title: C (alcohol-fed, fracture) #3 vs. D (alcohol-fed, no fracture) #3

city: Temple

first: H

middle: Wayne

last: Sampson

address: 702 SW HK Dodgen Loop

department: Systems Biology & Translational Medicine

institute: TAMHSC-College of Medicine

description: 4-week-old Weanling rats fed with alcohol-fed methods for 4 weeks, then treated with surgical fracture or no surgical fracture, then collected samples after 3 days healing period to study the effects of fracture healing.

hyb_protocol: Rat Array Ready Oligo Set (AROS) version 3.0 (Operon) were spotted to UltraGAPS coated glass slide (Corning), and went through a pre-hybridization process to remove the excess DNA and reduce background noises. The dye-coupled aRNA was fragmented to improve the hybridization kinetics and signals produced on microarrays through using RNA Fragmentation Reagents (Ambion Cat#8740). The fragmented aRNA was applied to the glass arrays and hybridized overnight for 17-19 hrs in an environmentally controlled oven at 42°C. After hybridization, the slides were washed by using Hyb Buffer Kits (Operon).

scan_protocol: Arrays were scanned using an Axon GenePix 4000a scanner and GenePix Pro software.

data_processing: The dye-swap replicates had been normalized and combined in GeneSpring GX (ver. 7.3.1) to get 6 pairs of data sets from original 12 pairs of microarray results. The detailed normalization order in GeneSpring GX is listed below in 5 steps. (1) Data Transformation: Set measurements < 1 to 1. (2) Data Transformation: Dye Swap (applied to half of the experiments). (3) Per Spot Per Chip: Intensity dependent (Lowess) normalization. (4) Per Chip: Normalize to a median or percentile. (5) Per Gene: Normalize to median. These 6 pairs of data sets were then quantile normalized in the R statistics environment and intensities were then log2-transformed. The TMeV program from TIGR (The Institute for Genomic Research) was then used for statistics test on the array data.  P-values were calculated by “Between subjects” T-test.

organism: Rattus norvegicus

source_name: 4 weeks alcohol-fed, surgical fracture, sample collected after 3 days

label_protocol: After purifying the aRNA (amplified antisenses RNA), the quality of the aRNA was analyzed again using the Agilent 2100 Bioanalyzer. Subsequently, coupling reactions of qualified aRNA (8-10ug) and Cy3 or Cy5 mono-reactive dyes (Amersham Bioscience) were performed with the procedures of Ambion kits (Cat# 1795-7).

growth_protocol: 4-week-old Weanling rats were placed on ethanol-containing or pair-fed Lieber & DeCarli diets for 4 weeks prior to fracture.

extract_protocol: The region of the fracture calluses were harvested from the right hind-limb and frozen. The frozen samples were homogenized in 2 ml Trizol reagent using Spex Freezer Mill. The powder was quantitatively transferred to culture centrifuge tubes containing Trizol and RNA was isolated according to manufacturer's directions for the Trizol kit.

treatment_protocol: A small skin incision was made in the rat right knee, and the patella deflected. A 1.0 mm diameter hole was drilled into the intercondylar notch, and a stainless steel pin, inserted into the medullary canal and recessed about 1mm. The skin was closed with wound clips. A closed mid-diaphyseal fracture was induced using Bonnarens and Einhorn fracture device.

value: Sprague-Dawley

value: fracture callus from right hind-limb

tag: replicate

value: #3 of C

source_name: 4 weeks alcohol-fed, no surgical fracture, sample collected after 3 days

value: non-fracture callus from right hind-limb

value: #3 of D


title: pTracer GFP(+)

status: Public on May 01 2011

type: RNA

city: Dallas

first: Bray

last: Denard

state: TX

address: 5323 Harry Hines Blvd. L5.226

department: Molecular Genetics

country: USA

institute: University of Texas Southwestern Medical Center

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software, version 1.0.0.046 using Affymetrix default analysis settings (MAS 5.0 algorithm) and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: HCV Replicon containing Huh7-K2040 cells, transfected with pTracer (control)

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

growth_protocol: Cells were maintianed in DMEM (High Glucose) supplemented with 10% Fetal Calf Serum and 1% Pennicillin/Streptomycin.

extract_protocol: Total RNA was extracted with Qiagen Rneasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: We transfected HCV Replicon containing Huh7-K2040 cells with pTracer-CREB3L1 or pTracer.  After overnight incubation, we isolated cells  by trypsinization and utilized FACS to isolate GFP(+) cells.

tag: infected cells

value: HCV-Replicon infected hepatocytes

tag: trasnfection protocol

value: empty vector control


title: B (pair-fed, no fracture) #3 vs. D (alcohol-fed, no fracture) #2

description: 4-week-old Weanling rats fed with pair-fed or alcohol-fed methods for 4 weeks, then treated with no surgical fracture, then collected samples after 3 days healing period to study the effects of fracture healing.

source_name: 4 weeks pair-fed, no surgical fracture, sample collected after 3 days

tag: strain

tag: tissue

value: #3 of B

value: #2 of D


title: HUH7

tag: cell line

tag: cell type

value: Hepatocyte

tag: permissiveness to hcv

value: Non-Permissive


title: A (pair-fed, fracture) #2 vs. C (alcohol-fed, fracture) #1

description: 4-week-old Weanling rats fed with pair-fed or alcohol-fed methods for 4 weeks, then treated with surgical fracture, then collected samples after 3 days healing period to study the effects of fracture healing.

source_name: 4 weeks pair-fed, surgical fracture, sample collected after 3 days

value: #2 of A

value: #1 of C


title: S. mutans mixed culture with Veillonella and S. gordonii at late log phase, biological rep2

city: Oklahoma City

first: Fengxia

last: Qi

state: OK

address: 975 NE 10th St. BRC366

department: microbiology/immunology

institute: university of Oklahoma Health sciences center

description:
8sm+va+sg
Gene transcription data from planktonic culture at late exponential phase.

hyb_protocol: Following fragmentation, 3 ug of cDNA were hybridized for 16 hr at 47℃ on a GeneChip S. mutans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a laser scanner 7G (Affymetrix).

data_processing: Data were analyzed with Gene Chip Operating Software version 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Streptococcus mutans UA159

source_name: S. mutans UA159, tri-species culture with Veillonella and S. gordonii

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were grown as static culture aerobically in BHI. Cells were grown to late-log phase (OD600 = 0.8) and harvested by centrifugation.

extract_protocol: Cells were lysed using beat-beater. Extraction of total RNA was performed using TRIzol reagent (Invitrogen) according to the manufacturer's protocol.

value: planktonic

tag: culture type


title: S. mutans mixed culture with Veillonella and S. gordonii at late log phase, biological rep1

description:
7sm+va+sg
Gene transcription data from planktonic culture at late exponential phase.

value: tri-species culture with Veillonella and S. gordonii


title: Cardiac Progenitor Clone 30

city: Miami

first: Lina

middle: A

last: Shehadeh

state: FL

address: 1600 NW 10th Ave

department: Medicine

institute: University of Miami Miller School of Medicine

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Hybridization was documented using a GeneChip Scanner 3000 7G and validated with Affymetrix Microarray Suite version 5.0 (MAS 5.0) software. Pearson correlation coefficients demonstrated high reproducibility.

data_processing: Subsequent statistical analysis was performed using GeneSpring software (Silicon Genetics, Redwood City, CA). Normalized expression values were calculated by the GC-Robust Multi-array Average (GC-RMA) method. The Gene Ontology annotation tool was used to generate functional classifications. Using Pearson Correlation as a similarity measure and Average Linkage as a clustering algorithm, supervised hierarchical clustering based on each of the 962 GO functions was also generated using GeneSpring 7.2.

organism: Mus musculus

source_name: heart left ventricle

label_protocol: Standard Affymetrix protocol.

growth_protocol:
CPC isolation, growth and cloning:
CPCs were isolated from 5-6 month old adult mouse left ventricles. Minced tissue was digested with collagenase II (Worthington Biomedical Corp.) for 30 minutes at 37oC under shaking. Undigested heart pieces were allowed to settle in the bottom of the tube. The supernatant was separated and filtered through a 70 um cell strainer. Sca-1+ CPCs were isolated by magnetic separation using anti-Sca-1 antibody conjugated to biotin (eBioscience) and streptavidin-coated magnetic Dynabeads (Invitrogen Life Science) according to the manufacturer's instructions. Cells were plated in 60 mm bacterial Petri dishes to allow the formation of cardiospheres in CPC medium and after 24-48h the suspension was distributed into 24 well culture plates to allow CPC attachment. All wells were checked daily for proliferating cells. Proliferating CPCs were expanded by gradual transfer from smaller to larger culture dishes. CPCs were initially cloned using cloning rings and then subcloned 1-2 times by seri  al dilution in 96 well plates. The presence of stem cell markers sca-1, c-kit and oct-4 was determined by immunostaining.

extract_protocol: RNA was extracted using Trizol Reagent followed by purification using RNAEasy kit(Qiagen).

value: heart left ventricle

value: c-kit+ cardiac progenitor cell

tag: clone


title: Cardiac Progenitor Clone 11B


title: A (pair-fed, fracture) #3 vs. D (alcohol-fed, no fracture) #1

description: 4-week-old Weanling rats fed with pair-fed or alcohol-fed methods for 4 weeks respectively, then treated with surgical fracture or no surgical fracture, respectively, then collected samples after 3 days healing period to study the effects of fracture healing.

value: Sprague-Dawley

value: #3 of A

value: #1 of D


title: Cardiac Progenitor Clone 42


title: S. mutans mixed culture with Veillonella at late log phase, biological rep1

description:
5Sm+Va
Gene transcription data from planktonic culture at late exponential phase.

source_name: S. mutans UA159, dual-species culture with Veillonella

value: dual-species culture with Veillonella


title: A (pair-fed, fracture) #1 vs. B (pair-fed, no fracture) #1

description: 4-week-old Weanling rats fed with pair-fed methods for 4 weeks, then treated with surgical fracture or no surgical fracture, then collected samples after 3 days healing period to study the effects of fracture healing.

value: fracture callus from right hind-limb

value: #1 of A

value: non-fracture callus from right hind-limb

value: #1 of B


title: Cardiac Progenitor Clone 20B


title: S. mutans mixed culture with S. gordonii at late log phase, biological rep2

description:
4sm+sg
Gene transcription data from planktonic culture at late exponential phase.

source_name: S. mutans UA159, dual-species culture with S. gordonii

value: dual-species culture with S. gordonii


title: S. mutans mixed culture with Veillonella at late log phase, biological rep2

description:
6sm+va
Gene transcription data from planktonic culture at late exponential phase.


title: Stimulated  S1

city: Cleveland

first: Jean-Eudes

last: Dazard

state: Ohio

address: 10900 Euclid Avenue

department: Proteomics and Bioinformatics

institute: Case Western Reserve University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were variance-stabilized and normalized with the help of the 'lumi' R package using Variance-Stabilizing Transformation (VST),  a generalized-log(.) transformation ensuring that the variance is approximately independent of the mean intensity, followed by a Robust Spline Normalization (RSN) algorithm.

source_name: Treated with Doxycycline

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

growth_protocol: Maintained in supplemented DMEM with antibiotics, and 10% fetal bovine serum (Tet system approved; Clontech). Shows E1A expression 8h after the addition of 100 ng/ml of doxycycline.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment (DNAfree, Ambion kit in accordance with the prescribed protocol provided with the kit). Quality control was assessed by NanoDrop 1000 (Thermo Scientific, Waltham, MA) and by Agilent Bioanalyzer.

treatment_protocol: Treatment with Doxicycline was for 8 hr, and total RNA harvested 1 hour after treatment. Untreated cell cultures were cultivated as for 8 h, and total RNA harvested 1 hour after at the same time as treated cells

value: Balb/c 3T3

value: Tet-on inducible cell line with a wild-type E1A gene (243 amino-acid)

tag: treatment

value: Doxycycline


title: Stimulated  S3

description: replicate 3


title: Stimulated  S2

description: replicate 2


title: Monocyte cell line, control 2

city: Copenhagen

first: Morten

last: Hansen

address: Blegdamsvej 3B

department: Department of Cellular and Melocular Medicine

country: Denmark

institute: Faculty of Health Sciences

description: Gene expression data from serum stimulation of a human monocyte cell line

hyb_protocol: The cRNA was fragmented and a hybridization mix was prepared, which included the fragmented target, probe array controls, bovine serum albumin (BSA) and herring sperm DNA. In this experiment, the Affymetrix GeneChip Human Genome U133 Plus 2.0 was applied. The hybridized probe array was subsequently stained with fluorescent protein streptavidin-phycoerythirn (SAPE).

scan_protocol: Scanned with a GeneArray scanner at the excitation wavelength of 488 nm.

data_processing: Scaled and normalized using robust multi-array analysis (RMA) in the statistical software R.

source_name: Monocyte cell line (CRL-9853)

label_protocol: In accordance with the Affymetrix protocol and the one cycle eukaryotic target labelling assay, double-stranded cDNA was synthesized from total RNA and an IVT reaction was subsequently performed to produce biotin-labelled cRNA from the cDNA.

growth_protocol: The monocytes were started up growing in Optimen + 10% FCS + antibiotics. At time 0 hours the monocytes were divided into 13 bottles with 3 x 10E6 cells in each bottle. 15 ml of Optimen medium + 10% FCS + antibiotics was added to each bottle. After 80 hours the medium was changed to 15 ml of Optimen medium + antibiotics (no FSC).

extract_protocol: RNA was extracted with the NucleoSpin® RNA/Protein mini kit (Macherey-Nagel, Düren, Germany) in accordance with the manufactures protocol

treatment_protocol: After 96 hours the bottles were marked into 3 groups and annotated control, serum + inhibitor and serum only. 15 ul of DMSO was added to control and serum only bottles. 15 ul of 10mM U0196 (inhibitor) dissolved in DMSO were added to serum + inhibitor bottles. 2 hours later, after 98 hours, 1.6 ml of fetal calf serum  were added to serum + inhibitor and serum only. After 120 hours each bottle were split equally into 2 centrifuge tubes and spun down.

value: monocyte

tag: condition

value: serum starved


title: S. mutans mixed culture with S. gordonii at late log phase, biological rep1

description:
3Sm+Sg
Gene transcription data from planktonic culture at late exponential phase.

value: planktonic


title: S. mutans monoculture at late log phase, biological rep1

description:
1Sm
Gene transcription data from planktonic culture at late exponential phase.

source_name: S. mutans UA159, monoculture

value: monoculture


title: S. mutans monoculture at late log phase, biological rep2

description:
2Sm
Gene transcription data from planktonic culture at late exponential phase.


title: Quiescent Q1

description: replicate 1

source_name: Control Without Doxycycline


title: B (pair-fed, no fracture) #2 vs. C (alcohol-fed, fracture) #2

description: 4-week-old Weanling rats fed with pair-fed or alcohol-fed methods for 4 weeks, then treated with no surgical fracture or surgical fracture, respectively, then collected samples after 3 days healing period to study the effects of fracture healing.

value: #2 of B

value: #2 of C


title: Cardiac Progenitor Clone 1D

value: heart left ventricle

value: c-kit+ cardiac progenitor cell


title: Quiescent Q3

description: replicate 3


title: SG200_drep1_CC-MMglc_w-AA_48h_1

city: Utrecht

first: Wieke

middle: R.

last: Teertstra

address: Padualaan 8

department: Biology

country: Netherlands

institute: University of Utrecht

description: Monitor the effects of the deletion of the repellent gene rep1 on expression profiles in SG200.

hyb_protocol: Affimetrix EukGE-WS2 on a GeneChip Fluidics Station 400

scan_protocol: Arrays were scanned twice using a GeneArray Scanner (Agilent/Affymetrix).

organism: Mycosarcoma maydis

source_name: Deletion of gene rep1 (um03924) in SG200 background, nourseothricin replacement, grown on NM+ charcoal plates for 48 h.

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labeling kit.

growth_protocol: For aerial hyphae formation cells were grown for 48h at 22 °C on nitrate minimal medium (NM+) (Holliday, 1974) containing 2 % agar (w/v), 1 % charcoal (w/v), 20 mg l-1 histidine, 380 mg l-1 leucine, 20 mg l-1 tryptophan, 50 mg l-1 uracil and 76 mg l-1 Yeast Synthetic Drop-out Medium Supplements (Sigma, Y2001). This was performed for three independently conducted replicates

extract_protocol:
RNA samples were frozen in liquid nitrogen for three independently conducted replicates.
Total RNA was extracted using TRIZOL (Invitrogen) according to the manufacturers instructions. RNA samples were column purified (Qiagen RNeasy) and the quality checked using a Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent Technologies).

tag: genotype

tag: genetic background

value: U. maydis strain SG200 (Bölker et al., 1995) is a haploid solopathogenic FB1 derivative


title: SG200_drep1_CC-MMglc_w-AA_48h_3


title: Patient 1 b

city: New York

first: Kristen

last: Brennand

state: NY

address: 1425 Madison Ave, 9-20B

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: As recommended by Affymetrix.

scan_protocol: GeneChip scanner 3000 7G

data_processing: Data in the sample data tables are rma background corrected, quantile normalized, log2 transformed and mean probeset summarized. Further processed data on the Series record were performed by Partek Genomics Suite.

source_name: hiPSC-derived 6-week-old neurons

label_protocol: GeneChip WT Sense Target Labeling and Control Reagents (900652) and GeneChip WT cDNA Synthesis and Amplification Kits (900672 and 900673)

growth_protocol: For neural differentiations, NPCs were dissociated with Accutase and plated in neural differentiation media (DMEM/F12-Glutamax, 1XN2, 1X B27-RA, 20 ng/ml BDNF, 20 ng/ml GDNF (Peprotech), 1 mm dibutyrl-cyclicAMP (Sigma), 200 nm ascorbic acid (Sigma) onto PORN/Laminin-coated plates. 200,000 cells/well of a 6-well plate. hiPSC derived-neurons were differentiated for 6 weeks.

extract_protocol: Cells were lysed in RNA BEE (Tel-test, Inc). RNA was chloroform extracted, pelleted with isopropanol, washed with 70% ethanol and resuspended in water. RNA was treated with RQ1 RNAse-free DNAse (Promega) for 30 minutes at 37C and then the reaction was inactivated by incubation with EGTA Stop buffer at 65C for 10 minutes.

tag: disease state

value: Schizophrenic

tag: gender

value: Male


title: Patient 1 c


title: Quiescent Q2

description: replicate 2


title: SG200_drep1_CC-MMglc_w-AA_48h_2


title: Patient 4 c


title: Patient 1 a


title: SG200_WT_CC-MMglc_w-AA_48h_3

description: Control experiment to measure the effects of the deletion of the repellent gene rep1 in SG200 during aerial hyphae formation.

source_name: U. maydis strain SG200_WT grown on NM+ charcoal plates for 48 h.

value: wild type


title: SG200_WT_CC-MMglc_w-AA_48h_2


title: Patient 4 b


title: Patient 4 a


title: SG200_WT_CC-MMglc_w-AA_48h_1


title: wke-sf-95-888-05-130308-u133p-2

city: Berlin

first: Susann

last: Förster

address: R. Rössle Str 10

country: Germany

institute: MDC

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000. Images were processed using GCOS 1.4.

data_processing: CEL data files were imported in GeneSpring GX 10.0.2 software (Agilent Technologies, Santa Clara, USA) and pre-processed using the GC-RMA algorithm. Statistical analysis for differentially expressed genes was performed using Welch-test.

source_name: gastric adenocarcinoma tissue of intestinal type

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: TRIzol (Invitrogen) extraction of total RNA, with RNeasy-based (Qiagen) cleanup and on-column DNase I (Qiagen) digest, was performed according to the manufacturer's instructions.

treatment_protocol: Tissue samples were snap-frozen immediately after pathological survey and stored constantly at -80 °C.

tag: histological type

value: intestinal


title: Patient 3 a

value: Female


title: wke-sf-93-1106-98-130308-u133p-2

source_name: gastric adenocarcinoma tissue of diffuse type

value: diffuse


title: wke-sf-90-1590-00-060208-u133p-2


title: wke-sf-89-860-95-060208-u133p-2


title: Patient 2 c


title: S_14_days_YFP_pos_3

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

hyb_protocol: Labeled samples were hybridized overnight to the Agilent 4X44 Whole Mouse Genome Array.

scan_protocol: Arrays were washed and then scanned with the model G2565B Agilent DNA microarray Scanner (Agilent Technologies).

data_processing: Median intensities of each element on the array were captured with Agilent Feature Extraction version 9.53 (Agilent Technologies). Quality control diagnostic plots were prepared for each array, and those failing to exhibit high-quality hybridizations were excluded from further analysis, resulting in the final dataset containing four biological replicates for each condition. The subsequent analysis was performed as previously (Rieck et al. 2009).

source_name: 14 days YFP pos

label_protocol: Amplified cDNA was prepared using the WT-Ovation Pico Amplification System (NuGEN Technologies). Amplified cDNA was directly labeled using the BioPrime Array CGH Genomic Labeling System with Cy3-labeled nucleotides (GE Amersham Biosciences).

growth_protocol: Foxl1-CRE mice were crossed with Rosa26R FYP reporter mice. Offspring were 6 to 10 weeks old.

extract_protocol: Total RNA was extracted from liver samples and sorted cells using Trizol and RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Foxl1-Cre; RosaYFP mice were fed a DDC diet for 3, 7, and 14 days, and YFP+ and YFP- were isolated from total non-parenchymal cells that are negative for CD45. Total non-parenchymal cells from chow-fed mice were used as controls.

value: Foxl1-CRE; RosaYFP mouse

tag: yfp expression

value: YFP positive

tag: days of ddc treatment

value: liver

value: non-parenchymal


title: Patient 3 b


title: Patient 2 b


title: Patient 3 c


title: wke-sf-86-2355-95-060208-u133p-2


title: Control 4 c

value: Control


title: Patient 2 a


title: S_14_days_YFP_pos_2


title: S_7_days_YFP_pos_3

source_name: 7 days YFP pos


title: S_7_days_YFP_pos_2


title: WKE_SF_72_170507_3661_03_U133_plus_2


title: Control 4 b


title: WKE_SF_68_170507_988_02_U133_plus_2


title: Control 4 a


title: WKE_SF_70_170507_1777_03_U133_plus_2


title: Control 3 c


title: WKE_SF_66_150507_2789_01_U133_plus_2


title: S_7_days_YFP_pos_1


title: S_3_days_YFP_pos_4

source_name: 3 days YFP pos


title: Control 3 b


title: S_7_days_YFP_pos_4


title: WKE_SF_62_100507_2864_02_U133_plus_2


title: S_3_days_YFP_pos_3


title: Control 2 c


title: Control 2 b


title: Control 3 a


title: WKE_SF_57_100507_176_01_U133_plus_2


title: S_3_days_YFP_pos_1


title: S_14_days_YFP_neg_3

source_name: 14 days YFP neg

value: YFP negative


title: WKE_SF_55_100507_1360_03_U133_plus_2


title: WKE_SF_56_100507_1817_01_U133_plus_2


title: S_3_days_YFP_pos_2


title: Control 2 a


title: Control 1 c


title: WKE_SF_61_100507_340_00_U133_plus_2


title: Control 1 b


title: WKE_SF_54_040507_1654_99_U133_plus_2


title: WKE_SF_53_040507_2582_99_U133_plus_2


title: S_7_days_YFP_neg_3

source_name: 7 days YFP neg


title: S_7_days_YFP_neg_2


title: S_7_days_YFP_neg_4


title: WKE_SF_52_040507_298_01_U133_plus_2


title: WKE_SF_50_040507_1955_98_U133_plus_2


title: Control 1 a


title: S_7_days_YFP_neg_1


title: S_14_days_YFP_neg_2


title: WKE_SF_47_040507_3066_96_U133_plus_2


title: WKE_SF_49_040507_2778_98_U133_plus_2


title: WKE_SF_46_240407_509_02_U133_plus_2


title: S_3_days_YFP_neg_4

source_name: 3 days YFP neg


title: S_3_days_YFP_neg_3


title: S_14_days_YFP_neg_1


title: WKE_SF_48_040507_1883_97_U133_plus_2


title: S_3_days_YFP_neg_1


title: S_3_days_YFP_neg_2


title: S_0_day_4

source_name: 0 day

value: pre-YFP


title: WKE_SF_43_240407_19_00_U133_plus_2


title: miR-302/367-iPS Clone 10

first: Frederick

last: Anokye-Danso

state: Pa

address: 421 Curie Blvd Room 938

description: Gene Expression data from miR-302/367-iPS cells

hyb_protocol: GeneChip WT Terminal Labeling and Hybridization kit from Affymetrix following manufacturer's instructions.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: Data was analyzed using Partek Genomics Suite v6.5.

source_name: Embryonic Fibroblast

label_protocol: Ambion WT Expression Kit was used following manufacturer's instruction

growth_protocol: Samples 1, 2, 3, 7, 8 and 9 were maintained in mouse ES media. Samples 4, 5 and 6 were maintain in fibroblast media. All samples were incubated at 37 degress Celsius in a humidified chamber containg 5% carbondioxide.

extract_protocol: Trizol was used following manufacturer's protocol

treatment_protocol: For samples 4, 5 and 6, cells were trypsinized and cells harvested by centrifugation. For the rest of the samples, feeders were eliminated before cells were harvested.

value: embryonic fibroblast


title: WKE_SF_42_240407_2610_98_U133_plus_2


title: miR-302/367-iPS Clone 6


title: S_0_day_3


title: WKE_SF_41_240407_2114_00_U133_plus_2


title: miR-302/367-iPS Clone 7


title: MEF2

description: Gene expression data from C57BL/6J cells


title: MEF3


title: S_0_day_1


title: WKE_SF_36_130407_1766_98_U133_plus_2


title: S_0_day_2


title: WKE_SF_35_130407_2506_99_U133_plus_2


title: WKE_SF_34_110407_1546_99_U133_plus_2


title: ES5

description: Gene expression data from R1 ES cells

source_name: Embryonic Stem Cells

value: embryonic stem cells


title: ES4

description: Gene expression data from R1 ES cells


title: ES6

description: Gene expression data from R1 ES cells


title: WKE_SF_31_110407_2754_97_U133_plus_2


title: female JAK2 KO liver sample 141

city: San Francisco

first: Ethan

middle: J

last: Weiss

state: CA

address: 555 Mission Bay Blvd South, Rm 382

department: CVRI

institute: UCSF

description:
gene expression data from female JAK2 KO mouse liver
FKO_141

hyb_protocol: Each sample was then hybridized to an Affymetrix Mouse Gene 1.0 ST array by standard procedures.

scan_protocol: Gene chips were scanned using the Affymetrix gene chip scanner 3000 7G

data_processing: Data were analyzed using the Affymetrix Expression Console (algorithm-name = rma-gene-default) and then furhter analyzed using Microsoft Excel

source_name: Mouse liver (8 weeks)

label_protocol: Total RNA from 3 8-week old male and 3 female JAK2L and littermate control livers was prepared as above. RNA was analyzed using the Agilent 2100 BioAnalyzer. All samples were prepared using Affymetrix WT cDNA Synthesis and Amplification Kits for cDNA.synthesis, cRNA amplification and conversion to sense strand DNA products according to manufacturer's instructions. Samples were then fragmented and end labeled using Affymetrix WT Target Labeling and Control Reagents Kits according to manufacturer's instructions.

growth_protocol: Animals were maintained on breeder chow

extract_protocol: Total RNA was isolated from mouse livers with TRIZOL (Invitrogen, Carlsbad CA) extraction, followed by purification with RNeasy Mini Column (QIAGEN, Valencia CA).

value: mixed (C57Bl/6:129Sv) background

value: female

value: Liver

tag: sample number

tag: genotype/variation

value: JAK2 KO

tag: age

value: 8 weeks


title: RORasg/sg WAT_HFD_rep5

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
Agilent TIFF High File = US23502387_251486824232_S01_H.tif
Agilent TIFF Low File = US23502387_251486824232_S01_L.tif
RNA samples from Staggerer mice fed with a HFD

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNA was fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters

source_name: Staggererer mice fed with a HFD for 6 weeks

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol

growth_protocol: Liver and white adipose tissue (WAT) from WT and RORasg/sg mice fed with a high fat diet (HFD; 35% fat) for 6 weeks

extract_protocol: Qiagen RNeasy mini kit with on-column DNAseI treatment

treatment_protocol: WT and RORasg/sg mice were fed with high fat diet (HFD; 35% fat)

tag: strain

value: RORasg/sg

value: male

value: 5 Month old

tag: tissue

value: White adipose tissue (WAT)

tag: diet

value: 35% Fat Diet (High Fat Diet; HFD)


title: S_14_days_YFP_pos_1

value: Foxl1-CRE; RosaYFP mouse

value: YFP positive

value: liver

tag: cell type


title: MEF1


title: WKE_SF_29_110407_535_02_U133_plus_2

value: diffuse


title: RORasg/sg WAT_HFD_rep3


title: WKE_SF_30_110407_939_95_U133_plus_2


title: WKE_SF_33_110407_1491_97_U133_plus_2

value: intestinal


title: female JAK2 KO liver sample 131

description:
gene expression data from female JAK2 KO mouse liver
FKO_131


title: RORasg/sg WAT_HFD_rep2

description:
Agilent TIFF High File = US23502387_251486824231_S01_H.tif
Agilent TIFF Low File = US23502387_251486824231_S01_L.tif
RNA samples from Staggerer mice fed with a HFD


title: RORasg/sg WAT_HFD_rep4


title: female JAK2 WT liver sample 132

description:
gene expression data from female JAK2 WT mouse liver
FWT_132

value: WT


title: WKE_SF_26_030407_1065_99_U133_plus_2


title: WKE_SF_21_050107_2044_96_U133_plus_2


title: female JAK2 WT liver sample 147

description:
gene expression data from female JAK2 WT mouse liver
FWT_147


title: WKE_SF_19_030107_2092_03_U133_plus_2


title: WT White adipose tissue (WAT)_HFD_rep5

description:
Agilent TIFF High File = US23502387_251486824232_S01_H.tif
Agilent TIFF Low File = US23502387_251486824232_S01_L.tif
RNA samples from WT mice fed with a HFD

source_name: WT mice fed with a HFD for 6 weeks

value: wild type


title: female JAK2 KO liver sample 102

description:
gene expression data from female JAK2 KO mouse liver
FKO_102

value: mixed (C57Bl/6:129Sv) background


title: wke-sf-81-2339-04-060208-u133p-2


title: WT White adipose tissue (WAT)_HFD_rep4

description:
Agilent TIFF High File = US23502387_251486824233_S01_H.tif
Agilent TIFF Low File = US23502387_251486824233_S01_L.tif
RNA samples from WT mice fed with a HFD


title: WKE_SF_20_050107_63_97_U133_plus_2


title: WT White adipose tissue (WAT)_HFD_rep3

description:
Agilent TIFF High File = US23502387_251486824231_S01_H.tif
Agilent TIFF Low File = US23502387_251486824231_S01_L.tif
RNA samples from WT mice fed with a HFD


title: RORasg/sg WAT_HFD_rep1

description:
Agilent TIFF High File = US23502387_251486824233_S01_H.tif
Agilent TIFF Low File = US23502387_251486824233_S01_L.tif
RNA samples from Staggerer mice fed with a HFD


title: male JAK2 KO liver sample 207

description:
gene expression data from male JAK2 KO mouse liver
MKO_207


title: female JAK2 WT liver sample 119

description:
gene expression data from female JAK2 WT mouse liver
FWT_119

value: female


title: WT White adipose tissue (WAT)_HFD_rep1


title: WT White adipose tissue (WAT)_HFD_rep2


title: male JAK2 KO liver sample 114

description:
gene expression data from male JAK2 KO mouse liver
MKO_114

value: Liver


title: RORasg/sg liver_HFD_rep5

description:
Agilent TIFF High File = US22502532_251486820888_S01_H.tif
Agilent TIFF Low File = US22502532_251486820888_S01_L.tif
RNA samples from Staggerer mice fed with a HFD


title: WKE_SF_15_081206_25_01_U133_plus_2


title: WKE_SF_14_081206_2480_03_U133_plus_2


title: WKE_SF_10_291106_2767_97_U133_plus_2


title: WKE_SF_16_081206_131_99_U133_plus_2


title: RORasg/sg liver_HFD_rep4


title: male JAK2 WT liver sample 126

description:
gene expression data from male JAK2 WT mouse liver
MWT_126


title: male JAK2 KO liver sample 122

description:
gene expression data from male JAK2 KO mouse liver
MKO_122

value: JAK2 KO


title: RORasg/sg liver_HFD_rep3

description:
Agilent TIFF High File = US22502532_251486820887_S01_H.tif
Agilent TIFF Low File = US22502532_251486820887_S01_L.tif
RNA samples from Staggerer mice fed with a HFD


title: WKE_SF_09_081106_1496-96_U133_plus_2


title: male JAK2 WT liver sample 116

description:
gene expression data from male JAK2 WT mouse liver
MWT_116

value: 8 weeks


title: WKE_SF_08_081106_613-98_U133_plus_2


title: RORasg/sg liver_HFD_rep2

value: RORasg/sg


title: RORasg/sg liver_HFD_rep1

value: male


title: St 35S::AtCBF3

city: East Lansing

first: Marcela

last: Carvallo

state: MI

address: 310 Plant Biology bldg

department: Plant Research Laboratory

institute: Michigan State University

description: St ox_2: 2 slides = 2 replicates

hyb_protocol: The slides were hybridized using the indirectly labeled aminoallyl probes hybridization method (http://www.jcvi.org/potato/sol_ma_protocols.shtml)

scan_protocol: Slides were scaned using a Affymetrix 428 Array scanner.

data_processing: Slide images were quantified using Genepix 3.0 (Axon Instruments, Union City, CA). GPR files were obtained. The data were normilized using the print tip loess method in the Limma package (Smyth 2004). A list of differentialy expressed clones were ranked based on p value, using false discovery rate to correct for multiple testing. Log2 ratios (M) were obtained from limma as average of the 3 biological replicates (with the exeption of St transgenic lines that were only 2). Then these Log2 ratios were averaged for the two clone technical replicates in each slide.

organism: Solanum tuberosum

source_name: St 35S::AtCBF3 lines experimental samples

label_protocol: 20 mg of total RNA were reverse transcribed and labeled with Cy5 or Cy3 by the indirect aminoallyl method (http://www.jcvi.org/potato/sol_ma_protocols.shtml)

growth_protocol: Sc and St wild type plants and transgenic lines were grown for 3 weeks at 25oC and 350 mmol m-2s-1 light intensity on 16:8 photoperiod.

extract_protocol: Total RNA was isolated from leaf tissue using Rneasy Plant Mini Kits (Qiagen).

treatment_protocol: Three independent experiments were done for cold treatments. Eight hours after dawn, plants were transfered to 2oC with 50 mmol m-2s-1 light intensity, tissue was harvested after 2h, 24h and 7d of cold. Control plants were kept at 25oC and 350 mmol m-2s-1 light intensity and tissue was harvested after 2h and 24h. For the 35S::AtCBF3 transgenic lines, three independent Sc lines and 2 St lines were used, 8h after dawn tissue was harvested. Tissue was frozen into liquid nitrogen and store at -80oC

value: Sc 35S::AtCBF3

source_name: St wild type control samples


title: Sc 35S::AtCBF3

description: Sc ox_3: 3 slides = 3 replicates

organism: Solanum commersonii

source_name: Sc 35S::AtCBF3 lines experimental samples

source_name: Sc wild type control samples


title: male JAK2 WT liver sample 112

description:
gene expression data from male JAK2 WT mouse liver
MWT_112


title: WT liver_HFD_rep4

description:
Agilent TIFF High File = US22502532_251486820842_S01_H.tif
Agilent TIFF Low File = US22502532_251486820842_S01_L.tif
RNA samples from WT mice fed with a HFD

value: 5 Month old


title: heart_KO_rep1

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

description: 1 week pressure overload by TAC

hyb_protocol: RNA samples were hybridizaed with Affymetrix expression arrays offering whole-transcript coverage. After hybridization, non-specific binding was washed off according to the manufacturer's protocol.

scan_protocol: Affymetrix arrays were scanned with the Affymetrix GeneArray scanner.

data_processing: In the Expression Console software, hybridization intensity data were normalized using the Robust Multichip Average (RMA) method.

source_name: mouse MAFbx KO heart

label_protocol: Biotinylated cRNA were prepared from total RNA as described by Affymetrix.

growth_protocol: No growth protocol. Samples were taken from animals in vivo.

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

treatment_protocol: No treatment prior to experiment was applied.

value: heart

value: MAFbx KO


title: heart_KO_rep3

description: 1 week pressure overload by TAC


title: heart_KO_rep2

description: 1 week pressure overload by TAC


title: St WT 2h cold

description: St C2h: 3 slides = 3 replicates

source_name: St wild type experimental samples 2h cold

source_name: St wild type control samples 2h warm


title: WT liver_HFD_rep5

description:
Agilent TIFF High File = US22502532_251486820887_S01_H.tif
Agilent TIFF Low File = US22502532_251486820887_S01_L.tif
RNA samples from WT mice fed with a HFD

value: 35% Fat Diet (High Fat Diet; HFD)


title: Sc WT 7 days cold

description: Sc C7d: 3 slides = 3 replicates

source_name: Sc wild type experimental samples 7 days cold

source_name: Sc wild type control samples 24h warm


title: St WT 24h cold

description: St C24h: 3 slides = 3 replicates

source_name: St wild type experimental samples 24h cold

source_name: St wild type control samples 24h warm


title: WT liver_HFD_rep3


title: heart_WT_rep1

description: 1 week pressure overload by TAC

source_name: mouse wildtype heart

value: wildtype


title: St WT 7 days cold

description: St C7d: 3 slides = 3 replicates

source_name: St wild type experimental samples 7 days cold


title: WT liver_HFD_rep1


title: WT vs ddlt

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

hyb_protocol: Agilent hybridization protocol for Two-color microarray-based Gene expression analysis. Version 5.5

scan_protocol: Scanned on an ScanArray Express 4000 scanner (Perkin Elmer, Wellesley, MA). Images were quantified using ImaGene Version 7.5 software (BioDiscovery Inc., Marina Del Rey, CA, USA).

data_processing: scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244). Interslide scaling was performed using Postprep

organism: Lactiplantibacillus plantarum

source_name: Wildtype strain grown in MRS, harvested in logarithmic phase

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: non-pH controlled Batch cultivation MRS-broth

extract_protocol: Quenching Buffer 66.7 mM HEPES (pH 6.5) 60%Methanol Extraction Mixture (Prepared in a screw-cap tube) -500 µl phenol/Chloroform -30 µl10% SDS -30 µl 3 M NaAc (pH 5.2) -500 mg glass-beads (75-150 µm) -400 µl TE buffer  1.For each sample prepare a tube with Extraction Mixture  2.Harvest cells and quench them immediately in Quenching Buffer. Add 4 volumes of Quenching Buffer ( 40°C) to 1 volume of cell culture  3.Mix and store the sample at -40°C  4.Centrifuge cells at -20°C at 9000 rpm for 10 minutes (Centrifuge RC5B)  5.Discard the supernatant; keep the cell pellet cooled and work quickly to prevent condensation of water. Transfer the pellet with a pre-cooled spatula to a screw-crap tube with Extraction Mixture  6.Mix the cell pellet thoroughly with Extraction Mixture by shaking by hand  7.Freeze the tube immediately in liquid nitrogen  8.Break cells in the Savant FastPrep FP120. Three times 40 seconds at speed 4.0 (cool cells between steps if necessary)  9.Centrifuge for 5 minutes at 4°C in an Eppendorf centrifuge at 10.000 rpm  10.Transfer 500 µl of the supernatant to a new tube. Add 400 µl chloroform (chloroform should be cooled at 4°C)  11.Centrifuge for 2 minutes in an Eppendorf centrifuge at full speed (4°C)  12.Continue with the High Pure RNA Isolation Kit from Roche (order # 1 828 665)  13.Incubate for 60 minutes with DnaseI, elute with 50 µl elution buffer   14.Store the RNA in at least 2 aliquots, one of 20 µl (for concentration and quality analysis and labelling) and one back-up of 30 µl at -80°C.

treatment_protocol: sampled at OD 1

tag: background strain

source_name: KO of dlt gene, grown in MRS, harvested in logarithmic phase

value: delta dlt


title: Sc WT 2h cold

description: Sc C2h: 3 slides = 3 replicates

source_name: Sc wild type experimental samples 2h cold

source_name: Sc wild type control samples 2h warm


title: ddlt vs dtagF1-2

source_name: KO of tagF1-F2 genes, grown in MRS, harvested in logarithmic phase

value: delta tagF1-F2


title: dtagF1-2 vs WT


title: Sc WT 24h cold

description: Sc C24h: 3 slides = 3 replicates

source_name: Sc wild type experimental samples 24h cold


title: Heart CSS3 uninfected 3

city: Montreal

first: Sean

last: Wiltshire

address: 3649 Sir william Osler, Rm 356

department: Human Genetics

country: Canada

institute: McGill University

description:
replicate 3
SVL042-1

data_processing: The data were normalized using FlexArray

source_name: Heart mock infection

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit (IL1791)

extract_protocol: Hearts were perfused with st. thomas solution, removed and placed immediately into RNAlater(ambion) RNA stabilization reagent. 30 mg were used to extract total RNA using Qiagen Rneasy Fibrous tissue, quality control by agilent bioanalyzer

treatment_protocol: Mice were infected with a dose of 400pfu per gram of CVB3(CG) or mock infected with sterile PBS

tag: Sex

value: Female

value: 7 weeks


title: Heart CSS3 uninfected 1

description:
replicate 1
SVL039-1


title: WT liver_HFD_rep2

source_name: WT mice fed with a HFD for 6 weeks

value: wild type


title: Heart CSS3 uninfected 2

description:
replicate 2
SVL040-1


title: Heart B6 uninfected 3

description:
replicate 3
SVL036-1


title: Heart B6 uninfected 2

description:
replicate 2
SVL034-1


title: in vivo C57J/B6 sugar diet_5

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: University of Michigan Medical School

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on custom GeneChip GPL9803. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Affymetrix Expression Console software using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Bacteroides ovatus

source_name: in vivo gnotobiotic mice fed defined sugar diet

label_protocol: Biotin-UDP end labeling.

growth_protocol: Bacteria were grown either in vitro to mid-exponential phase on the defined carbon source indicated; or, extracted from the ceca of gnotobiotic mice colonized with only B. ovatus.

extract_protocol: RNA was extracted directly from in vitro-grown bacteria. In vivo-grown cells were subjected to an initial phenol/chloroform bead-beating step. Both types of samples were subjected to final purification steps consisting of Qiagen RNAEasy extraction, Ambicon DNAEasy treatment; Final Qiagen RNAEasy cleanup.

treatment_protocol: In vitro-grown bacteria or mouse cecal contents were treated with RNAProtect reagent (Qiagen) and frozen at -80C until RNA extraction.

value: ATCC 8483

tag: treatment

value: sugar diet

tag: isolation source

value: cecum of C57BL/6 mouse fed simple sugar diet


title: in vivo C57J/B6 sugar diet_6


title: Heart B6 uninfected 1

description:
replicate 1
SVL033-1


title: 6.4P

city: Worcester

first: Mei

last: Xu

state: MA

address: 55 Lake Avenue, North

department: Information service

institute: university of Massachusetts

description: Gene expression data from Cpeb1 KO embryonic fibroblasts

hyb_protocol: Hybridization was @ 45C overnight in Affymetrix GeneChip Hybridization Oven 320. Washed using Affymetrix GeneChip Fluidics Station 450

scan_protocol: scanned with the GeneChip Scanner 3000 with 7G upgrade

data_processing: Matrix data was generated by GeneSpring GX11.5.1, guided workflow, meaning RMA was performed on the data and then the data are baseline transformed to median of all samples.

source_name: embryonic fibroblasts

label_protocol: labeling was performed using Enzo BioArray HighYield RNA Transcript Labeling Kit

growth_protocol: Fibroblasts (MEFs) isolated from WT and CPEB KO mice E12.5–E14.5 embryos (MEFs) were cultured in Dulbecco’s Modified Eagle’s Medium with 10% fetal bovine serum according to a 3T3 protocol. The cells were harvested in the presence of 100ug/ml cycloheximide and subjected to polysome fractionation. The lysate was layered onto a continuous sucrose gradient (15%-50%) and centrifuged for 2h at 40k RPM in a SW41 rotor. The RNA was isolated from polysomal fractions, pooled, and subjected to microarray analysis by UMass Medical School Genomics Core facility with Affymetrix GeneChip Mouse Genome 430A 2.0 array.  The gradients were performed with biologic triplicates.  The data were analyzed with DAVID Bioinformatics Resources 6.7, Panther pathway annotation.

extract_protocol: The RNA was extracted using Trizol reagent (Invitrogen) and subsequent RNAeasy (Qiagen) cleanup.

value: Cpeb KO

value: 12 weeks old


title: ∆SpoT_rep3

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

hyb_protocol: Labeled cDNA was hybridized to GeneChip CauloHi1 according to GeneChip Expression analysis technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: After hybridization for 16 hours at 50°C, arrays were washed using protocol PRO-GE-W52-V3 and stained on a GeneChipFluidics Station (Affymetrix)  according to the Genechip Expression analysis technical manual.

data_processing: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL intensity files were generated by GCOS (Gene Chip Operating Software ) v. 1.4.

organism: Caulobacter vibrioides

source_name: Caulobacter crescentus CB15N ∆SpoT

label_protocol: cDNA was column purified, fragmented using DNAseI (GE Life Sciences, Piscataway, NJ), and end labeled using GeneChip labeling reagent (Affymetrix, P/N 900542).

growth_protocol: Each strain was cultured in M2 glucose defined medium at 30 degrees C and grown to OD660=0.3, then washed in M2 media lacking glucose and incubated in M2 media lacking glucose for 5 minutes.

extract_protocol: Trizol RNA extraction, followed by DNAseI treatment.  RNA was re-extracted using acid phenol, alcohol precipitated, and resuspended in deionized water.

treatment_protocol: Experiment is measuring  differences in the transcriptomes of a CB15N wild-type strain and a CB15N∆SpoT strain in glucose starvation.

value: ∆SpoT


title: ∆SpoT_rep2


title: Heart CSS3 infected 2

description:
replicate 2
SVL029-1

source_name: Heart CVB3 infection


title: E7P-


title: Heart CSS3 infected 3

description:
replicate 3
SVL031-1


title: E7P+

description: Gene expression data from wild type embryonic fibroblasts


title: in vivo C57J/B6 sugar diet_4


title: in vivo C57J/B6 sugar diet_2


title: in vivo C57J/B6 sugar diet_3


title: WT_3

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Array data were analyzed using MAYDAY (Version 2.10). Array data were subjected to robust multi-array average (RMA) normalization. Normalized data were used for calculating fold changes of up- and down-regulated genes using Student's test. Only data with a false discovery rate (FDR) adjusted p-value <0.05 and at least 2x differential expression were included in the analysis. Data underwent z-score transformation for display.

source_name: Regulatory T-cells CD4+CD25+ from wild type mice

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).

tag: genotype

value: Wild type


title: Heart CSS3 infected 1

description:
replicate 1
SVL028-1


title: CB15N_rep3

source_name: Caulobacter crescentus CB15N

value: WT


title: WT_2


title: Heart B6 infected 3

description:
replicate 3
SVL027-1


title: CB15N_rep2


title: ∆SpoT_rep1


title: WT_1


title: 5.4P


title: Primary_Cholangocyte_Hyb4

treatment_protocol: Cells differentiated into cholaglocytes and hepatocytes in vitro.

value: Foxl1-CRE; RosaYFP mouse

value: primary cholanglocyte


title: CB15N_rep1


title: in vivo C57J/B6 plant diet_2

source_name: in vivo gnotobiotic mice fed defined plant diet

value: plant diet

value: cecum of C57BL/6 mouse fed defined plant diet


title: in vivo C57J/B6 plant diet_3


title: Heart B6 infected 1

description:
replicate 1
SVL023-1


title: in vivo C57J/B6 sugar diet_1


title: Heart B10.A infected 3

description:
replicate 3
SVL020-1

data_processing: Raw data was imported into FlexArray (http://genomequebec.mcgill.ca/FlexArray/) and processed with a log2, RMA and loess normalization, implemented within FlexArray through the 'lumi' bioconductor package.

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit (IL1791).

extract_protocol: Hearts were perfused with st. thomas solution, removed and placed immediately into RNAlater (Ambion) RNA stabilization reagent. 30 mg were used to extract total RNA using Qiagen RNeasy Fibrous tissue, quality control by agilent bioanalyzer.

treatment_protocol: Mice were infected with a dose of 400pfu per gram of CVB3(CG) or mock infected with sterile PBS.


title: HDAC6_3

source_name: Regulatory T-cells CD4+CD25+ from HDAC6 knock out mice

value: HDAC6 knock out


title: HDAC6_2


title: heart_CHIP(-/-)_TAB_rep4

city: Chapel Hill

middle: C

last: Schisler

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

description:
CHIPtab16
Biological replicate 4 of 4.

hyb_protocol: Cy5-labeled cRNA was co-hybridized to Agilent-014868 Whole Mouse Genome Microarrays with equimolar amounts of Cy3-labeled WMRR-derived cRNA. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.  After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner and processed using Agilent FeatureExtractor 9.1.3.1.

data_processing: Data files uploaded into GeneSpring 11.0.2 using a median value baseline transformation.  Entities where <50 percent of samples in any 1 out of 4 conditions have flags of Present or Marginal were filtered and removed.

source_name: Whole Mouse Reference RNA (WMRR)

label_protocol: 500 ng of WMRR (PMID 15470901) or heart RNA labeled with Cy3 or Cy5 (Perkin Elmer), respectively, and amplified using the Low Input RNA Amplification Kit (Agilent) as described by the manufacturer.

extract_protocol: Total RNA extracted using Trizol (Invitrogen) following manufacturer's instructions.

value: mixed 129Sv and C57BL/6

tag: developmental stage

value: neonatal

value: whole body

source_name: heart, 1 week post trans-aortic banding surgery

value: heart ventricle

tag: surgery

value: trans-aortic banding (TAB)

tag: time post-surgery

value: 1 week


title: homogalacturonan_2

source_name: in vitro bacterial culture, homogalacturonan

value: ATCC 8483

value: homogalacturonan

value: in vitro culture


title: homogalacturonan_1


title: Heart B6 infected 2

description:
replicate 2
SVL025-1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

value: Female

value: 7 weeks


title: Primary_Cholangocyte_Hyb3


title: Heart B10.A infected 2

description:
replicate 2
SVL019-1

value: heart


title: heart_CHIP(-/-)_TAB_rep3

description:
CHIPtab15
Biological replicate 3 of 4.


title: Primary_Hepatocyte_Hyb4

value: Foxl1-CRE; RosaYFP mouse

value: primary hepatocyte


title: beta-glucan_2

source_name: in vitro bacterial culture, beta-glucan

value: beta-glucan


title: Heart B10.A infected 1

description:
replicate 1
SVL018-1


title: in vivo C57J/B6 plant diet_1

value: plant diet

value: cecum of C57BL/6 mouse fed defined plant diet


title: heart_CHIP(-/-)_TAB_rep2

description:
CHIPtab14
Biological replicate 2 of 4.

value: mixed 129Sv and C57BL/6


title: Primary_Hepatocyte_Hyb3


title: Primary_Hepatocyte_Hyb2


title: beta-glucan_1


title: HDAC6_1

value: HDAC6 knock out


title: heart_CHIP(-/-)_TAB_rep1

description:
CHIPtab13
Biological replicate 1 of 4.

value: neonatal

value: whole body


title: Heart B10.A uninfected 3

description:
replicate 3
SVL015-1


title: Heart B10.A uninfected 2

description:
replicate 2
SVL013-1


title: heart_wild_type_TAB_rep4

description:
CHIPtab12
Biological replicate 4 of 4.

value: wild-type

value: heart ventricle

value: trans-aortic banding (TAB)


title: galactomannan_2

source_name: in vitro bacterial culture, galactomannan

value: ATCC 8483

value: galactomannan


title: heart_wild_type_TAB_rep3

description:
CHIPtab11
Biological replicate 3 of 4.

value: 1 week


title: Primary_Hepatocyte_Hyb1


title: Heart AJ infected 3

description:
replicate 3
SVL008-1

value: Female

value: A/J

value: 7 weeks


title: Heart AJ infected 2

description:
replicate 2
SVL007-1

value: heart


title: heart_wild_type_TAB_rep2

description:
CHIPtab10
Biological replicate 2 of 4.


title: glucomannan_2

source_name: in vitro bacterial culture, glucomannan

value: glucomannan

value: in vitro culture


title: Heart B10.A uninfected 1

description:
replicate 1
SVL012-1


title: Diff_Cholanglocyte_Hyb2

value: Foxl1-CRE; RosaYFP mouse

value: differentiated cholanglocyte


title: Diff_Cholanglocyte_Hyb3


title: Heart AJ infected 1

description:
replicate 1
SVL006-1


title: Diff_Hepatocyte_Hyb4

value: differentiated hepatocyte


title: Diff_Cholanglocyte_Hyb1


title: Heart AJ uninfected 3

description:
replicate 3
SVL004-1


title: Diff_Hepatocyte_Hyb3


title: xyloglucan_2

source_name: in vitro bacterial culture, xyloglucan

value: xyloglucan


title: Heart AJ uninfected 2

description:
replicate 2
SVL003-1

source_name: Heart mock infection


title: galactomannan_1


title: heart_CHIP(-/-)_sham_rep4

description:
CHIPtab08
Biological replicate 4 of 4.

value: mixed 129Sv and C57BL/6

value: neonatal

value: whole body

source_name: heart, 1 week post sham surgery

value: sham


title: xyloglucan_1

value: ATCC 8483


title: heart_CHIP(-/-)_sham_rep3

description:
CHIPtab07
Biological replicate 3 of 4.

value: heart ventricle


title: Heart AJ uninfected 1

description:
replicate 1
SVL002-1


title: heart_CHIP(-/-)_sham_rep2

description:
CHIPtab06
Biological replicate 2 of 4.

value: 1 week


title: Diff_Hepatocyte_Hyb2


title: arabinoxylan_2

source_name: in vitro bacterial culture, arabinoxylan

value: arabinoxylan


title: Diff_Hepatocyte_Hyb1


title: Undiff_Hyb4

source_name: Undiff

value: undifferentiated adult hepatic progenitor cells


title: heart_wild_type_sham_rep3

description:
CHIPtab03
Biological replicate 3 of 4.

value: wild-type


title: arabinoxylan_1


title: heart_CHIP(-/-)_sham_rep1

description:
CHIPtab05
Biological replicate 1 of 4.


title: oat spelt xylan_2

source_name: in vitro bacterial culture, oat spelt xylan

value: oat spelt xylan


title: Undiff_Hyb3


title: heart_wild_type_sham_rep4

description:
CHIPtab04
Biological replicate 4 of 4.


title: heart_wild_type_sham_rep2

description:
CHIPtab02
Biological replicate 2 of 4.


title: Undiff_Hyb2


title: heart_wild_type_sham_rep1

description:
CHIPtab01
Biological replicate 1 of 4.


title: oat spelt xylan_1


title: glucose_1

source_name: in vitro bacterial culture, glucose

value: glucose


title: Intestine_LPS injected chicken fed MOS (prebiotic)_replica 5

status: Public on Apr 30 2011

city: Ste Anne de Bellevue

first: Bushansingh

middle: Shyam

last: Baurhoo

state: Quebec

address: 21111, Lakeshore Road

department: Animal Science

description:
Slide 11_saline chicken_antibiotic group_ replica 5 (Cy3) vs LPS chicken_prebiotic group_ replica 5 (Cy5)
raw data file: Intestine Array_11.DAT

hyb_protocol: mix of 33 pmol of both samples was resuspended with 33 µl Pronto! Long Oligo Hybridization solution and applied to pre-hybrydized microarray slides with spotted area coved with a 25 X 40 mm glass coverslip; slides were hybridized in Corning Hybridization Chambers immersed in 42C water bath, protected from light, for 16h. After hybridization, slides were sequencenly washed according to manufacturer's instructions (Pronto! Universal Microarray Hybridization Kit, Corning Inc.)

scan_protocol: scanned on ScanArray Gx Plus (PerkinElmer) set to 65% lazer power Images were quantified using ScanAlyze Software (version 2.50).

data_processing: Log2 transformed data was submitted to ratio analysis and LOWESS normalization using JMP Genomics Software (SAS Institute).  Dual channel hybridizations were analyzed as single channel.  Raw data files are provided on the SERIES record, please see description above for associated Raw data file.  Results of comparison analysis are also provided on the Series record.

organism: Gallus gallus

source_name: Total RNA from intestine of LPS injected chicken fed MOS (prebiotic) labeled with Cyanine-5 (red).

label_protocol: 5µg of total RNA were primed with 3µg of random primers and 2µg of oligo(dt) primer, heated at 70 oC for 10 min, then reverse transcribed at 42 oC for 2h with 3.2 µl ChipShot Reverse Transcriptase and 4 µl aminoallyl-sNTPs; cDNA was indirectly labeled with CyDye NHS Esters (Cy3 or Cy5) by adding 60 µl of cDNA eluted to dried 40,000 pmol CyDye aliquot and hybrydized at room temperature for 1h, followed by purification steps as indicated by manufacturer's instructions (ChipShot Indirect Labeling System and Membrane Clean-Up System, Promega Corp)

growth_protocol: broiler chicks raised under standard conditions and fed prebiotic or antibiotic diet ad libitum

extract_protocol: Total RNA from liver, intestine and skeletal muscle tissues was extracted using Trizol reagent and Prelink RNA Mini Kit following manufacturer's instructions (Invitrogen)

treatment_protocol: at 14 d of age, chicks were injected i.p. with saline or Salmonella LPS. At 24 h post-injection, liver, intestine (jejunum) and skeletal muscle (breast) tissue samples were snap frozen in liquid nitrogen and stored at -80 oC for later RNA extraction and microarray analysis.

value: intestine

tag: status

value: MOS birds

tag: breed

value: Cobb 500 broiler chicken

tag: gender

value: male

value: 14 days


title: Intestine_saline injected chicken fed (VIRG (antibiotic)_replica 6

description:
Slide 12_LPS chicken_prebiotic group_ replica 6 (Cy3) vs saline chicken_antibiotic group_ replica 6 (Cy5)
raw data file: Intestine Array_12.DAT

source_name: Total RNA from intestine of saline injected chicken fed VIRG (antibiotic) labeled with Cyanine-5 (red).

value: VIRG birds


title: Intestine_LPS injected chicken fed VIRG (antibiotic)_replica 5

description:
Slide 9_saline chicken_prebiotic group_ replica 5 (Cy3) vs LPS chicken_antibiotic group_ replica 5 (Cy5)
raw data file: Intestine Array_9.DAT

source_name: Total RNA from intestine of LPS injected chicken fed VIRG (antibiotic) labeled with Cyanine-5 (red).


title: Intestine_saline injected chicken fed VIRG (antibiotic)_replica 3

description:
Slide 7_saline chicken_prebiotic group_ replica 3 (Cy3) vs saline chicken_antibiotic group_ replica 3 (Cy5)
raw data file: Intestine Array_7.DAT


title: Intestine_saline injected chicken fed MOS (prebiotic)_replica 4

description:
Slide 8_saline chicken_antibiotic group_ replica 4 (Cy3) vs saline chicken_prebiotic group_ replica 4 (Cy5)
raw data file: Intestine Array_8.DAT

source_name: Total RNA from intestine of saline injected chicken fed MOS (prebiotic) labeled with Cyanine-5 (red).


title: Intestine_LPS injected chicken fed MOS (prebiotic)_replica 3

description:
Slide 5_saline chicken_prebiotic group_ replica 1 (Cy3) vs LPS chicken_prebiotic group_ replica 3 (Cy5)
raw data file: Intestine Array_5.DAT


title: Intestine_saline injected chicken fed MOS (prebiotic)_replica 2

description:
Slide 6_LPS chicken_prebiotic group_ replica 4 (Cy3) vs saline chicken_prebiotic group_ replica 2 (Cy5)
raw data file: Intestine Array_6.DAT


title: Intestine_saline injected chicken fed MOS (prebiotic)_replica 6

description:
Slide 10_LPS chicken_antibiotic group_ replica 6 (Cy3) vs saline chicken_prebiotic group_ replica 6 (Cy5)
raw data file: Intestine Array_10.DAT


title: Intestine_LPS injected chicken fed VIRG (antibiotic)_replica 3

description:
Slide 3_LPS chicken_prebiotic group_ replica 1 (Cy3) vs LPS chicken_antibiotic group_ replica 3 (Cy5)
raw data file: Intestine Array_3.DAT


title: Intestine_LPS injected chicken fed MOS (prebiotic)_replica 2

description:
Slide 4_LPS chicken_antibiotic group_ replica 4 (Cy3) vs LPS chicken_prebiotic group_ replica 2 (Cy5)
raw data file: Intestine Array_4.DAT


title: Undiff_Hyb1

value: Foxl1-CRE; RosaYFP mouse


title: glucose_2

value: in vitro culture


title: Intestine_LPS injected chicken fed MOS (prebiotic)_replica 6

source_name: Total RNA from intestine of LPS injected chicken fed MOS (prebiotic) labeled with Cyanine-3 (green).


title: Intestine_saline injected chicken fed VIRG (antibiotic)_replica 5

source_name: Total RNA from intestine of saline injected chicken fed VIRG (antibiotic) labeled with Cyanine-3 (green).


title: Intestine_LPS injected chicken fed VIRG (antibiotic)_replica 1

description:
Slide 1_saline chicken_antibiotic group_ replica 1 (Cy3) vs LPS chicken_antibiotic group_ replica 1 (Cy5)
raw data file: Intestine Array_1.DAT


title: Intestine_saline injected chicken fed MOS (prebiotic)_replica 5

source_name: Total RNA from intestine of saline injected chicken fed MOS (prebiotic) labeled with Cyanine-3 (green).


title: Intestine_LPS injected chicken fed VIRG (antibiotic)_replica 6

source_name: Total RNA from intestine of LPS injected chicken fed VIRG (antibiotic) labeled with Cyanine-3 (green).


title: Intestine_saline injected chicken fed VIRG (antibiotic)_replica 4


title: Intestine_saline injected chicken fed MOS (prebiotic)_replica 3


title: Intestine_LPS injected chicken fed MOS (prebiotic)_replica 4


title: Intestine_LPS injected chicken fed VIRG (antibiotic)_replica 4


title: Intestine_LPS injected chicken fed MOS (prebiotic)_replica 1


title: Intestine_saline injected chicken fed VIRG (antibiotic)_replica 2

description:
Slide 2_LPS chicken_antibiotic group_ replica 2 (Cy3) vs saline chicken_antibiotic group_ replica 2 (Cy5)
raw data file: Intestine Array_2.DAT


title: Intestine_saline injected chicken fed VIRG (antibiotic)_replica 1


title: Intestine_saline injected chicken fed MOS (prebiotic)_replica 1


title: Intestine_LPS injected chicken fed VIRG (antibiotic)_replica 2


title: NY82

status: Public on Feb 17 2011

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing: After subtracting background signal intensities, data were normalized by median scaling, then a floor value of 20 was applied.

source_name: Human hepatocellular carcinoma

extract_protocol: Using fresh frozen HCC tissues, total RNA was extracted using TRIzol (Invitrogen).

tag: vascular invasion

tag: code

value: transplant

tag: class

value: Proliferation

tag: tp53 mutation

tag: ctnnb1 mutation

tag: immunohistochemistry

value: pRPS6 :1

value: pAkt :0

value: CTNNB1 :1

tag: used for prognostic prediction

value: no

tag: used for microrna profiling

value: Yes

tag: microRNA-based subclass


title: NY96

tag: age

tag: Sex

value: M

value: resection

value: pIGFR1 :0

value: CTNNB1 :0

value: yes

value: B


title: NY99

value: C

value: F

tag: afp

value: pAkt :1


title: NY70

value: pRPS6 :0


title: NY79

value: transplant


title: NY7

value: Inflammation


title: NY65

value: A

value: Proliferation

value: pRPS6 :1


title: NY6

value: pAkt :0

value: no


title: normal peripheral zone prostate glands

status: Public on Apr 15 2011

city: Bonn

first: Andreas

last: Lindstrot

address: Sigmund-Freud-Str. 25

department: Molekular Patholoy

institute: University of Bonn

hyb_protocol: The hybridization was performed according to Agilent 60mer oligo Microarray processing protocol using Agilent gene expression hybridization kit. Briefly Cy3-labeled fragmented cRNA in hybridization buffer was hybridyzed over nigth (17h 65°C ) to Agilent whole human genome oligo Micrarray 4x44k using Agilent recommended hybridization chamber and oven. Finally the microarray was washed once with the agilent gene expression wash buffer 1 for 1 minute at Room temperature followed by a second wash with preheated Agilent gene expression wash buffer 2 (37° for 1 Minutes). The last washing step was performed with acetonitrile

scan_protocol: Flourescence signals of the hydridysed agilent microarray were detected using the Agilent Microarray scanner system.

data_processing: the Agilent feature extraction software FES was used to read out and process the microarray image file. For the determination of differential gene expression FES derived output data files were further analyzed using the Rosetta resolver gene expression data analysis system (Rosetta biosoftware). All samples were labeled with Cy3, the ratio experiments are designated as control vs experiments. The ratios are always calculated by dividing sample signal intensity through control signal intensity.

source_name: prostate glands

label_protocol: For the linear T7 based amplification step, 0.26 - 0.3µg of total RNA sample was used. To produce Cy3-labebeld cRNA, the RNA samples were amplified and labeld using Agilent low RNA input linear Amp Kit (Agilent Technologies) following manufactures protocol.

extract_protocol: The extraction of the laser microdissected glands was performed according to the manual of the Qiagen Rneasy Micro Kit including a recommend DNAse digestion

tag: tumor stage

value: Gleason 0


title: MDS patient sample 3 diagnosis and relapse

status: Public on Apr 08 2011

type: genomic

city: Houston

first: Taichun

last: Qin

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description:
decitabine treatment: Patients with Myelodysplastic Syndrome were randomized to receive DAC in 20 mg/m2 intravenously over 1 hour daily for 5 days.  The patients were considered to have not responded only after having received at least 3 courses of therapy.
SAME MCA

hyb_protocol: Equimolar amounts of tumor and normal labeled amplicons were cohybridized to cohybridized to the HCGI12K-Human CpG 12K Array

scan_protocol: Hybridized slides were scanned with the GenePix 4000A scanner (Axon). The acquired images were analyzed with the software GenePix Pro3.0

data_processing:
Two-step global lowess normalization was done using the background-subtracted median intensity of each spot, and the resultant log2 ratios were averaged from duplicate experiments.
CpG island tags having a Cy5/Cy3 log2 ratio  > 1.3 (~2.5-fold enrichment) were chosen as hypermethylation-specific signals. This log2 ratio value was further supported by our validation experiments as the best cutoff to achieve optimal  sensitivity and specificity.

molecule: genomic DNA

source_name: Total DNA from bone marrow

label_protocol: Amplicons from patients with MDS after relapse were labeled with the Cy5 dye and cohybridized against amplicons from patients at diagnosis labeled with the Cy3 dye on Agilent Technologies 4 × 44K custom DNA microarrays (Agilent, Santa Clara, CA). Dye swaps were preformed for comparison.

growth_protocol: Collect patients bone marrow samples.

extract_protocol: Total DNA was extracted using DNA-Stat-60 using manufacturer's instructions. Biuslfite-methylation conversion was performed using manufacturer's instructions. DNA was digested by Sma1 and Xma1 enzymes and PCR amplification is required to amplify those DNA fragments before performing the CpG island methylation microarray.

tag: disease status

value: diagnosis

tag: tissue

value: bone marrow

value: Relapse


title: MDS patient sample 4 diagnosis and relapse

description:
decitabine treatment: Patients with Myelodysplastic Syndrome were randomized to receive DAC in 20 mg/m2 intravenously over 1 hour daily for 5 days.  The patients were considered to have not responded only after having received at least 3 courses of therapy.
Biological Replicates


title: NY44

value: CTNNB1 :1

value: Yes


title: MDS patient sample 3 diagnosis and relapse Dye Swap


title: MDS patient sample 2 diagnosis and relapse Dye Swap


title: MDS patient sample 4 diagnosis and relapse Dye Swap


title: heart_wild_type_TAB_rep1

description:
CHIPtab09
Biological replicate 1 of 4.

source_name: Whole Mouse Reference RNA (WMRR)

tag: strain

value: mixed 129Sv and C57BL/6

tag: developmental stage

value: neonatal

value: whole body

source_name: heart, 1 week post trans-aortic banding surgery

tag: genotype

value: wild-type

value: heart ventricle

tag: surgery

value: trans-aortic banding (TAB)

tag: time post-surgery

value: 1 week


title: MDS patient sample 1 diagnosis and relapse Dye Swap

description:
decitabine treatment: Patients with Myelodysplastic Syndrome were randomized to receive DAC in 20 mg/m2 intravenously over 1 hour daily for 5 days.  The patients were considered to have not responded only after having received at least 3 courses of therapy.
Biological replicate


title: MDS patient sample 1 diagnosis and relapse

value: Diagnosis


title: Huh7 cells treated with FH HDL, biological rep 2

status: Public on Mar 24 2011

city: Bethesda

first: Kasey

last: Vickers

state: MD

address: 10 Center Dr. Bldg. 10 8N222

department: National Heart, Lung and Blood Institute

institute: National Institutes of Health

description: Gene expression data from Huh7 cells treated with HDL from Normal or FH subjects in lipoprotein-depleted serum.

hyb_protocol: Following fragmentation, 15ug cRNA were hybridized 16 h @ 42oC to Affymetrix HG-U133 Plus 2.0 human whole genome microarrays. Arrays were washed and stained with Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner

data_processing: Low-level and high-level post-analyses of mRNA (LiWong method) expression were performed using GeneSpring GX11.0 (Agilent Technologies). LiWong summarization algorithm, quanitle normalization, no baseline transforamtion, filtered on expression (20.0-100.0)th percentile, and filtered on error CV<50.0%. Data presented here: all entities and summarization signal values

source_name: Human Huh7 cells, in culture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Huh7 cells were cultured in normal growth media (F12 Dulbecco’s modified Eagle’s medium, supplemented with 100U/mL penicillin, 100ug/mL streptomycin, and 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated by Qiazol extraction followed by miRNAeasy Column (Qiagen) purification

treatment_protocol: Huh7 cells were washed with warm 1X PBS and switched to a lipoprotein-depleted serum (10%) media prior to treatment. Cells were treated with 70ug/mL HDL for 48 h. Cells were washed 2X with 1X PBS and lysed with Qiazol

tag: cell line

tag: treatment

value: familial hypercholesterolemia HDL


title: NY41

tag: vascular invasion

tag: code

value: transplant

tag: class

value: Inflammation

tag: tp53 mutation

tag: ctnnb1 mutation

tag: immunohistochemistry

value: pRPS6 :1

value: pAkt :0


title: Huh7 cells treated with Normal HDL, biological rep 1

value: normal HDL


title: Huh7 cells treated with Normal HDL, biological rep 2


title: NY36

value: A

tag: age

tag: Sex

value: M

value: resection

tag: afp

value: pRPS6 :0

value: pIGFR1 :0

value: CTNNB1 :0

tag: used for prognostic prediction

value: no

tag: used for microrna profiling

tag: microRNA-based subclass


title: NY34

value: Yes


title: NY333

value: CTNNB1 :1

value: yes


title: Huh7 cells treated with FH HDL, biological rep 1


title: Huh7 cells treated with FH HDL, biological rep 3


title: NY331

value: No


title: glucomannan_1

source_name: in vitro bacterial culture, glucomannan

tag: strain

value: ATCC 8483

value: glucomannan

tag: isolation source

value: in vitro culture


title: Huh7 cells treated with Normal HDL, biological rep 3


title: NY39

value: transplant

value: Proliferation

value: pRPS6 :1


title: MDS patient sample 2 diagnosis and relapse

tag: disease status

value: Diagnosis

tag: tissue

value: bone marrow

value: Relapse


title: NY327

value: C

value: F

value: resection

value: pAkt :0


title: NY329

value: Yes

value: A

value: M

value: pRPS6 :0

value: pIGFR1 :1

value: pAkt :1


title: NY323

value: No

value: Inflammation

value: CTNNB1 :0

value: yes

value: B


title: NY325

value: Proliferation

value: pRPS6 :1


title: NY319

value: Polysomy chr7

value: pIGFR1 :0


title: NY321

value: C

value: F

value: resection


title: NY313

value: Yes

value: A

value: pAkt :0


title: NY309

value: M

value: CTNNB1 :1


title: NY317

value: No


title: NY26

value: transplant

value: Inflammation

value: pRPS6 :0

value: no


title: NY307

value: CTNNB1 :0

value: yes


title: NY224

value: Proliferation

value: pRPS6 :1

value: pAkt :1

value: B


title: NY226

value: F

value: resection

value: pIGFR1 :0


title: NY311

value: Yes

value: C

value: pIGFR1 :1

value: pAkt :0


title: NY222

value: M

value: A


title: NY216

value: CTNNB1 :1


title: NY204

value: No

value: pRPS6 :0


title: NY206

value: Polysomy chr7

value: yes


title: NY232

value: no


title: NY18

value: Inflammation

value: pAkt :1

value: CTNNB1 :0


title: NY2

value: resection


title: NY208

value: pIGFR1 :0


title: NY16

value: transplant

value: Yes

value: B


title: M96

value: F

value: pAkt :0


title: M98

value: A

value: M


title: NY228

value: pRPS6 :1


title: M94

value: No


title: NA18507_Clint_GGOCustomchip

city: Seattle

first: Tomas

last: Marques-Bonet

state: WA

address: 1705 NE Pacific St,

department: Genome Sciences

institute: University of Washington

hyb_protocol: As described in Nimblegen protocol

scan_protocol: As described in Nimblegen protocol

data_processing: Normalization (qspline) was performed using NimbleScan 2.4. Normalized log2 Cy3/Cy5.

label_protocol: As described in Nimblegen protocol

extract_protocol: As described in Nimblegen protocol

tag: name

organism: Pan troglodytes

source_name: Clint

value: Clint


title: M90

tag: vascular invasion

value: Polysomy chr7

value: pRPS6 :0

value: yes


title: M92

tag: code

value: Unannotated

value: pIGFR1 :1


title: M88

value: resection

tag: class

value: CTNNB1 :0


title: M81

tag: tp53 mutation

value: pIGFR1 :0

value: CTNNB1 :1


title: M71

value: Yes

tag: ctnnb1 mutation

value: no


title: M73

value: F

value: Inflammation

tag: immunohistochemistry

value: pAkt :0

value: B


title: Kwan_NA18507_GGOCustomchip

organism: Gorilla gorilla

source_name: Kwan

value: Kwan


title: M69

value: No

value: A

tag: age

value: Proliferation

value: pAkt :1


title: NY218

value: C

tag: Sex

value: pRPS6 :0

value: yes


title: M43

value: resection

tag: afp

value: pIGFR1 :1

value: CTNNB1 :0


title: M35

value: Yes

value: pRPS6 :1

value: pIGFR1 :0

tag: used for prognostic prediction


title: M17

value: M

value: CTNNB1 :1

tag: used for microrna profiling


title: M53

value: B

value: F

value: Unannotated

value: pAkt :0

tag: microRNA-based subclass


title: M104

value: A


title: M15

value: pAkt :1


title: M106

value: No


title: M100


title: M13


title: M102

value: Proliferation


title: M67

value: yes


title: B98

value: resection


title: B86

value: pRPS6 :0


title: B94


title: B88


title: B80

value: Polysomy chr7

value: CTNNB1 :0

value: no


title: B84

value: Yes

value: pIGFR1 :0


title: NA18507_Kwan_GGOCustomchip

value: Kwan


title: M11

value: pRPS6 :1

value: pIGFR1 :1

value: CTNNB1 :1


title: B82

value: F

value: Unannotated


title: B70

value: A

value: M

value: pAkt :0


title: B72

value: Inflammation

value: B


title: B78

value: No

value: resection

value: pRPS6 :0

value: yes


title: B90

value: Yes


title: B31

value: pIGFR1 :0

value: pAkt :1

value: CTNNB1 :0

value: no


title: B66

value: Proliferation

value: pRPS6 :1


title: B17

value: F

value: Unannotated


title: B29

value: A

value: M


title: B35

value: Inflammation

value: pAkt :0


title: B13

value: No

value: B


title: M31

value: resection

value: pRPS6 :0


title: B68

value: yes

value: Yes


title: B19

value: Polysomy chr7

value: pIGFR1 :1


title: B96

value: pIGFR1 :0

value: CTNNB1 :0


title: B33


title: Clint_Kwan_GGOCustomchip

value: Clint

value: Kwan


title: xeno_shTTL_sample8

status: Public on Feb 10 2011

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description: Gene expression data from leukemia xenograft samples

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing: The data were normalized using RMA algorithm in R software [www.r-ptoject.org], BioConductor package [www.bioconductor.org]

source_name: xenograft

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

growth_protocol: Xenograft A

extract_protocol: Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns

treatment_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation

tag: cell type

value: white blood cells

value: leukemia xenograft

value: xenograft


title: xeno_shTTL_sample10


title: xeno_loTTL_sample3


title: xeno_loTTL_sample6


title: xeno_shTTL_sample12


title: xeno_shTTL_sample9


title: B76

value: A

value: F

value: pRPS6 :1

value: CTNNB1 :1

value: no


title: xeno_loTTL_sample2


title: no relapse _ sample 197

description: Gene expression data from pediatric acute leukemia samples at diagnosis

source_name: no relapse

extract_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation. Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns.

value: pediatric acute leukemia

value: bone marrow


title: xeno_loTTL_sample4


title: no relapse _ sample 196


title: no relapse _ sample 182


title: no relapse _ sample 185


title: xeno_loTTL_sample7


title: no relapse _ sample 195


title: no relapse _ sample 183


title: xeno_shTTL_sample11


title: no relapse _ sample 186


title: no relapse _ sample 193


title: no relapse _ sample 190


title: xeno_loTTL_sample1


title: no relapse _ sample 188


title: B25

value: Yes

value: M

value: resection

value: Unannotated

value: pRPS6 :0

value: pAkt :0


title: B74

value: C

value: Proliferation

value: pIGFR1 :0

value: pAkt :1

value: CTNNB1 :0

value: B


title: M79

value: A

value: pRPS6 :1

value: pIGFR1 :1

value: yes


title: no relapse _ sample 179

value: white blood cells

value: pediatric acute leukemia

value: bone marrow


title: late relapse _ sample 177

source_name: late relapse


title: no relapse _ sample 174


title: no relapse _ sample 171


title: no relapse _ sample 170


title: late relapse _ sample 178


title: no relapse _ sample 169


title: no relapse _ sample 172


title: no relapse _ sample 180


title: no relapse _ sample 176


title: no relapse _ sample 175


title: no relapse _ sample 160


title: no relapse _ sample 162


title: no relapse _ sample 161


title: no relapse _ sample 158


title: no relapse _ sample 168


title: early relapse _ sample 173

source_name: early relapse


title: late relapse _ sample 159


title: B39

value: Yes

value: M

value: resection

value: Inflammation


title: no relapse _ sample 156


title: no relapse _ sample 155


title: no relapse _ sample 164


title: no relapse _ sample 184


title: no relapse _ sample 167


title: no relapse _ sample 163


title: no relapse _ sample 165


title: late relapse _ sample 153


title: no relapse _ sample 154


title: no relapse _ sample 194


title: no relapse _ sample 148


title: no relapse _ sample 151


title: no relapse _ sample 152


title: no relapse _ sample 150


title: late relapse _ sample 103


title: no relapse _ sample 101


title: no relapse _ sample 100


title: no relapse _ sample 104


title: no relapse _ sample 97


title: no relapse _ sample 105


title: no relapse _ sample 95


title: no relapse _ sample 102


title: early relapse _ sample 149


title: no relapse _ sample 88


title: no relapse _ sample 99


title: no relapse _ sample 98


title: no relapse _ sample 94


title: xeno_loTTL_sample5

value: leukemia xenograft

value: xenograft


title: early relapse _ sample 86


title: no relapse _ sample 93


title: early relapse _ sample 90


title: no relapse _ sample 89


title: no relapse _ sample 96


title: no relapse _ sample 87


title: early relapse _ sample 91


title: no relapse _ sample 92


title: no relapse _ sample 85


title: no relapse _ sample 83


title: no relapse _ sample 78


title: no relapse _ sample 76


title: early relapse _ sample 81


title: early relapse _ sample 84


title: no relapse _ sample 75


title: no relapse _ sample 70


title: no relapse _ sample 82


title: no relapse _ sample 68


title: no relapse _ sample 80


title: no relapse _ sample 69


title: no relapse _ sample 74


title: no relapse _ sample 65


title: no relapse _ sample 181


title: no relapse _ sample 72


title: late relapse _ sample 67


title: no relapse _ sample 63


title: early relapse _ sample 62


title: no relapse _ sample 61


title: no relapse _ sample 58


title: no relapse _ sample 71


title: no relapse _ sample 59


title: no relapse _ sample 66


title: no relapse _ sample 60


title: no relapse _ sample 57


title: early relapse _ sample 64


title: no relapse _ sample 54


title: no relapse _ sample 55


title: no relapse _ sample 56


title: no relapse _ sample 50


title: no relapse _ sample 43


title: late relapse _ sample 48


title: no relapse _ sample 44


title: no relapse _ sample 47


title: no relapse _ sample 49


title: no relapse _ sample 51


title: no relapse _ sample 46


title: no relapse _ sample 52


title: no relapse _ sample 77


title: no relapse _ sample 42


title: early relapse _ sample 53


title: no relapse _ sample 41


title: late relapse _ sample 38


title: no relapse _ sample 40


title: no relapse _ sample 37


title: late relapse _ sample 39


title: no relapse _ sample 79


title: no relapse _ sample 45


title: no relapse _ sample 30


title: no relapse _ sample 35


title: no relapse _ sample 33


title: no relapse _ sample 28


title: no relapse _ sample 32


title: late relapse _ sample 29


title: no relapse _ sample 27


title: no relapse _ sample 31


title: no relapse _ sample 25


title: no relapse _ sample 34


title: no relapse _ sample 26


title: early relapse _ sample 36


title: no relapse _ sample 24


title: no relapse _ sample 23


title: no relapse _ sample 22


title: no relapse _ sample 18


title: no relapse _ sample 19


title: no relapse _ sample 14


title: early relapse _ sample 17


title: early relapse _ sample 16


title: no relapse _ sample 21


title: no relapse _ sample 15


title: early relapse _ sample 11


title: early relapse _ sample 13


title: no relapse _ sample 6


title: early relapse _ sample 8


title: no relapse _ sample 12


title: late relapse _ sample 20


title: late relapse _ sample 4


title: early relapse _ sample 7


title: early relapse _ sample 5


title: no relapse _ sample 10


title: no relapse _ sample 3


title: early relapse _ sample 9


title: no relapse _ sample 2


title: Clone2_6Gy_rep1

status: Public on Feb 04 2011

city: Berlin

first: Artur

last: Muradyan

address: Ihnestr. 73

institute: Max Planck Institute for Molecular Genetics

description: Gene expression of clone 2

hyb_protocol: Labeled cRNA was hybridized on microarrays for 17h at 65oC in a rotating hybridization oven.

scan_protocol: Slides were scanned with the G2565BA Agilent Microarray Scanner System at 5µm resolution.

data_processing: Images were processed by Agilent Feature Extraction software (v9.1) and primary data were further analyzed by GeneSpring GX v7.3.1 software (Agilent, USA). All data underwent inter-experimental normalization processing (low intensity values below 0.01 were set to 0.01 and each measurement was divided by the 50th percentile of all measurements in that sample).

source_name: A549 cell line, clone 2, 6Gy

label_protocol: 500ng of high quality total RNA in combination with Agilent´s RNA Spike-In kit was amplified and labeled by Cy3-CTP. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The aneuploid A549 male non-small cell lung cancer (NSCLC) adenocarcinoma cell line was grown as monolayer in DMEM medium containing L-glutamine, 10% FCS (Invitrogen; Carlsbad, CA)

extract_protocol: Total RNA from cultured cells was isolated using the RNeasy® RNA extraction kit (Qiagen, Germany) in conjunction with QIAshredder® columns (Qiagen, Germany) following the manufacturer’s recommendations, including β-mercaptoethanol (Merck, Germany) to prevent RNA degradation.

treatment_protocol: Exponentially growing cells were irradiated at room temperature with 240 kV X rays (Isovolt 320/10; Seifert, Ahrensberg, Germany) filtered with 3 mm beryllium at a dose rate of 1 Gy/min at 13 mA. The absorbed dose was measured with a Duplex dosimeter (PTW, Freiburg, Germany). Thereafter, cells were serially diluted in fresh medium and aliquots of the suspension seeded in 96 well plates and incubated for two weeks in a 5% CO2 incubator with regular microscopic inspection. Wells that contained a viable cell clone were identified and four independent clones and one sham-irradiated clone were collected at random.

tag: gender

value: male

tag: cell line


title: Clone3_6Gy_rep1

description: Gene expression of clone 3

source_name: A549 cell line, clone 3, 6Gy


title: Clone0_sham_irradiated_rep1

description: Gene expression of clone 0

source_name: A549 cell line, clone 0, sham irradiated

treatment_protocol: Cells were serially diluted in fresh medium and aliquots of the suspension seeded in 96 well plates and incubated for two weeks in a 5% CO2 incubator with regular microscopic inspection. Wells that contained a viable cell clone were identified and four independent clones and one sham-irradiated clone were collected at random.


title: Clone4_6Gy_rep1

description: Gene expression of clone 4

source_name: A549 cell line, clone 4, 6Gy


title: no relapse _ sample 73

tag: tissue


title: early relapse _ sample 1


title: Clone1_6Gy_rep1

description: Gene expression of clone 1

source_name: A549 cell line, clone 1, 6Gy


title: 28 dpl laser captured CCP replicate 1

status: Public on Oct 22 2010

city: Cambridge

first: Julien

last: Bauer

state: Cambridgeshire

address: Tennis court road

country: United Kingdom

institute: Cambridge University

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays

data_processing: Data were filtered, removing any non expressed probes according to the detection p-value, then variance stabilization was applied and finally the data were normalised using quantile normalization.

source_name: Rat caudal cerebellar peduncle

label_protocol: Standard Illumina hybridisation protocol

extract_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays

treatment_protocol: Rat caudal cerebellar peduncles (CCP) were demyelinated using 0.1 % ethidium bromide.  The lesioned CCPs were selectively isolated from frozen brains using laser capture microdissections at 5, 14 and 28 days postlesion before RNA extraction and microarray analysis.

tag: strain

value: Sprague Dawley

value: 12 weeks at 0 dpl (days post lesion)

value: caudal cerebellar peduncles

tag: time

value: 28 dpl (days post lesion)


title: 28 dpl laser captured CCP replicate 2


title: Patient 25, before month24 IFN-beta injection_chipB

status: Public on Sep 29 2010

city: Rostock

first: Robert

last: Goertsches

address: Gehlsheimer Strasse 20

department: Neurology

institute: University

description: Gene expression data from a multiple sclerosis patient treated with IFN-beta

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on Affymetrix HG-U133A and B arrays, respectively. Microarrays were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The raw probe-level signals were converted to expression values using the MAS5.0 algorithm. Accordingly, probeset specific detection calls (Absent/Present) and changes with respect to baseline (Increase/Decrease/NoChange) were ascertained.

source_name: Peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 µg total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Patient blood samples were drawn immediately before first IFN-beta injection as well as two days, one, twelve and twenty-four months post therapy initiation.

extract_protocol: Blood was separated using isopycnic centrifugation (Ficoll), and peripheral blood mononuclear cells were lysed using chaotropic buffer and cleaned by RNeasy (Qiagen) according to the manufacturers' protocol.

treatment_protocol: Patients were treated with subcutaneous IFN-beta-1b (Betaferon, Bayer Healthcare) at standard dose (250 µg every other day).

tag: age at ifn-beta therapy onset (baseline blood sampling)

tag: duration from ms diagnosis to therapy initiation (in months)

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 5 years

tag: number of relapses during the year prior to treatment

tag: number of relapses during 1-year follow-up

tag: number of relapses during 2-year follow-up

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)

tag: completed years of ifn-beta therapy


title: Patient 24, before month12 IFN-beta injection_chipB

tag: gender

value: female


title: 28 dpl laser captured CCP replicate 3

tag: age


title: Patient 25, before second IFN-beta injection_chipB


title: Patient 23, before second IFN-beta injection_chipB


title: Patient 25, before month12 IFN-beta injection_chipB


title: Patient 23, before month1 IFN-beta injection_chipB


title: Patient 24, before month24 IFN-beta injection_chipB


title: Patient 24, before first IFN-beta injection_chipB


title: Patient 24, before month1 IFN-beta injection_chipB


title: Patient 23, before month12 IFN-beta injection_chipB


title: Patient 25, before month24 IFN-beta injection_chipA


title: Patient 25, before first IFN-beta injection_chipB


title: Patient 25, before month1 IFN-beta injection_chipA


title: JIL-1, rep2

status: Public on Feb 01 2011

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: Chip-chip S2 cells JIL-1

hyb_protocol: performed by imaGenes (www.imagenes-bio.de)

data_processing: raw signals of all channels in all replicate arrays were log2 transformed and quantile normalized in R/Bioconductor (normalize.quantiles in preprocessCore package).

organism: Drosophila melanogaster

source_name: Input DNA

growth_protocol: Cells were grown in Schneider Medium supplemented with 10% FCS, penicillin and streptomycin.

extract_protocol: ChIP DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C over night. After washing and crosslink revearsal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). IP DNA was amplified using the WGA kit (Sigma). Input DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. After crosslink revearsal, nucleic acids were purified on GFX columns (GE Healthcare). Input DNA was amplified using the WGA kit (Sigma).

treatment_protocol: no treatment

tag: cell type

value: Schneider line2 (S2) cells

tag: chip antibody

value: none, input DNA

source_name: JIL1 IP DNA

value: JIL1, R70 (custom rabbit anti JIL-1 antibody)


title: Patient 25, before month1 IFN-beta injection_chipB


title: Patient 24, before second IFN-beta injection_chipB


title: Patient 23, before first IFN-beta injection_chipB


title: Patient 25, before month12 IFN-beta injection_chipA


title: H4K16ac, rep1

description: Chip-chip S2 cells H4K16ac

scan_protocol: performed by imaGenes (www.imagenes-bio.de)

source_name: H4K16ac IP DNA

tag: chip antibody vendor

value: ACTIVE MOTIF

tag: chip antibody catalog #


title: H4K16ac, rep2

description: Chip-chip S2 cells H4K16ac

label_protocol: performed by imaGenes (www.imagenes-bio.de)


title: Patient 22, before month24 IFN-beta injection_chipB

tag: age at ifn-beta therapy onset (baseline blood sampling)

tag: duration from ms diagnosis to therapy initiation (in months)


title: JIL-1, rep1

description: Chip-chip S2 cells JIL-1


title: H3S10phK14ac, rep2

description: Chip-chip S2 cells H3S10phK14ac

source_name: H3S10phK14ac IP DNA

tag: chip antibody provider

value: Dr. Christian Seiser (see http://www.ncbi.nlm.nih.gov/pubmed/20442873)


title: Patient 23, before month24 IFN-beta injection_chipB

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years


title: Patient 24, before month24 IFN-beta injection_chipA

tag: edss after 5 years

tag: number of relapses during the year prior to treatment

tag: number of relapses during 1-year follow-up


title: Patient 22, before first IFN-beta injection_chipB

tag: number of relapses during 2-year follow-up

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)


title: Patient 22, before month12 IFN-beta injection_chipB

tag: gender

tag: completed years of ifn-beta therapy


title: Patient 22, before month1 IFN-beta injection_chipB


title: Patient 24, before month1 IFN-beta injection_chipA


title: Patient 25, before first IFN-beta injection_chipA


title: JIL-1, rep4

description: Chip-chip S2 cells JIL-1

tag: cell type

tag: chip antibody

value: JIL1, R69 (custom rabbit anti JIL-1 antibody)


title: Patient 24, before month12 IFN-beta injection_chipA