100).

organism: Saccharopolyspora erythraea

source_name: RNA extracted from Saccharopolyspora erythraea rif6 mutant after 72h of growth

label_protocol: The RNAs were processed following the Affymetrix Protocol Target Labeling for Prokaryotic GeneChip® Antisense Arrays (Affymetrix Procaryotic gene Expression Manual). The protocol consists in cDNA synthesis by reverse transcription (starting with 10 µg RNA), followed by cDNA fragmentation with DNase I and labeling with Terminal Deoxynucleotidyl Transferase.

growth_protocol: For shake-flask experiments, spores in frozen aliquots were collected by centrifugation, re-suspended in medium 707 (for rehydration), and readily separated by vortexing. Individual aliquots (about 5 x 108 spores) were used to inoculate each 500 ml buffled Erlenmeyer flask containing 50 ml liquid media above described. Cultures were incubated at 30°C with shaking at 250 rpm in R3 medium. R3 composition: 5 g yeast extract, 0.1 g casamino acids, 3 g L-proline, 10 g MgCl2 • 6H2O, 4 g CaCl2 • 2H2O, 0.2 g K2SO4, 0.05 g KH2PO4, 5.6 g TES, 10 g glucose, PH 7.2

extract_protocol: For each time point, RNA was extracted from mycelium pellets deriving fron 1 ml culture samples using the GeneElute™ total RNA Purification Kit (SIGMA), recovering it in 50 µl of Elution Solution.

value: NRRL 2338 rif6


title: Pericardial Mass Met 1A

description: Pericardial Mass Met 1A_BT_16128

source_name: Pericardial Mass Met 1A


title: A16 Pericardial Mets

description: A16 Pericardial Mets_BT_15954

source_name: A16 Pericardial Mets


title: Peritoneal Nodule pc1 Met

description: Peritoneal Nodule pc1 Met_BT_15963

source_name: Peritoneal Nodule pc1 Met


title: A12 R Pelvic LN Met

description: A12 R Pelvic LN Met_BT_16054

source_name: A12 R Pelvic LN Met


title: A21 Single Liver Met #8

description: A21 Single Liver Met #8_BT_16069

source_name: A21 Single Liver Met #8


title: Spleen NL_BT_16080

description: Spleen NL_BT_16080

source_name: Spleen NL

value: control


title: A16 L Pulm Hilar LN Met

description: A16 L Pulm Hilar LN Met_BT_15979

source_name: A16 L Pulm Hilar LN Met


title: Saccharopolyspora rif6 RNA at 72h biological rep.A


title: A16 R Temporal Subdural Met

description: A16 R Temporal Subdural Met_BT_15990

source_name: A16 R Temporal Subdural Met


title: A3 Pelvic Paraaortic LN Met

description: A3 Pelvic Paraaortic LN Met_BT_15953

source_name: A3 Pelvic Paraaortic LN Met


title: Saccharopolyspora rif6 RNA at 48h biological rep.B

description: Gene expression data from Saccharopolyspora erythraea rif6 after 48h of growth

source_name: RNA extracted from Saccharopolyspora erythraea rif6 mutant after 48h of growth


title: L Kidney NL_BT_16070

description: L Kidney NL_BT_16070

source_name: L Kidney NL

value: L Kidney NL


title: Spleen NL_BT_16076

description: Spleen NL_BT_16076


title: Liver NL_BT_16073

description: Liver NL_BT_16073

source_name: Liver NL


title: Liver NL_BT_16067

description: Liver NL_BT_16067


title: Saccharopolyspora rif6 RNA at 48h biological rep.A


title: Kidney NL_BT_16062

description: Kidney NL_BT_16062

source_name: Kidney NL

value: Kidney NL


title: Saccharopolyspora rif1 RNA at 48h biological rep.B

description: Gene expression data from Saccharopolyspora erythraea rif1 after 48h of growth

source_name: RNA extracted from Saccharopolyspora erythraea rif1 mutant after 48h of growth

value: NRRL 2338 rif1


title: Kidney NL_BT_16040

description: Kidney NL_BT_16040


title: Saccharopolyspora rif1 RNA at 24h biological rep.A

description: Gene expression data from Saccharopolyspora erythraea rif1 after 24h of growth

source_name: RNA extracted from Saccharopolyspora erythraea rif1 mutant after 24h of growth


title: Liver NL_BT_16059

description: Liver NL_BT_16059


title: Saccharopolyspora rif1 RNA at 48h biological rep.A


title: Saccharopolyspora rif1 RNA at 24h biological rep.B


title: Lymphs NL_BT_16007

description: Lymphs NL_BT_16007

source_name: Lymphs NL

value: Lymphs NL


title: Saccharopolyspora WT RNA at 48h biological rep.B

description: Gene expression data from Saccharopolyspora erythraea WT after 48h of growth

source_name: RNA extracted from Saccharopolyspora erythraea WT after 48h of growth

value: NRRL 2338


title: Saccharopolyspora WT RNA at 48h biological rep.A


title: Saccharopolyspora WT RNA at 24h biological rep.B

description: Gene expression data from Saccharopolyspora erythraea WT after 24h of growth

source_name: RNA extracted from Saccharopolyspora erythraea WT after 24h of growth


title: Saccharopolyspora WT RNA at 24h biological rep.A


title: A17 Subdural Met Fossa C

description: A17 Subdural Met Fossa C_BT_15982

source_name: A17 Subdural Met Fossa C

value: metastatic prostate cancer


title: 13279344 - wt vs hd1

status: Public on Apr 11 2009

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Different genes show an opposed expression profil in gcn5 compared to hd1. For these genes, the double mutant might show an expression similar to the wild type.

hyb_protocol: hd1 Cy5 / wt Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial - Seeds were sawn in vitro on 1/2 MS and synchronised 3 days at 4°C in the dark. After 3 days, dishes were exposed to light (Long days: 16h, hygrometry: 75%) until 1.03 boyes stadge (almost 10 days).

treatment_protocol: no treatment

tag: cultivar

value: Arabidopsis thaliana (wassilewskija)

tag: age

tag: developmental stage

value: (Boyes et al. Plant Cell 2001):boyes:1.03

source_name: wt


title: 13279345 - gcn5hd1 vs wt

hyb_protocol: wt Cy5 / gcn5hd1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13279342 - wt vs gcn5

hyb_protocol: gcn5 Cy5 / wt Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%


title: Medium-only control__24 h_rep3

city: Turku

first: Ilana

last: Saarikko

address: Linnankatu 55

country: Finland

institute: Genolyze Ltd

description: 1 µg total RNA was used as starting material for sample preparation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using Affymetrix scanning protocol

data_processing: Raw data was processed with R/Bioconductor and normalised with CG-RMA

source_name: Caco-2 cell line, medium-only control, 24 h

label_protocol: For biotinylated target synthesis, RNA was labeled using standard operating procedures supplied by the manufacturer (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA)

growth_protocol: Caco-2 cells (European Collection of Cell Cultures, ECACC, Salisbury, UK) passages p47 to p51 were used as a model for human intestinal epithelial cells (IEC). Cells were maintained in basal culture medium (BM) of Dulbecco’s Modified Eagle’s Medium (DMEM, Biochrom AG) supplemented with 10% FBS (Invitrogen), 2 mM glutamine (Biochrom AG), 1 x non-essential amino acids (Invitrogen), 20 U/ml penicillin (Invitrogen), 20 µg/ml streptomycin (Invitrogen), and 0.5 µg/ml amphotericin (Invitrogen) at +37ºC, in 5% CO2 atmosphere. For exposure experiments Caco-2 cells were differentiated on cell culture inserts with a 5-day protocol (Yamashita S, Konishi K, Yamazaki Y, Taki Y, Sakane T, Sezaki H, Furuyama Y: New and better protocols for a short-term Caco-2 cell culture system. J Pharm Sci 2002, 91:669-79). Probiotic starins were obtained from Danisco Global Culture Collection (DGCC). L. acidophilus NCFM™ (ATCC700396), B. animalis ssp. lactis 420 and L. salivarius Ls-33 were propagated at 37°C anaerobically in de Man, Rogosa and Sharpe (MRS) broth supplemented with 1.0 % glucose, and E. coli O157:H7, EHEC, (DSM 8579, DSMZ, Braunschweig, Germany) in Luria Bertani (LB) broth supplemented with 1.0 % glucose aerobically at 37°C until OD600 = 0.6-0.7. The bacterial cell densities were determined with flow cytometry (FACSCalibur, Becton Dickinson, San Jose, CA, US).

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.

treatment_protocol: Overnight cultures of probiotics were pelleted (25°C, 5 min, 3000 g), washed once with Caco-2 medium, and diluted into Caco-2 differentiation medium to correspond a  ratio of 20 to 100 bacterial cells to 1 Caco-2 cell. The cell-free supernatant (CFS) obtained from probiotic cultures after removal of bacterial cells was diluted 10 % (v/v) into Caco-2 differentiation medium, and sterile-filtered with 0.1 µM sterile filter unit (Sartorius, Goettingen, Germany) to remove any residual bacteria. For E. coli O157:H7 the bacteria were similarly pelleted and sterile-filtered but only experiments with CFS diluted 5 % (v/v) into Caco-2 differentiation medium was conducted. The bacteria as well as CFSs were used fresh in the experiments, and no antibiotics were used in the Caco-2 media in any step during handling the bacteria. To perform the experiments with Caco-2 cells, the differentiation on the basal side of the cells was changed to fresh Caco-2 differentiation medium, and on the apical side Caco-2 differentiation medium was changed to test media consisting of either DCE test medium composed of bacterial cells diluted in Caco-2 differentiation medium as described above or CFS test medium diluted either to 5% (v/v) or to 10% (v/v) in Caco-2 differentiation medium as described above. The DCE test media were incubated at +37ºC, in 5% CO2 atmosphere for 8 hours and the CFS test media in similar conditions for 24 hours. After incubation periods the test media was removed by aspiration from the apical side and cells were immediately lysed for RNA isolation.

tag: intestinal epithelial cells

value: differentiated Caco-2

tag: treatment time

value: 24 hrs


title: L. salivarius Ls-33_coculture_8 h_rep2

description: 5 µg total RNA was used as starting material for sample preparation

source_name: Caco-2 cell line, cocultured with L. salivarius Ls-33, 8 h

value: 8 hrs

tag: probiotic

value: Lactobacillus salivarius Ls-33


title: A12 Paraaortic LN Met

description: A12 Paraaortic LN Met_BT_15989

source_name: A12 Paraaortic LN Met

tag: disease state

value: pool of noncancerous samples, control


title: 13279341 - gcn5 vs wt

hyb_protocol: wt Cy5 / gcn5 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13279346 - wt vs gcn5hd1

hyb_protocol: gcn5hd1 Cy5 / wt Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13279343 - hd1 vs wt

hyb_protocol: wt Cy5 / hd1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: L. salivarius Ls-33_coculture_8 h_rep1


title: L. salivarius Ls-33_cell-free supernatant_24 h_rep2

source_name: Caco-2 cell line, treated with L. salivarius Ls-33 cell-free supernatant, 24 h


title: L. acidophilus NCFM™_coculture_8 h_rep2

source_name: Caco-2 cell line, cocultured with L. acidophilus NCFM™, 8 h

value: Lactobacillus acidophilus NCFM™


title: B. lactis 420_cell-free supernatant_24 h_rep2

source_name: Caco-2 cell line, treated with B. lactis 420 cell-free supernatant, 24 h

value: Bifidobacterium lactis 420


title: Medium-only control__24 h_rep1


title: L. acidophilus NCFM™_cell-free supernatant_24 h_rep1

source_name: Caco-2 cell line, treated with L. acidophilus NCFM™ cell-free supernatant, 24 h


title: E. coli O157:H7_cell-free supernatant_24 h_samle 1

source_name: Caco-2 cell line, treated with E. coli O157:H7 cell-free supernatant, 24 h

tag: pathogen

value: E. coli O157:H7


title: L. acidophilus NCFM™_coculture_8 h_rep1


title: B. lactis 420_cell-free supernatant_24 h_rep1


title: E. coli O157:H7_cell-free supernatant_24 h_sample 3


title: L. acidophilus NCFM™_cell-free supernatant_24 h_rep2


title: Medium-only control__8 h_rep2

source_name: Caco-2 cell line, medium-only control, 8 h


title: B. lactis 420_coculture_8 h_rep1

source_name: Caco-2 cell line, cocultured with B. lactis 420, 8 h


title: E. coli O157:H7_cell-free supernatant_24 h_sample 2


title: Medium-only control__24 h_rep2


title: B. lactis 420_coculture_8 h_rep2


title: Medium-only control__8 h_rep1


title: L. salivarius Ls-33_cell-free supernatant_24 h_rep1


title: Vps75 chrVI sample 1

city: South Mimms

first: Luke

last: Selth

state: Herts.

address: Blanch Lane

country: United Kingdom

institute: Cancer Research UK

description:
Analysis of the binding pattern of Vps75 along S. cerevisiae chromosome VI (First repeat)
Selth L, and Svejstrup JQ. (2007) Vps75, a new yeast member of the NAP histone chaperone family. J Biol Chem 282:12358-62.

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized in buffer containing SSPE, TritonX-100, denatured salmon sperm DNA and biotin-labelled control oligonucleotide, oligo B2. Samples were denatured at 95ºC for 10 minutes and then hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix)

scan_protocol: The washing and scanning protocol (FlexMidi_euk2v3_450), provided by Affymetrix, was performed automatically on a GeneChip Fluidics Station 450. Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Primary analysis of tiling chip data was performed using the Affymetrix GeneChip Operating Software (GCOS).

organism: Saccharomyces cerevisiae W303

source_name: ChIP DNA from yeast Saccharomyces cerevisiae cells

label_protocol: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl).

growth_protocol: Cells were grown at 30C in YPD medium and cross-linked at a density of 1 x 107 cells/mL.

extract_protocol: ChIP analyses were performed essentially as previously described (Selth et al, 2007). Cells were grown under the conditions described above, cross-linked with formaldehyde, disrupted by bead-beating in a FastPrep 24 instrument (MP Biomedicals), and whole cell extracts sonicated to obtain 400-600 bp genomic DNA fragments. Chromatin immunoprecipitation (ChIP) was performed with 9E11 antibody (monoclonal antibody against Myc tag of Vps75) coupled to protein A-sepharose beads. Immunoprecipates were eluted and incubated overnight at 65ºC to reverse cross-links. Then, as previously described (Katou et al 2003), the immunoprecipitated genomic DNA was incubated with proteinase K, extracted twice with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RNaseA. The DNA was purified, concentrated by ethanol precipitation and amplified by PCR after random priming. 10ug of the amplified DNA was digested with DNase I and end-labelled using TdT Terminal Transferase and Biotin-N6-ddATP.

treatment_protocol: ChIP and hybridization protocols were performed as previously described (Selth et al. 2007; Katou et al. 2003)

tag: genotype

tag: cell description

value: Cells expressing a C-terminally tagged version of Vps75 expressed from its own promoter (Selth et al., 2007)

tag: strain

value: Vps75-HTM (Selth et al., 2007)

tag: antibody

value: 9E11 anti-Myc

source_name: Input DNA from Saccharomyces cerevisiae cells from unbound fraction

treatment_protocol: ChIP and hybridization protocols were performed as previously described (Selth et al. 2005; Katou et al. 2003)


title: Vps75 chrVI sample 2

description:
Analysis of the binding pattern of Vps75 along S. cerevisiae chromosome VI (Second repeat)
Selth L, and Svejstrup JQ. (2007) Vps75, a new yeast member of the NAP histone chaperone family. J Biol Chem 282:12358-62.

label: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl)


title: 13689218 - mock_R3 vs TRV_R3

status: Public on Apr 10 2009

description: mRNA expression profile in virus-infected Arabidopsis.

hyb_protocol: TRV_R3 Cy5 / mock_R3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

growth_protocol: root - hygrometry : 75%	 Temperature : 22ºC	 Light : 50 lux sd (10-14h)

treatment_protocol: Name:TRV_infection_AU07-02_suite2 - environmental treatment - pathogen infection,trv or mock:time 8day .  Arabidopsis plants were sap inoculated using an inoculum prepared from N. benthamiana systemic infected leaves at 3 days post-infiltration. Leaves were ground in 100 mM phosphate buffer pH 7.2 and this extract was used to directly rub-inoculate whole leaves of 19 day old Arabidopsis plants that had been previously dusted with carborundum. Mock inoculation was performed with the phosphate buffer only. Total RNA was extracted from root tissue.

value: arabidopsis thaliana (columbia)

tag: development stage

value: (boyes et al. plant cell 2001):boyes = 3.6

tag: tissue

value: root


title: 13689631 - mock_R2 vs TRV_R2

hyb_protocol: TRV_R2 Cy5 / mock_R2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13419842 - TRV_R2 vs mock_R2

hyb_protocol: mock_R2 Cy5 / TRV_R2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

growth_protocol: aerial - medium : soil hygrometry : 75% temperature : 22°C light : 50 lux sd (10-14h)

treatment_protocol: Name:TRV_infection_AU07-02 - environmental treatment - pathogen infection,trv or mock:time 13day .

value: (boyes et al. plant cell 2001):boyes :6.7


title: 13415206 - mock_R2 vs TRV_R2


title: 13688451 - mock_R3 vs TRV_R3

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

growth_protocol: leaf - hygrometry : 75% temperature : 22°C light : 50 lux sd (10-14h)

treatment_protocol: Name:TRV_infection_AU07-02_suite - biotic stress - pathogen infection,trv or mock:time 8day .

value: leaf


title: 13415208 - mock_R1 vs TRV_R1

hyb_protocol: TRV_R1 Cy5 / mock_R1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13419816 - TRV_R3 vs mock_R3

hyb_protocol: mock_R3 Cy5 / TRV_R3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688452 - TRV_R3 vs mock_R3


title: 13689217 - TRV_R3 vs mock_R3


title: WGAAD-89

city: Miami

first: Amanda

last: Myers

state: FL

address: 1600 NW 10th Ave

department: Psychiatry and Behavioral Sciences

institute: Miller School of Medicine, University of Miami

description: Human Cortex from Alzheimer's Disease

hyb_protocol: RNA: Illumina Whole Genome Gene Expression Rev. F (Illumina Doc #11763837)

scan_protocol: RNA: Illumina Beadstation

data_processing: RNA: Beadstudio software v 1.5.0.34, rank invariant normalization to extract

source_name: Alzheimer's Disease frozen cortical tissue

label_protocol: RNA: per ambion manual for cat #IL1791, biotinylated cRNA created from in vitro translation targeting poly A tail, cy3 used to image RNA signal

extract_protocol: total RNA (Qiagen Rneasy Lipid Tissue cat #cat 74804, Qiagen Rnase free dnase set- cat # 79254)

tag: gender

value: Female

tag: pmi


title: 13688339 - mock_R2 vs TRV_R2


title: 13689629 - mock_R1 vs TRV_R1


title: 13689626 - TRV_R1 vs mock_R1

hyb_protocol: mock_R1 Cy5 / TRV_R1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689630 - TRV_R2 vs mock_R2


title: 13688436 - TRV_R1 vs mock_R1


title: 13688443 - TRV_R2 vs mock_R2


title: 13688435 - mock_R1 vs TRV_R1


title: 13415211 - mock_R3 vs TRV_R3


title: HUES9 SB-431542 outgrowth culture passage 5

city: Odense

first: Amer

last: Mahmood

address: Fyrreparken 66, 2 tv

department: Department of Endocrinology

country: Denmark

institute: University Hospital of Odense &  University of South Denmark

description:
hESCs are from Harvard and are HUES9 passage 32
All protocols were from Affymatrix Gene Expression Analysis Technical Manual

hyb_protocol: Eukaryotic Target Hybridization method was used according to Affymatrix protocol

scan_protocol: GeneChip® Scanner 3000 was used according to Affymatrix protocol

label: Biotin

source_name: SB-EB day 10 outgrowth passage 5 in CDM

label_protocol: GeneChip IVT Labeling Kit was used for labelling

growth_protocol:
EB formation:
To induce differentiation of hESCs into embryoid bodies (EB), hESC were disaggregated, using trypsin/EDTA (0.1%/ 1 mM, Gibco, 25300-0549), into small clumps containing 5-10 cells, and transferred to low-adhesion plastic Petri dishes (Costar Ultra Low Attachment; Corning Life Sciences, Acton, MA) in KO-Media without addition of bFGF and β-mercaptoethanol.  However, the cells were induced with SB-431542      ([10 uM]). Embryoid bodies were formed after 3 days in culture and media change was performed at days 3, 6 and 8 by gravity sedimentation for 10 minutes at 37oC, 5% CO2.
EB-explant outgrowth culture:
At day 10, hEBs (SB) were transferred to fibronectin-precoated (10 µg/ml, Sigma) plates in chemically defined medium (CDM) that allowed cellular outgrowth and formation of a monolayer. CDM was composed of DMEM/F-12 (Invitrogen) supplemented with bovine serum albumin (0.5%) (Fraction V BSA, Sigma), penicillin/Streptomyocin (1%), lipids (1%) and ITS (10%) (All Invitrogen). The cultures were treated with SB-431542 ([1 uM]) at all time. The hEB-derived outgrowth cultures (OG) in the presence of SB-431542 (SB-OG) were allowed to grow to confluency; subsequent passaging was performed using trypsin/EDTA (0.05% trypsin + 0.53 mM EDTA).

extract_protocol: Frozen samples using RNeasy Mini kit (Qiagen, Copenhagen, Denamrk) for gene expression analysis.

treatment_protocol: hESCs were treated with 10uM SB-431542 and described as SB-EB further at day 10 the EBs were plated and grown in 1uM SB-431542 and recalled as SB-OG.

tag: cell line


title: WGAAD-69

description: Human Cortex from Alzheimer's Disease

value: Alzheimer's Disease frozen cortical tissue

value: Male


title: WGAAD-394

description: Human Cortex from Alzheimer's Disease


title: WGAAD-45

description: Human Cortex from Alzheimer's Disease


title: WGAAD-391

description: Human Cortex from Alzheimer's Disease


title: WGAAD-386

description: Human Cortex from Alzheimer's Disease


title: WGAAD-71

description: Human Cortex from Alzheimer's Disease


title: WGAAD-62

description: Human Cortex from Alzheimer's Disease


title: Control EB outgrowth passage 5

data_processing: All protocols were from Affymatrix Gene Expression Analysis Technical Manual

source_name: hESCs EB day 10 outgrowth passage 5 control condition in CDM

growth_protocol:
EB formation
To induce differentiation of hESCs into embryoid bodies (EB), hESC were disaggregated, using trypsin/EDTA (0.1%/ 1 mM, Gibco, 25300-0549), into small clumps containing 5-10 cells, and transferred to low-adhesion plastic Petri dishes (Costar Ultra Low Attachment; Corning Life Sciences, Acton, MA) in KO-Media without addition of bFGF and β-mercaptoethanol.  However, the cells were cultured in presence of control vehicle (DMSO [0.01%]). Embryoid bodies (EB) were formed after 3 days in culture and media change was performed at days 3, 6 and 8 by gravity sedimentation for 10 minutes at 37oC, 5% CO2.
EB-explant outgrowth culture
At day 10, hEBs (control) were transferred to fibronectin-precoated (10 µg/ml, Sigma) plates in chemically defined medium (CDM) that allowed cellular outgrowth and formation of a monolayer. CDM was composed of DMEM/F-12 (Invitrogen) supplemented with bovine serum albumin (0.5%) (Fraction V BSA, Sigma), penicillin/Streptomyocin (1%), lipids (1%) and ITS (10%) (All Invitrogen). The cultures were incubated in presence of vehicle (control). The hEB-derived outgrowth cultures (OG) in the presence of vehicle (control-OG) were allowed to grow to confluency; subsequent passaging was performed using trypsin/EDTA (0.05% trypsin + 0.53 mM EDTA).

treatment_protocol: hESCs were treated with 0.01% DMSO and considered as control


title: WGAAD-76

description: Human Cortex from Alzheimer's Disease


title: WGAAD-305

description: Human Cortex from Alzheimer's Disease


title: WGAAD-188

description: Human Cortex from Alzheimer's Disease


title: WGAAD-304

description: Human Cortex from Alzheimer's Disease


title: WGAAD-480

description: Human Cortex from Alzheimer's Disease


title: WGAAD-117

description: Human Cortex from Alzheimer's Disease


title: WGAAD-297

description: Human Cortex from Alzheimer's Disease


title: WGAAD-104

description: Human Cortex from Alzheimer's Disease


title: WGAAD-463

description: Human Cortex from Alzheimer's Disease


title: WGAAD-449

description: Human Cortex from Alzheimer's Disease


title: WGAAD-118

description: Human Cortex from Alzheimer's Disease


title: WGAAD-272

description: Human Cortex from Alzheimer's Disease


title: WGAAD-178

description: Human Cortex from Alzheimer's Disease


title: WGAAD-478

description: Human Cortex from Alzheimer's Disease


title: WGAAD-346

description: Human Cortex from Alzheimer's Disease


title: WGAAD-189

description: Human Cortex from Alzheimer's Disease


title: WGAAD-156

description: Human Cortex from Alzheimer's Disease


title: WGAAD-444

description: Human Cortex from Alzheimer's Disease


title: WGAAD-243

description: Human Cortex from Alzheimer's Disease


title: WGAAD-271

description: Human Cortex from Alzheimer's Disease


title: WGAAD-195

description: Human Cortex from Alzheimer's Disease


title: WGAAD-456

description: Human Cortex from Alzheimer's Disease


title: WGAAD-316

description: Human Cortex from Alzheimer's Disease


title: WGAAD-158

description: Human Cortex from Alzheimer's Disease


title: WGAAD-329

description: Human Cortex from Alzheimer's Disease


title: WGAAD-340

description: Human Cortex from Alzheimer's Disease


title: WGAAD-330

description: Human Cortex from Alzheimer's Disease


title: WGAAD-280

description: Human Cortex from Alzheimer's Disease


title: WGAAD-194

description: Human Cortex from Alzheimer's Disease


title: WGAAD-196

description: Human Cortex from Alzheimer's Disease


title: WGAAD-165

description: Human Cortex from Alzheimer's Disease


title: 13415207 - TRV_R1 vs mock_R1

tag: cultivar


title: WGAAD-148

description: Human Cortex from Alzheimer's Disease

tag: age


title: WGAAD-24

description: Human Cortex from Alzheimer's Disease


title: WGAAD-20

description: Human Cortex from Alzheimer's Disease


title: WGAAD-399

description: Human Cortex from Alzheimer's Disease


title: WGAAD-389

description: Human Cortex from Alzheimer's Disease


title: WGAAD-201

description: Human Cortex from Alzheimer's Disease


title: WGAAD-18

description: Human Cortex from Alzheimer's Disease


title: WGAAD-486

description: Human Cortex from Alzheimer's Disease


title: WGAAD-238

description: Human Cortex from Alzheimer's Disease


title: WGAAD-187

description: Human Cortex from Alzheimer's Disease


title: WGAAD-413

description: Human Cortex from Alzheimer's Disease


title: WGAAD-25

description: Human Cortex from Alzheimer's Disease


title: WGAAD-236

description: Human Cortex from Alzheimer's Disease


title: WGAAD-411

description: Human Cortex from Alzheimer's Disease


title: WGAAD-202

description: Human Cortex from Alzheimer's Disease


title: WGAAD-15

description: Human Cortex from Alzheimer's Disease


title: WGAAD-382

description: Human Cortex from Alzheimer's Disease


title: WGAAD-28

description: Human Cortex from Alzheimer's Disease


title: WGAAD-347

description: Human Cortex from Alzheimer's Disease


title: WGAAD-375

description: Human Cortex from Alzheimer's Disease


title: WGAAD-35

description: Human Cortex from Alzheimer's Disease


title: WGAAD-407

description: Human Cortex from Alzheimer's Disease


title: WGAAD-390

description: Human Cortex from Alzheimer's Disease


title: WGAAD-237

description: Human Cortex from Alzheimer's Disease


title: WGAAD-476

description: Human Cortex from Alzheimer's Disease


title: WGAAD-379

description: Human Cortex from Alzheimer's Disease


title: WGAAD-10

description: Human Cortex from Alzheimer's Disease


title: WGAAD-393

description: Human Cortex from Alzheimer's Disease


title: WGAAD-402

description: Human Cortex from Alzheimer's Disease


title: WGAAD-29

description: Human Cortex from Alzheimer's Disease


title: WGAAD-171

description: Human Cortex from Alzheimer's Disease


title: WGAAD-166

description: Human Cortex from Alzheimer's Disease


title: WGAAD-387

description: Human Cortex from Alzheimer's Disease


title: WGAAD-137

description: Human Cortex from Alzheimer's Disease


title: WGAAD-186

description: Human Cortex from Alzheimer's Disease


title: WGAAD-135

description: Human Cortex from Alzheimer's Disease


title: WGAAD-179

description: Human Cortex from Alzheimer's Disease


title: WGAAD-262

description: Human Cortex from Alzheimer's Disease


title: WGAAD-251

description: Human Cortex from Alzheimer's Disease


title: WGAAD-428

description: Human Cortex from Alzheimer's Disease


title: WGAAD-377

description: Human Cortex from Alzheimer's Disease


title: WGAAD-31

description: Human Cortex from Alzheimer's Disease


title: WGAAD-123

description: Human Cortex from Alzheimer's Disease


title: WGAAD-144

description: Human Cortex from Alzheimer's Disease


title: WGAAD-199

description: Human Cortex from Alzheimer's Disease


title: WGAAD-378

description: Human Cortex from Alzheimer's Disease


title: WGAAD-124

description: Human Cortex from Alzheimer's Disease


title: WGAAD-395

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: MDA-MB-435s (Batch 2)

city: Singapore

first: Seiichi

last: Mori

state: Singapore

address: Centre for Life Sciences #02-07, 28 Medical Drive

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6976_h133+_Q.MDA.MB.435S

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

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

data_processing: Data were normalized by RMA using R with Bioconductor. ComBat standardization was then used to remove the batch effect.

source_name: Breast Cancer Cell Line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Snap-frozen samples in liquid nitrogen were used for extraction.  Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

tag: cell type

value: Breast Cancer

tag: colony number

tag: batch


title: WGAAD-133

description: Human Cortex from Alzheimer's Disease


title: WGAAD-200

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: MDA-MB-453 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6978_h133+_S.MDA.MB.453


title: Breast cancer cell line: MDA-MB-231 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6977_h133+_R.MDA.MB.231


title: WGAAD-401

description: Human Cortex from Alzheimer's Disease


title: WGAAD-130

description: Human Cortex from Alzheimer's Disease


title: WGAAD-417

description: Human Cortex from Alzheimer's Disease


title: WGAAD-385

description: Human Cortex from Alzheimer's Disease


title: WGAAD-132

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: HCC1428 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6974_h133+_O.HCC1428


title: Breast cancer cell line: HCC38 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6975_h133+_P.HCC38


title: Breast cancer cell line: HCC1806 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6973_h133+_N.HCC1806


title: WGAAD-293

description: Human Cortex from Alzheimer's Disease


title: WGAAD-140

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: HCC1143 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6972_h133+_M.HCC1143


title: Breast cancer cell line: ZR75 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6971_h133+_L.ZR.75.1


title: WGAAD-192

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: T47D (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6970_h133+_K.T.47D


title: WGAAD-126

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: BT549 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6968_h133+_I.BT.549


title: WGAAD-284

description: Human Cortex from Alzheimer's Disease


title: WGAAD-295

description: Human Cortex from Alzheimer's Disease


title: WGAAD-78

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: Hs578T (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6963_h133+_D.HS578T


title: WGAAD-287

description: Human Cortex from Alzheimer's Disease


title: WGAAD-282

description: Human Cortex from Alzheimer's Disease


title: WGAAD-190

description: Human Cortex from Alzheimer's Disease


title: WGAAD-128

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: BT483 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6967_h133+_H.BT.483


title: WGAAD-191

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: BT474 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6961_h133+_A.BT.474


title: WGAAD-193

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: SKBR3 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6969_h133+_J.SK.BR.3


title: Breast cancer cell line: MDA-MB-361 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6965_h133+_F.MDA.MB.361


title: WGAAD-127

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: MDA-MB-361 (Batch 1)

description:
Gene expression data from breast cancer cell line
0159_6162_h133+_MDA.MB.361


title: Breast cancer cell line: MCF7 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6962_h133+_C.MCF7


title: WGAAD-289

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: SKBR3 (Batch 1)

description:
Gene expression data from breast cancer cell line
0159_6161_h133+_SKBR3


title: Breast cancer cell line: MDA-MB-157 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6966_h133+_G.MDA.MB.157


title: WGAAD-441

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: BT549 (Batch 1)

description:
Gene expression data from breast cancer cell line
0159_6160_h133+_BT549


title: Breast cancer cell line: MDA-MB-231 (Batch 1)

description:
Gene expression data from breast cancer cell line
0159_6158_h133+_MDA.MB.231


title: WGAAD-437

description: Human Cortex from Alzheimer's Disease


title: WGAAD-431

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: MCF7 (Batch 1)

description:
Gene expression data from breast cancer cell line
0159_6157_h133+_MCF7


title: WGAAD-268

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: BT474 (Batch 1)

description:
Gene expression data from breast cancer cell line
0159_6159_h133+_BT474


title: WGAAD-263

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: CAMA1 (Batch 2)

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6964_h133+_E.CAMA.1


title: WGAAD-425

description: Human Cortex from Alzheimer's Disease


title: WGAAD-269

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: T47D (Batch 1)

description:
Gene expression data from breast cancer cell line
0159_6152_h133+_T47D


title: WGAAD-422

description: Human Cortex from Alzheimer's Disease


title: WGAAD-423

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: BT483 (Batch 1)

description:
Gene expression data from breast cancer cell line
0159_6154_h133+_BT483


title: Breast cancer cell line: ZR75 (Batch 1)

description:
Gene expression data from breast cancer cell line
0159_6155_h133+_ZR75


title: WGAAD-421

description: Human Cortex from Alzheimer's Disease


title: Breast cancer cell line: MDA-MB-435s (Batch 1)

description:
Gene expression data from breast cancer cell line
0159_6156_h133+_MDA.MB.435


title: Calu-6 TSC 0.001 Bio replicate 3

city: Bethesda

first: maocheng

last: yang

address: 10 Center Drive

department: NCI

institute: National Institutes of Health

description: TSC 0.001 puffs/ml

hyb_protocol: Standard Affymetrix hyb on Affymetrix.GeneChip.HG-U133_Plus_2

scan_protocol: Affymetrix 3000G Scaner

data_processing: Genespring GX was used for data normalization following standard protocol with RMA normalization. ANOVA identified significanly-regulated genes (filter of 2 fold change genes against control - see series supplementary file).

source_name: Calu-6 TSC 0.001

label_protocol: Affymetrix labeling

growth_protocol: Human cancer cell lines Calu-6 and A549 cell culture in standard RPMI 1640 medium at 37 degree

extract_protocol: Qiagen RNaEasy mini protocol

treatment_protocol: Treat cells with diffierent concentration of Tobacco smoking condensate

tag: TSC 0.001 puffs/ml


title: WGAAD-274

description: Human Cortex from Alzheimer's Disease


title: WGAAD-46

description: Human Cortex from Alzheimer's Disease


title: Calu-6 TSC 0.0005 Bio replicate 3

description: TSC 0.0005puffs/ml

tag: TSC 0.0005puffs/ml


title: WGAAD-273

description: Human Cortex from Alzheimer's Disease


title: WGAAD-275

description: Human Cortex from Alzheimer's Disease


title: Calu-6 0 Bio replicate 3

description: Control

source_name: Calu-6 TSC 0

tag: Control (no TSC)


title: Calu-6 TSC 0.003 Bio replicate 3

description: TSC 0.003 puffs/ml

source_name: Calu-6 TSC 0.003

tag: TSC 0.003 puffs/ml


title: WGAAD-396

description: Human Cortex from Alzheimer's Disease


title: A549 0 Bio replicate 3

description: Control

source_name: A549 TSC 0


title: WGAAD-231

description: Human Cortex from Alzheimer's Disease


title: A549 TSC 0.0005 Bio replicate 3

description: TSC 0.0005puffs/ml


title: microsatellite instable colorectal tumor 24853

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Ann Arbor quantile-normalized trimmed-mean method

label_protocol: 3-5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue lysate using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen)

tag: sex

tag: Dukes stage

value: B


title: Calu-6 TSC 0.0005 Bio replicate 2

description: TSC 0.0005puffs/ml


title: A549 TSC 0.003 Bio replicate 3

description: TSC 0.003 puffs/ml


title: WGAAD-462

description: Human Cortex from Alzheimer's Disease


title: microsatellite instable colorectal tumor 24889


title: microsatellite instable colorectal tumor 33683

value: C


title: Calu-6 TSC 0.003 Bio replicate 2

description: TSC 0.003 puffs/ml


title: Calu-6 TSC 0.001 Bio replicate 2

description: TSC 0.001 puffs/ml


title: WGAAD-230

description: Human Cortex from Alzheimer's Disease


title: Calu-6 0 Bio replicate 2

description: Control


title: microsatellite instable colorectal tumor 33667


title: A549 TSC 0.003 Bio replicate 2

description: TSC 0.003 puffs/ml


title: microsatellite instable colorectal tumor 24859


title: WGAAD-249

description: Human Cortex from Alzheimer's Disease


title: A549 TSC 0.0005 Bio replicate 2

description: TSC 0.0005puffs/ml


title: A549 TSC 0.001 Bio replicate 3

description: TSC 0.001 puffs/ml


title: A549 TSC 0.001 Bio replicate 2

description: TSC 0.001 puffs/ml


title: Calu-6 TSC 0.003 Bio replicate 1

description: TSC 0.003 puffs/ml


title: WGAAD-248

description: Human Cortex from Alzheimer's Disease


title: microsatellite instable colorectal tumor 24844


title: microsatellite instable colorectal tumor 4298

value: A


title: A549 TSC 0.001 Bio replicate 1

description: TSC 0.001 puffs/ml


title: A549 TSC 0.0005 Bio replicate 1

description: TSC 0.0005puffs/ml


title: A549 0 Bio replicate 2

description: Control


title: WGAAD-184

description: Human Cortex from Alzheimer's Disease


title: microsatellite instable colorectal tumor 4393


title: Calu-6 0 Bio replicate 1

description: Control


title: A549 TSC 0.003 Bio replicate 1

description: TSC 0.003 puffs/ml


title: A549 0 Bio replicate 1

description: Control


title: WGAAD-264

description: Human Cortex from Alzheimer's Disease


title: Calu-6 TSC 0.001 Bio replicate 1

description: TSC 0.001 puffs/ml


title: microsatellite instable colorectal tumor 4291


title: WGAAD-384

description: Human Cortex from Alzheimer's Disease


title: Calu-6 TSC 0.0005 Bio replicate 1

description: TSC 0.0005puffs/ml


title: WGAAD-261

description: Human Cortex from Alzheimer's Disease


title: microsatellite instable colorectal tumor 4330


title: microsatellite instable colorectal tumor 4255


title: microsatellite instable colorectal tumor 4329


title: WGAAD-260

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 33677


title: WGAAD-436

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 33684


title: WGAAD-232

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 33700


title: WGAAD-234

description: Human Cortex from Alzheimer's Disease


title: microsatellite instable colorectal tumor 4284


title: WGAAD-460

description: Human Cortex from Alzheimer's Disease


title: WGAAD-481

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 33699


title: microsatellite stable colorectal tumor 24893


title: microsatellite stable colorectal tumor 24894


title: microsatellite stable colorectal tumor 33691

value: D


title: microsatellite stable colorectal tumor 24937


title: WGAAD-247

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 24896


title: WGAAD-446

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 33696


title: microsatellite stable colorectal tumor 24875


title: WGAAD-245

description: Human Cortex from Alzheimer's Disease


title: WGAAD-80

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 24951


title: microsatellite stable colorectal tumor 24877


title: microsatellite stable colorectal tumor 4266


title: microsatellite stable colorectal tumor 4254


title: WGAAD-239

description: Human Cortex from Alzheimer's Disease


title: WGAAD-50

description: Human Cortex from Alzheimer's Disease


title: WGAAD-72

description: Human Cortex from Alzheimer's Disease


title: WGAAD-83

description: Human Cortex from Alzheimer's Disease


title: WGAAD-477

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 4278


title: WGAAD-53

description: Human Cortex from Alzheimer's Disease

tag: pmi:


title: WGAAD-43

description: Human Cortex from Alzheimer's Disease


title: WGAAD-54

description: Human Cortex from Alzheimer's Disease


title: WGAAD-44

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 4312


title: microsatellite stable colorectal tumor 4310


title: WGAAD-381

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 4326


title: microsatellite stable colorectal tumor 4403


title: WGAAD-52

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 4321


title: microsatellite stable colorectal tumor 4389


title: WGAAD-68

description: Human Cortex from Alzheimer's Disease


title: WGAAD-51

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 4397


title: WGAAD-380

description: Human Cortex from Alzheimer's Disease


title: WGAAD-383

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 4387


title: WGAAD-397

description: Human Cortex from Alzheimer's Disease


title: WGAAD-61

description: Human Cortex from Alzheimer's Disease


title: WGAAD-90

description: Human Cortex from Alzheimer's Disease


title: WGAAD-65

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 4338


title: microsatellite stable colorectal tumor 4342


title: microsatellite stable colorectal tumor 4337


title: microsatellite stable colorectal tumor 4350


title: microsatellite stable colorectal tumor 4306


title: microsatellite stable colorectal tumor 4385


title: microsatellite stable colorectal tumor 4345


title: WGAAD-459

description: Human Cortex from Alzheimer's Disease


title: WGAAD-474

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 24832


title: WGAAD-442

description: Human Cortex from Alzheimer's Disease


title: WGAAD-49

description: Human Cortex from Alzheimer's Disease


title: WGAAD-242

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 24831


title: WGAAD-66

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 4281


title: microsatellite stable colorectal tumor 24840


title: WGAAD-86

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 4280


title: WGAAD-79

description: Human Cortex from Alzheimer's Disease


title: microsatellite stable colorectal tumor 4288


title: microsatellite stable colorectal tumor 4282


title: WGAAD-398

description: Human Cortex from Alzheimer's Disease


title: Empty vector-transfected 3Y1 cells grown in vitro, biological replicate 1

city: Chicago

first: Sean

middle: Pravin

last: Pitroda

state: IL

address: 5841 South Maryland Avenue, MC 1105

department: Radiation and Cellular Oncology

institute: The University of Chicago

description: gene expression data from empty vector-transfected 3Y1 cells grown in vitro

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on GeneChip® Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 700.

growth_protocol: Rat 3Y1 embryonic fibroblasts were stably transfected by an empty vector (3Y1/Vector) or one expressing the cytoplasmic domain of MUC1 (3Y1/MUC1-CD) as previously described (PMID: 16288032). Transfected 3Y1 cells were cultured in DMEM media with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mmol/L L-glutamine and maintained at 37 ˚C in a humidified environment containing 5% CO2. 3Y1/Vector and 3Y1/MUC1-CD cells were injected subcutaneously into the hindlimbs of female athymic mice (FCRI-Taconic, Frederick, MD) in increasing concentrations from 10^2 to 10^7 cells in 100 µl of PBS per mouse. Mice were euthanized using CO2 followed by cervical dislocation.

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

treatment_protocol: Tumors were excised, snap-frozen in liquid nitrogen, and stored at -80 ˚C. Frozen xenografts were sectioned into pieces approximately 5 mm^3 in size and soaked overnight in RNAlater®-ICE solution (Applied Biosystems-Ambion, Austin, TX, USA). Samples were spun, washed in RLT buffer (QIAGEN, Valencia, CA, USA) and homogenized on ice using a mechanical glass-Teflon homogenizer set at 3000 rpm. Further purification was performed using a combination of RNeasy spin columns and TRIzol reagent, as previously described (PMID: 11848408).

tag: non-transformed embryonic fibroblasts


title: Empty vector-transfected 3Y1 cells grown in vitro, biological replicate 2


title: MUC1-CD-transfected 3Y1 cells grown in vivo, biological replicate 1

description: gene expression data from MUC1-CD-transfected 3Y1 cells grown in vivo

tag: transformed embryonic fibroblasts


title: WGAAD-278

description: Human Cortex from Alzheimer's Disease

tag: tissue

tag: gender


title: WGAAD-418

description: Human Cortex from Alzheimer's Disease

tag: pmi


title: MUC1-CD-transfected 3Y1 cells grown in vitro, biological replicate 1

description: gene expression data from MUC1-CD-transfected 3Y1 cells grown in vitro


title: MUC1-CD-transfected 3Y1 cells grown in vivo, biological replicate 2


title: Patient 8, post-treatment

status: Public on Apr 09 2009

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

address: Via Rita Montalcini 4

department: Biomedical Sciences

institute: Humanitas University

description: Responder

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

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

data_processing: The data were processed using the RMA methodology without background correction using the affy package in R/Bioconductor.

source_name: Biopsy, Patient 8, post-treatment_Paclitaxel

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Samples with less than 1 ug quantities were amplified using 10 ng of total RNA.

extract_protocol: RNA was extracted using RNA-Easy kit from Qiagen according to manufacturer's instructions.

tag: treatment

value: Paclitaxel

tag: response

value: sensitive

tag: clinical group

tag: ca-125 coefficient


title: Patient 4, post-treatment

description: Non-responder

source_name: Biopsy, Patient 4, post-treatment_Carboplatin

value: Carboplatin

value: resistant


title: Patient 7, post-treatment

description: Responder

source_name: Biopsy, Patient 7, post-treatment_Paclitaxel


title: Patient 43, post-treatment

description: Responder

source_name: Biopsy, Patient 43, post-treatment_Paclitaxel


title: Patient 40, post-treatment

description: Non-responder

source_name: Biopsy, Patient 40, post-treatment_Paclitaxel


title: Patient 42, post-treatment

description: Non-responder

source_name: Biopsy, Patient 42, post-treatment_Paclitaxel


title: Patient 41, post-treatment

description: Responder

source_name: Biopsy, Patient 41, post-treatment_Paclitaxel