title: treated_3h_rep2

city: Tuebingen

first: Alexander

last: Herbig

address: Ruemelinstr. 23

department: Archaeo- and Paleogenetics

institute: University of Tuebingen

hyb_protocol: 3 μg of cDNA were hybridized for 16 hours at 50°C and arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: The microarray raw data were normalized and summarized using robust multi-array analysis (RMA) (Irizarry et al., 2003), which is integrated in the transcriptome analysis software Mayday-Seasight (Battke and Nieselt, 2011). Expression profile analysis was done using Mayday (Battke et al., 2010).

organism: Staphylococcus aureus

source_name: S. aureus SA113 daptomycin treated culture sampled after 3 hours

label_protocol: Biotinylated cDNA was prepared after fragmentation according to the standard Affymetrix protocol from 3 μg total RNA (Prokaryotic Sample and Array Processing, Technical Manual 701030 Rev. 5, 2004, Affymetrix)

growth_protocol: Cells were grown over night at 37°C with aeration and shaking (150 rpm) in tryptic soy broth (TSB, Sigma) at an approximate 1:6 culture-to-flask volume ratio.

extract_protocol: Cells were collected by centrifugation at 4,700 rpm for 10 min at 4°C and resuspended in 1 ml Trizol (Invitrogen/Life Technologies, Darmstadt, Germany) for further RNA isolation. Cells were lysed with 0.1 mm glass beads (Roth, Karlsruhe, Germany) in a homogenizer (FastPrep-24, MP Biomedicals, Eschwege, Germany) for 2x20 s at 6,500 rpm. The samples were mixed with 200 µl chloroform for 60 s and incubated for another 3 min at room temperature to extract RNA. After centrifugation at 12,000 g for 15 min at 4°C, the upper phase was collected and 500 µl isopropanol was added. After incubation for 10 min at room temperature, the samples were centrifuged at 12,000 g for 30 min at 4°C and washed with 500 µl 70% ethanol. Pellets collected by centrifugation at 7,500 g for 5 min at 4°C were air-dried for about an hour. After suspension in 50 µl sodium citrate buffer (1 mM, pH 6.4) (Ambion/Life Technologies, Darmstadt, Germany) and incubation for 10 min at 55°C, RNA quality and quantity was determined photometrically at λ=260 and λ=280 nm.

treatment_protocol: Two stationary growth phase SA113 liquid cultures in 2.24 ml TSB each were treated with 100-fold MIC of daptomycin for 10 min or 3 h, respectively, and then pooled to obtain a sufficient number of cells for downstream analysis. Otherwise identical cultures without antibiotics served as controls.

tag: daptomycin treated

value: treated


title: AG_48644

status: Public on Jun 06 2014

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description: Methylation data from anaplastic glioma tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 2.0) package minifi (Version 1.10) using function 'preprocessIllumina'
Unmethylated and methylated signal intensities are available on series level

label: biotin/DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary brain tumor tissue

label_protocol: Illumina protocol.

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: 1p/19q status

value: intact

tag: molecular classification

value: CIMP-A

tag: tissue

value: brain


title: untreated_3h_rep3

type: RNA

label: biotin

molecule: total RNA

source_name: S. aureus SA113 untreated culture sampled after 3 hours

tag: strain

value: untreated


title: treated_3h_rep1


title: AG_50782

tag: idh status

value: mut


title: AG_43904


title: untreated_3h_rep2


title: treated_10min_rep3

source_name: S. aureus SA113 daptomycin treated culture sampled after 10 minutes


title: AG_43940


title: untreated_3h_rep1


title: treated_10min_rep2


title: AG_43846

value: wt


title: treated_10min_rep1


title: AG_43894


title: untreated_10min_rep3

source_name: S. aureus SA113 untreated culture sampled after 10 minutes


title: treated_3h_rep3


title: AG_43864


title: AG_43738


title: untreated_10min_rep2


title: AG_43824


title: kyp suvh5 suvh6

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: UT Southwestern

hyb_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

data_processing: Each probe in the array was assigned a score define by the log2 ratio between Cy5 and Cy3 signal.

organism: Arabidopsis thaliana

source_name: kyp suvh5 suvh6 3 week old mature leaves HeK9me2 ChIP

growth_protocol: plants were grown in long day conditions

extract_protocol: H3K9me2 ChIP experiments were performed using 3 week old leaves of wild type Col-0 and suvr5-1 plants, as previously described [Johnson L, Cao X, Jacobsen S (2002) Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr Biol 12: 1360-1367]. The ChIP-chip was performed as described in [Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE (2008) Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One 3: e3156], the results show a comparison of the abundance of DNA pulled down with the anti-H3K9me2 antibody (#1220, monoclonal anti-H3K9m2 antibody, Abcam) versus INPUT. Each probe in the array was normalized by taking the log2 ratio of H3K9m2 to INPUT intensities, and the scores were scaled so that the average score across the arrays were zero.  H3K9me2 hypomethylated regions were defined by tiling the genome into 500bp bins (250bp overlap), and computing the log2 ratios of the scores of suvr5 vs Col-0, and Z-score transformed.  A Z<-3 cutoff was applied, and regions within 2.5kb were merged.

tag: genotype

value: kyp suvh5 suvh6

tag: chip antibody

source_name: suvr5-1 3 week old mature leaves genomic DNA (INPUT)

value: no antibody

value: 3 week old mature leaves


title: Col0 for kyp suvh5 suvh6

scan_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

source_name: Col0 3 week old mature leaves HeK9me2 ChIP

treatment_protocol: as previously described [Johnson L, Cao X, Jacobsen S (2002)

value: Col0 WT

value: anti-H3K9me2 antibody (#1220, monoclonal anti-H3K9m2 antibody, Abcam)

source_name: Col0 3 week old mature leaves genomic DNA (INPUT)


title: AG_43796


title: untreated_10min_rep1


title: AG_43858


title: AG_43862


title: Col0 for suvr5-1

label_protocol: According to standard NimbleGen protocols (www.nimblegen.com)


title: AG_43732


title: AG_43826


title: Yap Expressing Liver 6 wk.3

city: Boston

first: Dean

last: Yimlamai

state: MA

address: 300 Longwood Ave

department: Medicine

institute: Boston Children's Hospital

hyb_protocol: Performed at BCH microarray core accoding to stander proceedures.

scan_protocol: standard Affymetrix protocol

data_processing: Data was processed at www.genepattern.org, v3.5 using the public website according to default settings (RMA normalization).

organism: Mus musculus

label_protocol: Nugen Pico WT kits was used for labeling

extract_protocol: Qiagen microRNEasy kit was used according to the manufeacters directions

treatment_protocol: Yap expression was induced by administration of doxycycline for one or six weeks in Yap inducible mice.  These were combined and analyzed against GSM305568, GSM305569, GSM305570 as controls

tag: strain background

tag: genotype/variation

value: Rosa26-lsl-YFP mice

tag: cell type

value: FACS sorted Yap expressing liver cells

tag: time point

value: 6 wks after induction


title: Yap Expressing Liver 6 wk.1


title: suvr5-1

source_name: suvr5-1 3 week old mature leaves HeK9me2 ChIP


title: AG_43756


title: AG_43698


title: AG_43714


title: kidney_OpeA_minus

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

country: Japan

institute: kyushu university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8×60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensitieswere log2-transformed and normalized by the quantile algorithm with the Bioconductor.  Then the normalized data were converted to linear scale ('un-log2-transormed') for intuitive readability.

source_name: kidney, Ope, A-

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: ICR

tag: gender

value: male

tag: feeding

value: retinol-free (-) feeding

value: kidney


title: AG_43660

value: intact

value: CIMP-A


title: AG_43702

value: brain


title: kidney_ShamA_plus [re-anlysis]

description: reanalysis

source_name: kidney, sham, A+

value: wild type

tag: operation

value: sham

value: retinol (+) feeding


title: Yap Expressing Liver 1 wk.2

value: 1 wk after induction


title: kidney_ShamA_minus [re-analysis]

description: reanalysis

source_name: kidney, sham, A-


title: kidney_OpeA_plus

source_name: kidney, Ope, A+


title: AG_43692

value: mut


title: Clock5_6_Nx_kidney_133

description: SAMPLE 2

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.   The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensitieswere log2-transformed and normalized by the quantile algorithm with the Bioconductor.  Then the normalized data were converted to linear scale ('un-log2-transormed') for intuitive readability.

source_name: kidney, Clock, 5/6Nx

value: Clock mutant mice (homo)

value: 5/6 nephrectomized


title: Yap Expressing Liver 1 wk.1

value: Rosa26-lsl-YFP mice


title: Yap Expressing Liver 1 wk.3

value: FACS sorted Yap expressing liver cells


title: AG_43666


title: AG_43632

value: wt


title: kidney_ShamA_minus

description: SAMPLE 4

value: ICR


title: Clock_Sham_kidney_132

description: SAMPLE 1

source_name: kidney, Clock, sham

value: male


title: kidney_ShamA_plus

description: SAMPLE 3


title: AG_43628


title: AG_43704


title: AG_43634


title: AG_43620


title: AG_43640


title: Control siRNA [7d]

description: SAMPLE 5

source_name: liver_siRNA_control_7 days

growth_protocol: Male ICR mice (5 weeks old) were purchased from Kyudo Co. Ltd. (Tosu, Japan). Mice were housed in a light-controlled room (lights on from 07:00 to 19:00) at 24 ± 1°C and 60 ± 10% humidity with food and water ad libitum. The animals were adapted to the environmental conditions for 1 week before the experiments.

treatment_protocol: DEN (Tokyo Chemical Industry, Tokyo, Japan) was administered in the drinking water (80 mg/L) at approximately 400 µg/day. ATRA (Wako Pure Chemical Industries, Osaka, Japan) was dissolved in ethanol and dimethyl sulfoxide and administered in the drinking water (30 mg/L) at approximately 150 µg/day or in the culture medium. As a control, the vehicle-treated group was administered water. On the day before DEN treatment, G0s2 siRNA or control siRNA (1.6 nmol) was administered to mice intravenously using LipoTrust EX Oligo in vivo (Hokkaido System Science, Sapporo, Japan).

tag: age

value: 5 wks

value: control

tag: treated with

value: control_siRNA (negative control)

value: 7 days after treatment

value: liver


title: Yap Expressing Liver 6 wk.2

value: 6 wks after induction


title: Yap Organoid Plus Dox 2

growth_protocol: Organoids were grown for 2 weeks prior to RNA analysis.  Wt-wildtype, Minus Dox - 3 weeks Yap ON (in vivo) 2 weeks Yap Off (in vitro), Plus Dox 3 weeks Yap ON (in vivo) 2 weeks Yap ON (in vitro).

value: Organoids; cultured cells

tag: culture condition

value: 3 wks Yap ON (in vivo) 2 wks Yap ON (in vitro)


title: Yap Organoid Plus Dox 1


title: G0s2 siRNA [7d]

description: SAMPLE 6

source_name: liver_siRNA_G0s2_7 days

value: G0s2 knockdown

value: G0s2_siRNA (G0s2 knockdown)


title: Yap Organoid Minus Dox 3

value: 3 wks Yap ON (in vivo) 2 wks Yap Off (in vitro)


title: AG_43616

source_name: Primary brain tumor tissue

tag: 1p/19q status

value: intact

value: mut

value: CIMP-A

value: brain


title: DEN [7d]

description: SAMPLE 2

source_name: liver_DEN_7 days

value: ICR

value: wild type

value: all-trans-retinoic acid (ATRA)


title: Yap Organoid Minus Dox 2


title: AG_43582

tag: molecular classification


title: ATRA+DEN [7d]

description: SAMPLE 3

source_name: liver_ATRA+DEN_7 days

value: male

value: 5 wks

value: diethylnitrosamine (DEN)

tag: tissue


title: vecicle [7d]

description: SAMPLE 1

source_name: liver_vehicle_7 days

tag: strain

value: water (vehicle)

value: 7 days after treatment

value: liver


title: ATRA [7d]

description: SAMPLE 4

source_name: liver_ATRA_7 days


title: G0s2 siRNA [2d]

description: SAMPLE 6

source_name: liver_siRNA_G0s2_2 days

treatment_protocol:
DEN (Tokyo Chemical Industry, Tokyo, Japan) was administered in the drinking water (80 mg/L) at approximately 400 µg/day. ATRA (Wako Pure Chemical Industries, Osaka, Japan) was dissolved in ethanol and dimethyl sulfoxide and administered in the drinking water (30 mg/L) at approximately 150 µg/day or in the culture medium. As a control, the vehicle-treated group was administered water. On the day before DEN treatment, G0s2 siRNA or control siRNA (1.6 nmol) was administered to mice intravenously using LipoTrust EX Oligo in vivo (Hokkaido System Science, Sapporo, Japan).
Genes induced by the following treatment in mice liver were investigated at 2 days after treatment;
DEN: diethylnitrosamine (treatment of DEN (drinking water 80 mg/L))
ATRA: retinoic acid (treatment of ATRA (drinking water 30 mg/L))
G0s2 siRNA : G0s2 knockdown mouse liver (treatment of G0s2 siRNA)
Control siRNA: treatment of scramble siRNA (negative control)

value: 2 days after treatment


title: ATRA+DEN [2d]

description: SAMPLE 4

source_name: liver_ATRA+DEN_2 days


title: AG_43540

tag: idh status


title: Yap Organoid Minus Dox 1

value: Organoids; cultured cells


title: AG_43580


title: DEN [2d]

description: SAMPLE 3

source_name: liver_DEN_2 days


title: Wild-type Organoid 3

value: wild-type conditions (WT)


title: ATRA [2d]

description: SAMPLE 2

source_name: liver_ATRA_2 days


title: vehicle [2d]

description: SAMPLE 1

source_name: liver_vehicle_2 days


title: Yap Organoid Plus Dox 3

value: 3 wks Yap ON (in vivo) 2 wks Yap ON (in vitro)


title: CD8 IL-15 Rep#3

city: Portland

first: Michael

last: McNamara

state: Oregon

address: 4805 NE Glisan St

department: EACRI - Cancer Research

institute: Providence Portland Medical Center

description: Ambion MessageAmp Premier (3' IVT)

hyb_protocol: Affymetrix Mouse 430 2.0 GeneChip array protocol.

scan_protocol: Affymetrix GeneChip Command Console (AGCC) v. 3.1.1 and Affymetrix Expression Console v.1.1 software.

data_processing: Affymetrix Expression Console and RMA normalization.

source_name: Murine OT-I CD8 T Cells

label_protocol: Ambion MessageAmp Premier Protocol

growth_protocol: Antigen activated OT-I CD8 T cells cultured for 24 hours in complete RPMI media supplemented with various gamma chain cytokines

extract_protocol: TRIzol+DirectZol miniprep

treatment_protocol: Soluble recombinant murine IL-2, IL-4, IL-7, IL-15 or IL-21, all at a concentration of 100 ng/ml

tag: cytokines

value: Male

value: OT-I TCR Tg


title: CD8 IL-21 Rep#2

description: Ambion MessageAmp Premier (3' IVT)

extract_protocol: Rneasy miniprep


title: AG_43670

value: intact

value: mut

value: CIMP-A


title: Uninduced YFP+ Hepatocyte3

value: FACS sorted Liver Cells


title: Wild-type Organoid 1


title: CD8 IL-15 Rep#1

description: Ambion MessageAmp Premier (3' IVT)


title: CD8 IL-15 Rep#2

description: Ambion MessageAmp Premier (3' IVT)


title: AG_43516

value: brain


title: Uninduced YFP+ Hepatocyte2


title: AG_43512


title: CD8 IL-7 Rep#2

description: Ambion MessageAmp Premier (3' IVT)


title: CD8 IL-21 Rep#3

description: Ambion MessageAmp Premier (3' IVT)


title: AG_43534


title: CD8 IL-7 Rep#1

description: Ambion MessageAmp Premier (3' IVT)


title: CD8 IL-4 Rep#3

description: Ambion MessageAmp Premier (3' IVT)


title: AG_43536


title: CD8 IL-21 Rep#1

description: Ambion MessageAmp Premier (3' IVT)


title: Wild-type Organoid 2


title: Uninduced YFP+ Hepatocyte1


title: AG_43484


title: AG_43488


title: AG_43626


title: CD8 IL-4 Rep#2

description: Ambion MessageAmp Premier (3' IVT)


title: CD8 IL-2 Rep#1

description: Ambion MessageAmp Premier (3' IVT)


title: CD8 Media Control Rep#3

description: Ambion MessageAmp Premier (3' IVT)

value: Media Control


title: CD8 IL-2 Rep#2

description: Ambion MessageAmp Premier (3' IVT)


title: AG_43456


title: AG_43478

value: codel


title: CD8 IL-4 Rep#1

description: Ambion MessageAmp Premier (3' IVT)


title: CD8 IL-2 Rep#3

description: Ambion MessageAmp Premier (3' IVT)


title: AG_43436


title: CD8 Media Control Rep#1

description: Ambion MessageAmp Premier (3' IVT)


title: Retnla-Tg 6

city: Seoul

first: GooTaeg

last: Oh

address: 52, Ewhayeodae-gil

department: Department of Life Sciences

country: South Korea

institute: Ewha Womans University

description: L-6-WD T

hyb_protocol: RNA samples derived from single animals were hybridized in recommended buffer to microarrays (Affymetrix Murine Genome Array U430 2.0) at 45°C for 16 hours. The samples were stained and washed according to the manufacturer’s protocol on a Fluidics Station 400 (Affymetrix).

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000.

data_processing: Data normalization was performed using GCOS, global scaling in GenPlex software (Istech Corp., Korea).To identify differentially expressed transcripts, pairwise comparisons were carried out using GenPlex software (Istech Corporation).

source_name: liver from HFD-fed Retnla-Tg mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All mice used in the experiment were given water and food ad libitum and were kept in a room with a light cycle lasting from 7:00 AM to 7:00 PM. The animal study was conducted in accordance with protocols approved by the IACUC of Ewha Womans University.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: All mice used in the experiment were switched from a standard diet (SD) to a HFD at eight weeks of age and maintained on that diet. The HFD consisted of 0.15% cholesterol and 21% fat. Mice were euthanized by cervical dislocation, and livers was removed.

value: Retnla transgenic (Tg)

value: male

value: 3 months

tag: diet

value: high fat diet (HFD) for 4 wks


title: CD8 Media Control Rep#2

description: Ambion MessageAmp Premier (3' IVT)


title: Retnla-non-Tg 3

description: L-3-WD nonT

source_name: liver from HFD-fed Retnla-non-Tg mice

tag: strain background

value: non-transgenic (non-Tg)

value: liver


title: AG_42866


title: Retnla-non-Tg 2

description: L-2-WD nonT

tag: genotype/variation


title: Retnla-Tg 5

description: L-5-WD T


title: Retnla-Tg 7

description: L-7-WD T


title: Retnla-non-Tg 1

description: L-1-WD nonT


title: Jemalong_Callus_4weeks_rep1

status: Public on Jun 05 2014

city: Sydney

first: Sergey

last: Kurdyukov

address: Reserve Road

country: Australia

institute: Kolling Institute of Medical Research

hyb_protocol: Samples were hybridized with GPL4652 Arrays (Affymetrix) and scanned at the Australian Genome Research Facility (AGRF).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data processing was performed as described in Imin N, Goffard N, Nizamidin M, Rolfe BG: Genome-wide transcriptional analysis of super-embryogenic Medicago truncatula explant cultures. BMC Plant Biol 2008, 8:110. Raw data were background corrected, normalized, summarized and log2 transformed using the GCRMA algorithm (ver. 2.2.0) using the affy package of the bioconductor software (Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge YC, Gentry J et al: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5: R80) with default parameters.

organism: Medicago truncatula

source_name: Medicago truncatula, Jemalong variety (WT), 4weeks old callus

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The standard tissue culture procedure was as described in Nolan KE, Irwanto RR, Rose RJ: Auxin up-regulates MtSERK1 expression in both Medicago truncatula root-forming and embryogenic cultures. Plant Physiol 2003, 133:218-230.. Explants were cultured on P4 10:4 on agar plates for 3 weeks (10 µM NAA, 4 µM BAP) before transfer to P4 10:4:1 (10 µM NAA, 4 µM BAP, 1 µM ABA) for additional 1 week. Cultures were incubated in the dark.

extract_protocol: RNA was isolated using RNAqueous™-4PCR Kit (Ambion, http://www.ambion.com/. Hybridisations were performed according to the Affymetrix manual (Affymetrix, http://www.affymetrix.com/).

value: 4 week old callus

tag: line

value: Jemalong variety (WT)


title: 2HA_Callus_4weeks_rep1

source_name: Medicago truncatula, 2HA seedline, 4weeks old callus

value: 2HA seedline


title: 2HA_Callus_4weeks_rep3


title: Jemalong_Callus_4weeks_rep3


title: Jemalong_Callus_4weeks_rep2


title: control siRNA [2d]

description: SAMPLE 5

source_name: liver_siRNA_control_2 days

value: ICR

value: control

value: control_siRNA (negative control)

tag: time point

value: 2 days after treatment


title: 2HA_Callus_4weeks_rep2


title: blood at T24h, S. aureus infected, vancomycin treated, biological rep5

city: Durham

first: Sun Hee

last: Ahn

state: NC

address: Stead Bldg, RM 1546A

institute: Duke University

hyb_protocol: Biotin-labeled cDNA was hybridized to the arrays for 16 hours at 45°C according to the manufacturer’s instruction. Arrays were then washed and labeled with streptavidinphycoerythrin (strep-PE), and the signal was amplified using biotinylated antistreptavidin followed by another round of staining with strep-PE. These steps were performed on the Affymetrix fluidics station according to the recommended protocol.

scan_protocol: Amplification and microarray hybridization were performed at the Duke University Microarray Core. Labeled gene chips were scanned using an Affymetrix Genechip Scanner 7G (Santa Clara, CA).

data_processing: Data processing was conducted using the Robust Multichip Average (RMA) generated by Affymetrix Expression Console software. Gene expression data were imported into Partek Genomics Suite 6.5 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average analysis, and expression data were log2 transformed. Differential expression analysis for the whole blood cells was performed using 1-way ANOVA (either infection status or drug treatment alone). Gene lists were created using a cutoff of P < .05, 2-fold change, although second-level analysis using a false-discovery rate of <0.05, 2-fold change was also performed.

source_name: mouse blood after 24h of S. aureus infection (i.p.) with vancomycin treatment (i.v.)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Affymetrix).

growth_protocol: One methicillin-resistant S. aureus strain (USA300) was used.  Overnight S. aureus cultures were inoculated into fresh tryptic soy broth and incubated aerobically at 30°C to log-phase growth (optical density 600nm of ~1.0) (Rice et al., 2003).  Cells were harvested by centrifugation, rinsed, and resuspended in phosphate-buffered saline (PBS).

extract_protocol: Total RNA was extracted from mouse blood using the Mouse RiboPure Blood RNA kit (Ambion, Austin, TX) according to the manufacturer’s instructions. Globin mRNA was removed from whole blood RNA using the Globinclear kit (Ambion, Austin, TX). All samples passed the quality criteria of the Agilent Bioanalyzer and were used for microarray analysis. Since the total RNA yield of many samples was low, one round of linear amplification was performed for all samples using the MessageAmp Premier kit (Ambion, Austin, TX).

treatment_protocol: To mimic the natural course of S. aureus infection in humans, which typically arises from a primary focus of infection and disseminates to other sites, we employed an intraperitoneal (i.p.) route of infection in our animal model. Briefly, blood from 5 individual mice from A/J will be collected by intracardiac puncture after infection with USA300, and 24h post-treatment of linezolid vs vancomycin (i.v.) and stored in RNAlater at -20oC

tag: inbred strain

value: A/J

tag: pathogen strain

value: S. aureus USA300

tag: drug treatment  (linezolid/vancomycin/no)

value: vancomycin

tag: time (0h/2h/24h post infection)

tag: replicate

tag: host gender

value: 8-10 weeks


title: blood at T24h, S. aureus infected, linezolid treated, biological rep5

source_name: mouse blood after 24h of S. aureus infection (i.p.) with linezolid treatment (i.v.)

value: linezolid

tag: age


title: blood at T0, biological rep5

source_name: mouse blood of uninfected control

value: no

value: male


title: AG_42162

source_name: Primary brain tumor tissue

tag: 1p/19q status

value: intact

tag: molecular classification

value: CIMP-A

value: brain


title: blood at T0, linezolid treated, biological rep5

source_name: mouse blood after linezolid treatment (i.v.)


title: blood at T24h, S. aureus infected, biological rep5

source_name: mouse blood after 24h of S. aureus infection (i.p.)


title: blood at T0, vancomycin treated, biological rep5

source_name: mouse blood after vancomycin treatment (i.v.)


title: blood at T24h, S. aureus infected, biological rep4


title: blood at T24h, S. aureus infected, vancomycin treated, biological rep4


title: AG_41402

value: mut

tag: tissue


title: AG_41546

tag: idh status


title: blood at T0, vancomycin treated, biological rep4


title: blood at T2h, S. aureus infected, biological rep5

source_name: mouse blood after 2h of S. aureus infection (i.p.)


title: AG_41790


title: AG_41590


title: AG_40642


title: blood at T24h, S. aureus infected, vancomycin treated, biological rep3


title: AG_25752


title: blood at T0, linezolid treated, biological rep4


title: blood at T0, vancomycin treated, biological rep3


title: CD8 IL-7 Rep#3

description: Ambion MessageAmp Premier (3' IVT)

tag: cytokines

tag: gender

value: Male

tag: strain

value: OT-I TCR Tg


title: blood at T24h, S. aureus infected, biological rep3


title: blood at T24h, S. aureus infected, vancomycin treated, biological rep2


title: blood at T24h, S. aureus infected, linezolid treated, biological rep3


title: AG_41336


title: AG_25548


title: blood at T2h, S. aureus infected, biological rep3


title: blood at T0, linezolid treated, biological rep3


title: blood at T24h, S. aureus infected, linezolid treated, biological rep2


title: blood at T0, biological rep3


title: blood at T24h, S. aureus infected, linezolid treated, biological rep4


title: blood at T24h, S. aureus infected, vancomycin treated, biological rep1


title: AG_22966


title: blood at T24h, S. aureus infected, linezolid treated, biological rep1


title: blood at T2h, S. aureus infected, biological rep2


title: blood at T24h, S. aureus infected, biological rep2


title: blood at T0, linezolid treated, biological rep2


title: blood at T0, biological rep2


title: blood at T2h, S. aureus infected, biological rep1


title: blood at T0, vancomycin treated, biological rep2


title: blood at T0, vancomycin treated, biological rep1


title: blood at T0, biological rep1


title: blood at T0, linezolid treated, biological rep1


title: AG_43348


title: blood at T24h, S. aureus infected, biological rep1


title: blood at T0, biological rep4


title: blood at T2h, S. aureus infected, biological rep4


title: Muscle biospy sample 11

city: Singapore

first: Joanna

last: Holbrook

address: 30 Medical Drive

country: Singapore

institute: SICS

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The image data were processed with the Genome Studio™ Methylation Module software. Further data processing was performed as described previously (Pan et al., 2012).  Probes were filtered for detection p-value <0.05 and NBEADS>3 in Matlab (MathWorks). Data were normalised amongst samples using quantile normalization.

organism: Macaca fascicularis

source_name: Muscle

label_protocol: 1 mg was bisulfite converted using EZ-96 DNA Methylation™ Gold Kit (Catalogue No.: D5007, Zymo Research).

extract_protocol: Genomic DNA was extracted according to standard procedures

value: muscle


title: Muscle biospy sample 9


title: ItalianWolf2

city: Barcelona

first: Oscar

last: Ramirez

state: APO/FPO EUROPE / ATLANTIC

address: Dr. Aiguader, 88

country: Spain

institute: Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra)

data_processing:
Standard NimbleGen protocols (http://www.nimblegen.com/products/lit/05434483001.pdf)
We assessed the performance of our CNV genotyping using a two-stage procedure. In a first discovery stage, we identified CNVs using a conservative approach based onthe combination on two methods: a Reversible Jump hidden Markov Model and the procedure described in Berglund et al. 2012. In the second stage, we genotyped our samples for each of these discovered CNV regions.

organism: Canis lupus

source_name: Italian Wolf

extract_protocol: Genomic DNA were extracted using Quiagen's QIAamp DNA and the quality of the DNA was analyzed by spectrophotometry and agarose gel electrophoresis.

tag: breed

value: Italian Wolf

organism: Canis lupus familiaris

source_name: Boxer

value: Boxer


title: SwedenWolf

hyb_protocol: Standard NimbleGen protocols (http://www.nimblegen.com/products/lit/05434483001.pdf)

source_name: Sweden Wolf

value: Sweden Wolf


title: IsraelWolf

scan_protocol: Standard NimbleGen protocols (http://www.nimblegen.com/products/lit/05434483001.pdf)

source_name: Israel Wolf

value: Israel Wolf


title: Muscle biospy sample 10


title: GoldenJackal

organism: Canis aureus

source_name: Golden Jackal

label_protocol: Standard NimbleGen protocols (http://www.nimblegen.com/products/lit/05434483001.pdf)

value: Golden Jackal


title: RedWolf

organism: Canis rufus

source_name: Red Wolf

value: Red Wolf


title: Dingo

source_name: Dingo

value: Dingo


title: IberianWolf

source_name: Iberian Wolf

value: Iberian Wolf


title: PortugueseWolf

source_name: Portuguese Wolf

value: Portuguese Wolf


title: IranianSelf

source_name: Iranian Wolf

value: Iranian Wolf

source_name: Iranian wolf

value: Iranian wolf


title: MongolianWolf2

source_name: Mongolian Wolf2

value: Mongolian Wolf2


title: MexicanWolf

source_name: Mexican Wolf

value: Mexican Wolf


title: Basenji

source_name: Basenji

value: Basenji


title: IranianWolf


title: Beagle

source_name: Beagle

value: Beagle


title: BoxerSelf


title: Dachshund

source_name: Dachshund

value: Dachshund


title: IsraelWolf2


title: YellowstoneWolf

source_name: Yellowstone Wolf

value: Yellowstone Wolf


title: SSEA-4+ cells,biological rep2

city: Shanghai

first: WU

last: ZHANG

address: No.197,  Ruijin 2nd Road

country: China

institute: RuiJin Hospital Shanghai Jiao Tong University school of Medicine

description: Gene expression data from SSEA-4+

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US)

source_name: sorted SSEA-4+

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA

growth_protocol: The fresh osteosarcoma samples were cut up into small pieces (<3×3×1.5 mm3) within an hour after surgery.And then incubated with Collagenase Type V (Invitrogen) in IMDM medium (250 units/ml) at 37°C for 1 hour.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: Sorted SSEA-4+ or SSEA-4- osteosarcoma cells suspended in PBS.

tag: cell type

value: sorted SSEA-4+ osteosarcoma cells


title: Muscle biospy sample 8

source_name: Muscle

value: male

value: muscle


title: ItalianWolf

source_name: Italian Wolf

value: Italian Wolf

source_name: Boxer

value: Boxer


title: SSEA-4+ cells,biological rep3

description: Gene expression data from SSEA-4+


title: ChineseWolf

source_name: Chinese Wolf

value: Chinese Wolf


title: Boxer


title: Muscle biospy sample 7


title: Coyote

organism: Canis latrans

source_name: Coyote

value: Coyote


title: SSEA-4- cells,biological rep3

description: Gene expression data from SSEA-4-

source_name: sorted SSEA-4-

value: sorted SSEA-4- osteosarcoma cells


title: Muscle biospy sample 6


title: SSEA-4+ cells,biological rep1

description: Gene expression data from SSEA-4+


title: CHO Chr6 hybridoma

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

hyb_protocol: 200 µl hybridization mix was hybridized to genotyping microarrays for 16 h at 50°C.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were processed with R v3.0.1 and Bioconductor extension packages; microarray CDF and CEL files were read with affxparser, non-polymorphic probes were retained for analysis; the limma package was used to perform between-sample loess normalization of log2-transformed signal values.

organism: Cricetulus griseus

source_name: Chinese hamster ovary cells monosomal for human chromosome 6

label_protocol: 500 ng total genomic DNA was precessed with the Genome-Wide Human SNP Nsp/Sty Assay Kit 6.0 (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Cells were cultured in RPMI 1640 medium containing 10% FCS, 2mM l-glutamine, 10 μg/mL streptomycin, 100 IU/mL penicillin, and 300 IU/mL rhIL-2.

extract_protocol: Genomic DNA was isolated with the QIAamp DNA Mini Kit (Qiagen)  following the manufactuer's protocol.

tag: cell line

value: CHO Chr6


title: SSEA-4- cells,biological rep1

description: Gene expression data from SSEA-4-


title: parental CHO

source_name: Chinese hamster ovary cells

value: CHO


title: Muscle biospy sample 5


title: Muscle biospy sample 1 replicate


title: Muscle biospy sample 4


title: IndianWolf

source_name: Indian Wolf

value: Indian Wolf


title: GreatlakesWolf

source_name: Greatlakes Wolf

value: Greatlakes Wolf


title: SSEA-4- cells,biological rep2

description: Gene expression data from SSEA-4-


title: Muscle biospy sample 3


title: shNsl1 ESC rep1_B

status: Public on Jun 04 2014

city: Illkirch

first: Sarina

last: Ravens

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

description: Experiment B: gene expression data from shNsl1 ESCs

hyb_protocol: Following fragmentation and end-labeling, 3 ug of cDNAs were hybridized on GeneChip Mouse Gene 2.0 ST arrays (Affymetrix) for whole-transcript expression profiles.

scan_protocol: Washed and stained chips were scanned with the GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7um.

data_processing: Obtained raw data (.CEL intensity files) were processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: ESC E14wt

label_protocol: Biotinylated cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat 4411974) and the Affymetrix GeneChip WT Terminal Labeling Kit (Cat 900671) according to Affymetrix recommendations.

growth_protocol: Wild type male mESCs (E14.wt) were cultivated on 0.1% gelatin and CD1 feeder cells (37°C, 5% CO2) in DMEM (4.5g/L), 15% foetal calf serum, leukemia inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino acids. To work under feeder-free conditions cells were treated with 1mg/ml Collagenase (GIBCO) and 2mg/ml Dispase (GIBCO) and cultivated for one passage without feeder cells. Experiments were conducted at passage 26-29.

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

treatment_protocol: shRNA approaches were conducted with pLKO.1 puro shRNA vectors (Sigma-Aldrich, France) of the TRC2 library. For Ns1 KD the TRCN0000241466 shRNA clone and for Msl1 KD the TRCN0000241378 shRNA clone was used. In addition, the shRNA Non-Target Control (Product No. SHC002) was applied. Production of lentiviral particles as well as infection of mESCs was conducted according to the manufacturer’s protocol.

tag: transduction

value: shNsl1 expression vector

tag: background


title: shNsl1 ESC rep3_B


title: shNsl1 ESC rep2_B


title: Muscle biospy sample 2


title: MongolianWolf

source_name: Mongolian Wolf

value: Mongolian Wolf


title: shcontrol ESC rep3_B

description: Experiment B: gene expression data from shcontrol ESCs

value: shcontrol (non-target) expression vector


title: shcontrol ESC rep1_A

description: Experiment A: gene expression data from shcontrol ESCs


title: shcontrol ESC rep2_A


title: shMsl1 ESC rep3_A

description: Experiment A: gene expression data from shMsl1 ESCs

value: shMsl1 expression vector


title: Muscle biospy sample 1


title: shcontrol ESC rep1_B


title: shcontrol ESC rep2_B


title: shMsl1 ESC rep1_A


title: shcontrol ESC rep3_A


title: mTET1-CD

city: Houston

first: CHUNLEI

last: JIN

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description: Sample 6

hyb_protocol: Affymetrix GeneChip Human Gene 2.0 ST arrays were hybridized to 5.5ug of biotin labeled cDNA, washed and stained according to Affymetrix protocol.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were analyzed using the Affymetrix Gene Expression Console (v.1.3.1) with RMA (Robust Multi-array Average) normalization algorithm.

source_name: HEK293T_mTET1-CD expression plasmid

label_protocol: 100 ng of total RNA were amplified using the Ambion WT Expression Kit and cDNA were biotin labelled using Affymetrix GeneChip WT Terminal Labeling protocol.

growth_protocol: HEK293T cells were cultured in Dulbecco's Modified Eagle Medium modified with 10% fetal bovine serum and 100 μg/ml streptomycin-penicillin.

treatment_protocol: mTET1-CD, TET1-CD, mTET1-FL, TET1-FL expression plasmid or empty vector was transfected into HEK293T cells by using OPTI-MEM (Invitrogen) and FuGene HD transfection reagent (Roche). Three days after transfection, overexpressed cells were purified with fluorescent activated cell sortng. Lentiviral shRNA-mediated TET1 knockdown were also established in HEK293T cells, and one control and two TET1 knockdown clones were identified.

tag: transfected with

value: mTET1-CD expression plasmid


title: mTET1-FL

description: Sample 8

source_name: HEK293T_mTET1-FL expression plasmid

value: mTET1-FL expression plasmid


title: Vector control

description: Sample 4

source_name: HEK293T_empty vector

value: empty vector


title: shMsl1 ESC rep2_A


title: TET1-CD

description: Sample 5

source_name: HEK293T_TET1-CD expression plasmid

value: TET1-CD expression plasmid


title: shTET1#1

description: Sample 2

source_name: HEK293T_TET1 shRNA

value: TET1 shRNA#1


title: shTET1#2

description: Sample 3

value: TET1 shRNA#2


title: TET1-FL

description: Sample 7

source_name: HEK293T_TET1-FL expression plasmid

value: TET1-FL expression plasmid


title: shControl

description: Sample 1

source_name: HEK293T_control shRNA

value: control shRNA


title: Liver_microsomic_females

city: Utrecht

first: Alberto

last: Miranda Bedate

address: Yalelaan 104

country: Netherlands

institute: Universiteit Utrecht

hyb_protocol: Samples were hybridized using the Agilent Whole Genome Oligo Microarray (Agilent Technologies, Palo Alto, CA) by using Agilent SureHyb hybridization chambers

scan_protocol: The processed slides were scanned with the Agilent DNA microarray scanner using the settings recommended by Agilent Technologies.

data_processing: Agilent Feature Extraction Software

source_name: Liver

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.5 mg of total RNA using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer’s instructions. The RNA content was measured using a Nanodrop ND-1000 spectrophotometer, and denaturing gel electrophoresis was conducted. Next, the samples were amplified, labeled using the Agilent Quick Amp labeling kit.

extract_protocol: Liver from each experimental group (Normal or microsomal litter) was extracted from fetus E20. Total RNA was prepared following the manufacturer's instructions using the TRIzol® Reagent Kit (Invitrogen). Samples were additionally treated with RNeasycolumn purification kit (QIAGEN) in order to completely remove genomic DNA. Immediately after extraction, total RNA was stored to -80ºC until it was processed for the mycroarray experiment

value: Female

tag: developmental stage

value: Embryonic Day 20

value: Whole liver


title: 24_YS_N_48H

city: Lund

first: Gustaf

last: Lindgren

address: Lasarettsgatan 21

department: Depoartment of Otolaryngology/Head and Neck surgery

country: Sweden

institute: Lund University

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The raw data provided in the submitted file was log2 transformed and  set for detection p-value <= 0.05. Probes that did not have a gene symbol were also removed and the remaining probes were median centered.

label_protocol: standard Illumina protocol

extract_protocol: Trizol

tag: nr [a]

tag: surgery [a]

value: TRUE

tag: epo_nacl [a]

value: NaCl

tag: timepoint [a]

tag: row_pos [a]

tag: group [a]

value: H

tag: project

tag: column name mev

value: xenografted human Head and Neck squamous Cell Cancer (HNSCC) tumours on Balb/c nude mice

tag: treatment

value: Surgery (=TRUE) + Nacl  48 hours after surgical transection


title: Liver_control_females

tag: gender

tag: tissue

tag: strain


title: Liver_control_males

value: Male


title: 23_YS_N_48H


title: CGH: FN0190009.01.01.03.M5_v_M92-220

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 9.1)

scan_protocol: Slides were scanned on the NimbleGen MS 200 Scanner (Roche/NimbleGen, Madison,WI) according to the array manufacturer instructions (NimbleGen CGH User Guild Ver 9.1)

data_processing: Data was analyzed using the Roche NimbleGen DEVA software.

organism: Glycine max

source_name: DNA from soybean line FN0190009.01.01.03.M5

label_protocol: 500 ng of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 9.1.

growth_protocol: single plant leaf tissue

extract_protocol: Genomic DNA samples were isolated using the Qiagen Plant DNeasy protocol

tag: genotype

value: single plant leaf

source_name: DNA from soybean line M92-220


title: 22_YS_N_48H


title: 20_YS_N_48H


title: CGH: FN0190076.01.02.M4_v_M92-220

source_name: DNA from soybean line FN0190076.01.02.M4


title: 29_YS_E_48H

value: epo

value: G

value: Surgery (=TRUE) + Epo  48 hours after surgical transection


title: 21_YS_N_48H


title: Liver_microsomic_males


title: CGH: FN0190144.01.04.M4_v_M92-220

source_name: DNA from soybean line FN0190144.01.04.M4


title: CGH: M92-220.x2.54.WT_v_M92-220

source_name: DNA from soybean line M92-220.x2.54.WT


title: CGH: FN0190100.01.M3_v_M92-220

source_name: DNA from soybean line FN0190100.01.M3


title: CGH: FN0190007.02.M3_v_M92-220

source_name: DNA from soybean line FN0190007.02.M3


title: 25_YS_E_48H


title: CGH: FN0190119.01.02.M4_v_M92-220

source_name: DNA from soybean line FN0190119.01.02.M4


title: 27_YS_E_48H


title: CGH: FN0190107.01.03.M4_v_M92-220

source_name: DNA from soybean line FN0190107.01.03.M4


title: CGH: FN0190004.01.02.M4_v_M92-220

source_name: DNA from soybean line FN0190004.01.02.M4


title: CGH: FN0164472.x3.06.01.M5_v_M92-220

source_name: DNA from soybean line FN0164472.x3.06.01.M5


title: 10_YS_N_24H

value: F

value: Surgery (=TRUE) + NaCl 24 hours after surgical resection


title: 09_YS_N_24H


title: CGH: FN0190080.01.M3_v_M92-220

source_name: DNA from soybean line FN0190080.01.M3


title: CGH: FN0190069.01.01.M4_v_M92-220

source_name: DNA from soybean line FN0190069.01.01.M4


title: CGH: FN0190018.01.M3_v_M92-220

source_name: DNA from soybean line FN0190018.01.M3


title: 26_YS_E_48H


title: CGH: FN0175143.05.06.01.M5_v_M92-220

source_name: DNA from soybean line FN0175143.05.06.01.M5


title: RL-PDGFAA3G3-3

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

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

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label: Biotin

source_name: Uterine cancer cells

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: cell line


title: CGH: FN0173217.03.09.01.M5_v_M92-220

source_name: DNA from soybean line FN0173217.03.09.01.M5


title: RL-PDGFAA3G3-2


title: CGH: FN0190101.01.M3_v_M92-220

source_name: DNA from soybean line FN0190101.01.M3


title: CGH: FN0190020.02.M3_v_M92-220

source_name: DNA from soybean line FN0190020.02.M3

source_name: DNA from soybean line M92-220


title: 08_YS_N_24H


title: RL-PDGFAA3G3-1


title: 14_YS_E_24H

value: E

value: Surgery (=TRUE) + Epo 24 hours after surgical transection


title: 11_YS_E_24H


title: CGH: FN0190055.02.M3_v_M92-220

source_name: DNA from soybean line FN0190055.02.M3


title: 04_NS_N_01H

value: FALSE

value: B

value: No surgery (=FALSE) +  NaCl


title: 02_NS_N_01H


title: 12_YS_E_24H

value: TRUE


title: RL-PDGFAA-3

value: PDGFAA


title: 28_YS_E_48H


title: RL-PDGFAA-2


title: 05_NS_N_01H

value: NaCl


title: 07_YS_N_24H

value: xenografted human Head and Neck squamous Cell Cancer (HNSCC) tumours on Balb/c nude mice


title: CGH: FN0172932.09.08.01.M5_v_M92-220

source_name: DNA from soybean line FN0172932.09.08.01.M5


title: 19_NS_E_01H

value: A

value: No surgery (=FALSE) + Epo


title: CGH: FN0172728.01.01.M4_v_M92-220

source_name: DNA from soybean line FN0172728.01.01.M4

value: single plant leaf


title: 17_NS_E_01H

value: epo


title: 18_NS_E_01H


title: RL-PDGFAA-1


title: 03_NS_N_01H


title: RL-Ctr.IgG-2

value: Control IgG


title: RL-Ctr.IgG-1


title: CGH: FN0190013.01.M3_v_M92-220

source_name: DNA from soybean line FN0190013.01.M3


title: 16_NS_E_01H


title: 15_NS_E_01H


title: RL-Ctr.IgG-3


title: CGH: FN0171501.01.02.M4_v_M92-220

source_name: DNA from soybean line FN0171501.01.02.M4


title: H1A-PDGFAA3G3-2


title: H1A-PDGFAA-3


title: H1A-PDGFAA3G3-1


title: H1A-PDGFAA-1


title: H1A-Ctr.IgG-3


title: H1A-Ctr.IgG-2


title: CGH: FN0171154.08.01.02.02.M6_v_M92-220

source_name: DNA from soybean line FN0171154.08.01.02.02.M6


title: H1A-PDGFAA-2


title: H1A-Ctr.IgG-1


title: CGH: FN0170714.03.01.02.M5_v_M92-220

source_name: DNA from soybean line FN0170714.03.01.02.M5


title: CGH: FN0170228.07.35.01.M5_v_M92-220

source_name: DNA from soybean line FN0170228.07.35.01.M5


title: CGH: FN0171208.01.07.M4_v_M92-220

source_name: DNA from soybean line FN0171208.01.07.M4


title: 2012-01-27A10_11-43_527821_Area1_532

city: Los Angeles

first: Paul

last: Webster

state: CA

address: 804 Bloom Walk

department: CEMMA

institute: University of Southern California

description: Biofilm, not treated

hyb_protocol: Hybridization was performed by  Functional Genomic Core, City of Hope, Duarte,CA, USA following Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Functional Genomic Core, City of Hope, Duarte,CA, USA, following Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Haemophilus influenzae

source_name: Haemophilus influenzae Biofilm, not treated

label_protocol: Labeling was performed by Functional Genomic Core, City of Hope, Duarte,CA, USA, following Nimblegen standard operating protocol. See www.nimblegen.com.

growth_protocol: 50 μl from frozen stock cultures of non-typeable Haemophilus influenzae strain PittGG were spread onto chocolate agar plates and incubated at 37°C in an atmosphere of 5% CO2 with 95% relative humidity. After 24-hour incubation, multiple colonies were used to inoculate BHI broth supplemented with hemin at 10 μg/ml and nicotinamide adenine dinucleotide (NAD) at 2 μg/ml (sBHI). The bacterial suspension was grown to stationary phase (1 x 109 CFU/ml) at 37˚C, 5% CO2, with 95% relative humidity. Biofilms in this study were prepared by diluting 1:200 bacterial suspensions at stationary phase with fresh sBHI, aliquoting into culture vessels appropriate for subsequent applications, and incubating at 37˚C with 5% CO2 and 95% relative humidity for 24 hours.

extract_protocol: NTHi PittGG bacteria were suspended in sBHI and added to 20x100mm tissue culture-treated polystyrene dishes and incubated for 24 hr at 37°C. Three biological replicates per condition were prepared (plus or minus 170 ng/mL ampicillin) and the experiment was carried out as follows.     Briefly, the biofilms were gently washed in PBS to remove culture medium and then removed from the plastic substrate by scraping in 4 mL of PBS. The scraped biofilm suspensions were placed in 50 mL Falcon tubes, evenly dispersed and aliquoted for further processing. The aliquots were centrifuged at 8,000 rpm in a benchtop centrifuge for 3 min. and the supernatant was discarded. The pellets were re-suspended in RNAwiz and total RNA was extracted using Ambion RiboPure-Bacteria kit following the manufacturer’s instructions.     cDNA was synthesized using Invitrogen SuperScript Double-Stranded cDNA Synthesis Kit. Both RNA and cDNA quality was checked using Agilent 2100 Bioanalyzer and Agilent RNA 6000 nano and DNA1000 chips. cDNA (0.5-1 µg) was used to start the amplification and labeling reaction using the Roche NimbleGen One-Color DNA Labeling kit, in which Cy3 was randomly incorporated in the newly synthesized DNA by Klenow fragment (3’ -> 5’ exo-).     Two µg of labeled DNA derived from each RNA sample was hybridized to each array for over 16-18 hours. DNA microarray gene expression was carried out using Roche NimbleGen custom whole genome arrays according to the standard NimbleGen procedure (NimbleGen Arrays User’s Guide: Gene Expression Analysis v5.1).     The slides/arrays were washed and spun dry and then scanned using a NimbleGen MS200 Microarray scanner with a resolution of 2 µm. The normalization was done using NimbleScan 2.6.0.0 built-in normalization function. Microarray data analysis was performed using Partek Genomics Suite v6.5 (Partek Inc., St. Louis, MO, USA). Differentially expressed genes were determined using fold-change (≥1.5) plus P (≤ 0.05, T-test) with FDR ≤ 0.05.

treatment_protocol: Biofilms were prepared in tissue culture-treated polystyrene petri dishes with beta-lactam antibiotics at designated concentration ranges. Control biofilms were formed in perti dishes containing sBHI with no antibiotics. The bacteria were incubated at 37°C in an atmosphere of 5% CO2 and 95% relative humidity for 24 hours before biofilm quantification using crystal violet assay.

tag: protocol

value: Biofilm, not treated


title: 2012-01-27A09_11-43_527821_Area1_532

description: Planktonic, not treated

source_name: Haemophilus influenzae Planktonic, not treated

value: Planktonic, not treated


title: CGH: M92-220.x1.04.WT_v_M92-220

source_name: DNA from soybean line M92-220.x1.04.WT


title: CGH: FN0170142.07.01.01.M5_v_M92-220

source_name: DNA from soybean line FN0170142.07.01.01.M5


title: 2012-01-27A08_11-43_527821_Area1_532

description: Ampicillin treated

source_name: Haemophilus influenzae Ampicillin treated

value: Ampicillin treated


title: CGH: FN0175501.x2.02.01.M5_v_M92-220

source_name: DNA from soybean line FN0175501.x2.02.01.M5


title: 2012-01-27A12_11-43_527821_Area1_532

description: Ampicillin treated


title: CGH: FN0164166.03.06.M4_v_M92-220

source_name: DNA from soybean line FN0164166.03.06.M4


title: 2012-01-27A07_11-43_527821_Area1_532

description: DMSO treated

source_name: Haemophilus influenzae DMSO treated

value: DMSO treated


title: H1A-PDGFAA3G3-3

source_name: Uterine cancer cells


title: CGH: FN0190074.01.M3_v_M92-220

source_name: DNA from soybean line FN0190074.01.M3

source_name: DNA from soybean line M92-220


title: 2012-01-27A11_11-43_527821_Area1_532

description: DMSO treated


title: 2012-01-27A05_11-43_527821_Area1_532

description: Planktonic, not treated


title: CGH: FN0164084.01.04.M4_v_M92-220

source_name: DNA from soybean line FN0164084.01.04.M4


title: CGH: FN0164160.03.02.01.M5_v_M92-220

source_name: DNA from soybean line FN0164160.03.02.01.M5


title: CGH: FN0164160.03.02.01.01.M6_v_M92-220

source_name: DNA from soybean line FN0164160.03.02.01.01.M6


title: CGH: FN0190067.01.M3_v_M92-220

source_name: DNA from soybean line FN0190067.01.M3


title: CGH: FN0170712.06.41.01.M5_v_M92-220

source_name: DNA from soybean line FN0170712.06.41.01.M5


title: 2012-01-27A03_11-43_527821_Area1_532

description: DMSO treated


title: 2012-01-27A02_11-43_527821_Area1_532

description: Biofilm, not treated


title: CGH: FN0163955.05.01.M4_v_M92-220

source_name: DNA from soybean line FN0163955.05.01.M4


title: 2012-01-27A01_11-43_527821_Area1_532

description: Planktonic, not treated


title: 2012-01-27A04_11-43_527821_Area1_532

description: Ampicillin treated


title: 2012-01-27A06_11-43_527821_Area1_532

description: Biofilm, not treated

source_name: Haemophilus influenzae Biofilm, not treated


title: CGH: FN0190069.01.M3_v_M92-220

source_name: DNA from soybean line FN0190069.01.M3


title: CGH: FN0163764.04.01.M4_v_M92-220

source_name: DNA from soybean line FN0163764.04.01.M4


title: CGH: FN0190009.01.M3_v_M92-220

source_name: DNA from soybean line FN0190009.01.M3


title: CGH: FN0190008.02.M3_v_M92-220

source_name: DNA from soybean line FN0190008.02.M3


title: CGH: FN0163764.04.03.M4_v_M92-220

source_name: DNA from soybean line FN0163764.04.03.M4


title: shEbf1 Hairpin 2_repeat1

first: Evan

last: Rosen

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

description: shEbf1 Hairpin 2

hyb_protocol: As manufacturer's instruction

scan_protocol: As manufacturer's instruction

data_processing: RMA procedure in BioConductor package for summarization and normalization

source_name: shEbf1 Hairpin 2

label_protocol: labeling with Encore Biotin Module.

extract_protocol: amplification with the NuGEN Ovation WTA Pico kit

treatment_protocol: Mature 3T3-L1 cells were subjected to 3-4 serial infections with virus, and selected with 5 μg/ml puromycin for at least 8 days prior to harvest.

tag: cell type

tag: lentivirus

value: shEbf1 Hairpin 2


title: CGH: FN0153903.26.M3_v_M92-220

source_name: DNA from soybean line FN0153903.26.M3


title: shEbf1 Hairpin 1_repeat3

description: shEbf1 Hairpin 1

source_name: shEbf1 Hairpin 1

value: shEbf1 Hairpin 1


title: CGH: FN0190006.01.M3_v_M92-220

source_name: DNA from soybean line FN0190006.01.M3


title: CGH: FN0163764.04.26.M4_v_M92-220

source_name: DNA from soybean line FN0163764.04.26.M4

source_name: DNA from soybean line M92-220


title: CGH: FN0163764.04.02.M4_v_M92-220

source_name: DNA from soybean line FN0163764.04.02.M4


title: shEbf1 Hairpin 2_repeat3

description: shEbf1 Hairpin 2


title: shEbf1 Hairpin 1_repeat2

description: shEbf1 Hairpin 1


title: Normal PBMC_sample 5

first: Kam

last: Hui

address: 11 Hospital Drive

institute: National Cancer Centre Singapore

description:
Gene expression data from PBMC sample of  healthy volunteer
NOR-PBMC-05

hyb_protocol: The final cRNA obtained was hybridized to the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, USA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data was analyzed using Partek Genomics Suite version 6.6. CEL files were imported into Partek with GCRMA background correction, quantile normalization and log2 transformation.

source_name: PBMC sample from healthy volunteer

label_protocol: Five micrograms of total RNA were reverse-transcribed and labeled with biotin.

growth_protocol: Patients with hepatocellular carcinoma were recruited at diagnosis and patients with chronic hepatitis B were recruited according to the protocol approved by the Institutional Review Board.  Informed consent was obtained from all subjects before blood samples were collected.  A total of 10 ml of blood was collected into BD Vacutainer® Plus K2EDTA tubes (Becton-Dickinson, USA).

extract_protocol: Total RNA was extracted from PBMC and WBC using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.

treatment_protocol: Within 6 hours of collection, blood was processed by density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare, Sweden).  Residual red blood cells were lysed and washed with phosphate buffered saline (PBS).  The isolated peripheral blood mononuclear cells (PBMC) were stored at -80 oC.

tag: disease state

value: healthy control

value: Peripheral blood mononuclear cells


title: shEbf1 Hairpin 2_repeat2

description: shEbf1 Hairpin 2


title: shEbf1 Hairpin 1_repeat1

description: shEbf1 Hairpin 1


title: CGH: FN0153903.04.M3_v_M92-220

source_name: DNA from soybean line FN0153903.04.M3


title: Scrambled_repeat3

description: Scrambled

source_name: Scrambled

value: scrambled control


title: CGH: FN0153903.02.M3_v_M92-220

source_name: DNA from soybean line FN0153903.02.M3


title: CGH: FN0190065.01.M3_v_M92-220

source_name: DNA from soybean line FN0190065.01.M3


title: Normal PBMC_sample 3

description:
Gene expression data from PBMC sample of  healthy volunteer
NOR-PBMC-03


title: Normal PBMC_sample 4

description:
Gene expression data from PBMC sample of  healthy volunteer
NOR-PBMC-04


title: CGH: FN0153903.01.M3_v_M92-220

source_name: DNA from soybean line FN0153903.01.M3


title: Normal PBMC_sample 1

description:
Gene expression data from PBMC sample of  healthy volunteer
NOR-PBMC-01


title: Scrambled_repeat2

description: Scrambled


title: Normal PBMC_sample 2

description:
Gene expression data from PBMC sample of  healthy volunteer
NOR-PBMC-02


title: CHB PBMC_sample 12

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-12

source_name: PBMC sample from Chronic hepatitis B carriers

value: Chronic hepatitis B


title: Olig2 wt (+/+) rep5

city: Paris

first: Adrien

last: Clavairoly

address: 47 Boulevard de l'Hôpital

institute: ICM

description: Gene expression data from E13.5 embryos olig2wt(+/+)

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

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

data_processing: Raw image files were processed using Affymetrix GCOS and the Microarray Suite (MAS) 5.0 algorithm. The probe   signal levels were quantile-normalized, summarized and then transformed to the log 2 expression using   GCRMA (gcrma R-package, Irizarry et al., 2003)

source_name: E13.5 mouse ventral telencephalon

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

extract_protocol: RNA samples were prepared by pooling RNAs extracted from 3 brains to constitute one replicate and each   sample type was prepared in five replicates. cRNA hybridization probes were hybridized to Affymetrix   Mouse Whole Genome MOE430 2.0 arrays.

value: ventral telencephalon

tag: genotype/variation


title: CGH: FN0163955.03.01.M4_v_M92-220

source_name: DNA from soybean line FN0163955.03.01.M4


title: CGH: FN0152921.08.02.M4_v_M92-220

source_name: DNA from soybean line FN0152921.08.02.M4


title: CHB PBMC_sample 11

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-11


title: Scrambled_repeat1

city: Boston

description: Scrambled


title: CHB PBMC_sample 10

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-10


title: Olig2 ko (-/-) rep5

description: Gene expression data from E13.5 embryos olig2ko(-/-)


title: Olig2 ko (-/-) rep4


title: CGH: FN0153165.01.03.M4_v_M92-220

source_name: DNA from soybean line FN0153165.01.03.M4


title: Olig2 wt (+/+) rep1


title: CGH: FN0152809.04.01.M4_v_M92-220

source_name: DNA from soybean line FN0152809.04.01.M4


title: Olig2 wt (+/+) rep4


title: CGH: FN0151669.02.01.M4_v_M92-220

source_name: DNA from soybean line FN0151669.02.01.M4


title: CGH: FN0151601.04.M3_v_M92-220

source_name: DNA from soybean line FN0151601.04.M3


title: CGH: FN0151601.26.M3_v_M92-220

source_name: DNA from soybean line FN0151601.26.M3


title: CHB PBMC_sample 9

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-09


title: CGH: FN0151601.23.M3_v_M92-220

source_name: DNA from soybean line FN0151601.23.M3

source_name: DNA from soybean line M92-220


title: CHB PBMC_sample 8

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-08


title: Olig2 ko (-/-) rep2


title: CHB PBMC_sample 7

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-07


title: CHB PBMC_sample 6

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-06


title: CHB PBMC_sample 5

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-05


title: CGH: FN0153903.03.M3_v_M92-220

source_name: DNA from soybean line FN0153903.03.M3


title: CGH: FN0151549.03.04.x1.M5_v_M92-220

source_name: DNA from soybean line FN0151549.03.04.x1.M5


title: Seedling_X4102 Replicate 2

city: Beaucouzé

first: Jean-Marc

last: Celton

address: 42 rue Georges Morel

institute: INRA-IRHS

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Malus domestica

source_name: Open pollinated X4102 seedling

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: orchard conditions

extract_protocol: Macherey-Nagel NucleoSpin RNA Plant

tag: tissus

value: Whole seedling

tag: genetic background

value: Open pollinated X4102

value: Wild-type

tag: phenotype

tag: age

value: 10 days old

tag: growth protocol

value: orchard conditions


title: CGH: FN0151601.03.M3_v_M92-220

source_name: DNA from soybean line FN0151601.03.M3

value: single plant leaf


title: Seed_X3069xX922 Replicate 1

source_name: Seed derived from cross between X3069 and X922

value: whole seed

value: derived from cross X3069 x X922

value: dormant seed


title: CHB PBMC_sample 4

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-04


title: CGH: FN0151601.02.M3_v_M92-220

source_name: DNA from soybean line FN0151601.02.M3


title: Seed_X3069xX922 Replicate 2


title: CHB PBMC_sample 3

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-03

source_name: PBMC sample from Chronic hepatitis B carriers


title: CGH: FN0151549.03.04.01.M5_v_M92-220

source_name: DNA from soybean line FN0151549.03.04.01.M5


title: CGH: FN0143867.02.03.M4_v_M92-220

source_name: DNA from soybean line FN0143867.02.03.M4


title: CHB PBMC_sample 2

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-02


title: CHB PBMC_sample 1

description:
Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-01


title: 45.gpr

first: Alan

last: Branco

address: 665 Huntington Ave.

department: Environmental Health

institute: Harvard School of Public Health

description: Biological replicate

hyb_protocol: 3DNA procedure

scan_protocol: Scanned on an Axon 400B scanner. Images were quantified using Genepix.

data_processing: LOESS normalized, VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Drosophila melanogaster

source_name: Total RNA from D melanogaster exposed to BPA + high sugar

label_protocol: 3DNA procedure

extract_protocol: TriZol procedure

tag: Sex

value: male (XY)

value: 2 days old, unmated


title: Seedling_X4102 Replicate 1


title: 44.gpr

description: Biological replicate

source_name: Total RNA from D melanogaster exposed to BPA


title: Seed_X4442xX2596 Replicate 2

source_name: Seed derived from cross between X4442 and X2596

value: derived from cross X4442 x X2596


title: CGH: FN0151549.03.04.M4_v_M92-220

source_name: DNA from soybean line FN0151549.03.04.M4


title: 43.gpr

description: Biological replicate

source_name: Total RNA from D melanogaster exposed to high sugar


title: Seed_X4442xX2596 Replicate 1


title: CGH: FN0141766.02.02.M4_v_M92-220

source_name: DNA from soybean line FN0141766.02.02.M4


title: Seedling_GD Replicate 2

source_name: Open pollinated 'Golden Delicious' seedling

growth_protocol: in vitro

value: Open pollinated 'Golden Delicious'

value: in vitro


title: HCC PBMC_sample 10

description:
Gene expression data from PBMC sample of  hepatocellular carcinoma patient
HCC-PBMC-10

source_name: PBMC sample from hepatocellular carcinoma patient

value: hepatocellular carcinoma

value: Peripheral blood mononuclear cells


title: 41.gpr

description: Biological replicate


title: 42.gpr

description: Biological replicate


title: HCC PBMC_sample 9

description:
Gene expression data from PBMC sample of  hepatocellular carcinoma patient
HCC-PBMC-09


title: Seedling_GD Replicate 1


title: CGH: FN0140972.01.03.M4_v_M92-220

source_name: DNA from soybean line FN0140972.01.03.M4

source_name: DNA from soybean line M92-220


title: HCC PBMC_sample 8

description:
Gene expression data from PBMC sample of  hepatocellular carcinoma patient
HCC-PBMC-08


title: 40.gpr

description: Biological replicate


title: CGH: FN0140856.05.02.04.M5_v_M92-220

source_name: DNA from soybean line FN0140856.05.02.04.M5


title: CGH: FN0141075.03.05.M4_v_M92-220

source_name: DNA from soybean line FN0141075.03.05.M4


title: HCC PBMC_sample 7

description:
Gene expression data from PBMC sample of  hepatocellular carcinoma patient
HCC-PBMC-07


title: Stem_GD Replicate 2

source_name: Wild type 'Golden Delicious' stem

value: stem

value: “Golden Delicious”

value: fully developed


title: Stem_GD Replicate 1

value: Wild-type


title: HCC PBMC_sample 5

description:
Gene expression data from PBMC sample of  hepatocellular carcinoma patient
HCC-PBMC-05


title: 39.gpr

description: Biological replicate


title: CGH: FN0140856.05.01.06.03.M6_v_M92-220

source_name: DNA from soybean line FN0140856.05.01.06.03.M6


title: HCC PBMC_sample 6

description:
Gene expression data from PBMC sample of  hepatocellular carcinoma patient
HCC-PBMC-06


title: CGH: FN0140313.02.03.M4_v_M92-220

source_name: DNA from soybean line FN0140313.02.03.M4


title: HCC PBMC_sample 4

description:
Gene expression data from PBMC sample of  hepatocellular carcinoma patient
HCC-PBMC-04


title: Root_X8877 Replicate 1

source_name: Wild type X8877 root

value: in vitro root

value: Hybrid X8877

value: growing root tip


title: Root_X8877 Replicate 2


title: CGH: FN0151601.01.M3_v_M92-220

source_name: DNA from soybean line FN0151601.01.M3

value: single plant leaf


title: CGH: FN0134069.03.01.01.02.M6_v_M92-220

source_name: DNA from soybean line FN0134069.03.01.01.02.M6


title: HCC PBMC_sample 3

description:
Gene expression data from PBMC sample of  hepatocellular carcinoma patient
HCC-PBMC-03


title: Stem_X8877 Replicate 2

source_name: Wild type X8877 stem

value: orchard conditions


title: Stem_X8877 Replicate 1


title: 35.gpr

description: Biological replicate

source_name: Total RNA from D melanogaster exposed to BPA

source_name: Total RNA from D melanogaster control


title: CGH: FN0143022.01.03.01.M5_v_M92-220

source_name: DNA from soybean line FN0143022.01.03.01.M5


title: HCC PBMC_sample 2

description:
Gene expression data from PBMC sample of  hepatocellular carcinoma patient
HCC-PBMC-02


title: CGH: FN0133361.03.01.M4_v_M92-220

source_name: DNA from soybean line FN0133361.03.01.M4


title: 34.gpr

description: Biological replicate

source_name: Total RNA from D melanogaster exposed to BPA + high sugar


title: 38.gpr

description: Biological replicate

source_name: Total RNA from D melanogaster exposed to high sugar


title: Root_GD Replicate 2

source_name: Wild type 'Golden Delicious' root


title: CGH: FN0190004.01.M3_v_M92-220

source_name: DNA from soybean line FN0190004.01.M3

source_name: DNA from soybean line M92-220


title: Root_GD Replicate 1


title: 27.gpr

description: Biological replicate


title: CGH: FN0140219.01.02.M4_v_M92-220

source_name: DNA from soybean line FN0140219.01.02.M4


title: 36.gpr

description: Biological replicate


title: CD56+ NK-cells from peripheral blood (ND53)

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

institute: Charité

description: Gene expression data of purified CD56+ NK-cells from peripheral blood of a healthy donor

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.

data_processing: MAS 5.0 signals, detection calls and p-values; TGT 150; MAS 5.0 pairwise comparisons, SLR, change calls, p-values; BioRetis platform group comparisons (PMID: 19265543)

label_protocol: Double-stranded complementary DNA was synthesized from 3–5 µg total RNA using reagents recommended in the technical manual GeneChip Expression Analysis (Affymetrix, Santa Clara, CA). The in vitro transcription necessary for the synthesis of biotinylated complementary RNA (cRNA) was performed using the Enzo RNA Transcript Labeling kit (Affymetrix).

growth_protocol: cells were isolated immediately after drawing blood

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen). Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen). The amount and integrity of RNA isolated were assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: Peripheral blood (50 ml) was collected in Vacutainer tubes containing heparin (Becton Dickinson) and processed within 120 minutes. Briefly, blood was fractionated simultaneously in 4 major leukocyte populations (monocytes, CD4  and CD8 lymphocytes, and natural killer cells) by a combination of erythrocyte lysis, magnetic-activated cell sorting (MACS; Miltenyi Biotec, Bergisch Gladbach, Germany), and high-speed fluorescence-activated cell sorting (FACS). This procedure was optimized in order to obtain cell populations with purities and viabilities of  95%. Temperature- and Ficoll-induced transcriptional alterations were reduced as much as possible by maintaining a temperature of 4°C and by avoiding any density gradient medium for the preenrichment of PBMCs (40).  Erythrocytes were lysed at 4°C with EL buffer, according to the recommendations of the manufacturer (Qiagen). After lysis was completed, leukocytes were washed twice with 50 ml phosphate buffered saline (PBS)–bovine serum albumin containing 5 mM EDTA. Leukocytes were quantified with a CASY cell counter (Schärfe System, Reutlingen, Germany) and incubated with an appropriate amount of CD15-conjugated microbeads (MACS; Miltenyi Biotec). Separation was performed using an automated separation system (autoMACS; Miltenyi Biotec) using the separation program “possel_s.” The fraction of CD15-negative cells was counted and prepared for 4-channel high-speed FACS (FACSVantage SE equipped with a FACSDiVa option; Becton Dickinson). Cells were stained for 15 minutes at 10°C with an antibody cocktail containing CD3-APC (Becton Dickinson), CD56-PE (Miltenyi Biotec), CD14-FITC (Becton Dickinson), CD4–PE-Cy5 (Caltag, Hamburg, Germany) and CD8–PE-Cy7 (Caltag) mAb. After washing, cells were filtered using 30-µm nylon mesh filters (Miltenyi Biotec), and 4',6-diamidino-2-phenylindole was added to identify dead cells during FACS analysis. Stained cells were sorted under continuous cooling at a sorting rate of 25,000 events/second and an operating system pressure of 35 psi. After sorting, cell populations showed purities of  97% and cell viabilities of  99%. Sorted cells were immediately lysed in buffer RLT containing 1% beta-mercaptoethanol, and lysates were stored at  80°C until RNA isolation.

value: sorted CD56+ NK-cell population


title: HCC PBMC_sample 1

description:
Gene expression data from PBMC sample of  hepatocellular carcinoma patient
HCC-PBMC-01

source_name: PBMC sample from hepatocellular carcinoma patient


title: CD56+ NK-cells from peripheral blood (ND52)

source_name: purified CD56+ NK-cells from peripheral blood of a healthy donor


title: 26.gpr

description: Biological replicate

value: male (XY)


title: CGH: FN0132370.07.02.M4_v_M92-220

source_name: DNA from soybean line FN0132370.07.02.M4


title: Fruit_M74_harvest Replicate 2

source_name: Wild type M74 fruit

extract_protocol: derived from the pine tree RNA isolation method (Chang et al., 1993)

value: Fruit flesh at harvest

value: Hybrid M74

value: harvested at maturity


title: Fruit_M74_harvest Replicate 1


title: 37.gpr

description: Biological replicate

value: 2 days old, unmated


title: CD56+ NK-cells from peripheral blood (ND51)


title: CGH: FN0132338.01.01.M4_v_M92-220

source_name: DNA from soybean line FN0132338.01.01.M4


title: 24.gpr

description: Biological replicate


title: CD19+ B-cells from peripheral blood (ND53)

description: Gene expression data of purified CD19+ B-cells from peripheral blood of a healthy donor

value: sorted CD19+ B-cell population


title: leaf_M49 Replicate 1

source_name: Wild type M49 leaf

value: whole leaf

value: Hybrid M49


title: CGH: FN0140162.01.x1.M4_v_M92-220

source_name: DNA from soybean line FN0140162.01.x1.M4


title: Fruit_M20_harvest Replicate 2

source_name: Wild type M20 fruit

value: Hybrid M20


title: 69.gpr

description: Biological replicate

source_name: Total RNA from D. melanogaster exposed to BPA for 48 hours.

source_name: Total RNA from D. melanogaster exposed to DEHP for 48 hours.


title: 25.gpr

description: Biological replicate

source_name: Total RNA from D melanogaster exposed to BPA

source_name: Total RNA from D melanogaster control


title: CD19+ B-cells from peripheral blood (ND52)

source_name: purified CD19+ B-cells from peripheral blood of a healthy donor


title: CD19+ B-cells from peripheral blood (ND51)


title: CGH: FN0124748.01.01.M4_v_M92-220

source_name: DNA from soybean line FN0124748.01.01.M4


title: Fruit_M20_harvest Replicate 1


title: CGH: FN0130342.12.02.M4_v_M92-220

source_name: DNA from soybean line FN0130342.12.02.M4


title: CGH: FN0124702.03.03.M4_v_M92-220

source_name: DNA from soybean line FN0124702.03.03.M4

source_name: DNA from soybean line M92-220


title: CGH: FN0124367.02.02.M4_v_M92-220

source_name: DNA from soybean line FN0124367.02.02.M4


title: CGH: FN0124543.02.01.02.M5_v_M92-220

source_name: DNA from soybean line FN0124543.02.01.02.M5


title: Leaf_M14 Replicate 2

source_name: Wild type M14 leaf

value: Hybrid M14

value: fully developed


title: 68.gpr

description: Biological replicate

source_name: Total RNA from D. melanogaster exposed to high sugar for 48 hours.


title: 67.gpr

description: Biological replicate

source_name: Total RNA from D. melanogaster exposed to BPA+DEHP+high sugar for 48 hours.


title: CD15+ neutrophils from peripheral blood (ND53)

description: Gene expression data of purified CD15+ neutrophils from peripheral blood of a healthy donor

value: sorted CD15+ neutrophil population


title: CGH: FN0132790.05.03.M4_v_M92-220

source_name: DNA from soybean line FN0132790.05.03.M4


title: 70.gpr

description: Biological replicate

source_name: Total RNA from D. melanogaster control.


title: CD15+ neutrophils from peripheral blood (ND52)

source_name: purified CD15+ neutrophils from peripheral blood of a healthy donor


title: 65.gpr

description: Biological replicate

source_name: Total RNA from D. melanogaster exposed to BPA for 48 hours.


title: Fruit_M20_100daa Replicate 2

source_name: Wild type M20 fruit

value: Fruit flesh 100 days post anthesis

value: Wild-type

value: 100 days after anthesis


title: 66.gpr

description: Biological replicate


title: leaf_M49 Replicate 2

source_name: Wild type M49 leaf

value: orchard conditions


title: CGH: FN0123951.01.01.M4_v_M92-220

source_name: DNA from soybean line FN0123951.01.01.M4

value: single plant leaf


title: CGH: FN0131139.02.03.M4_v_M92-220

source_name: DNA from soybean line FN0131139.02.03.M4


title: CGH: FN0123694.10.M3_v_M92-220

source_name: DNA from soybean line FN0123694.10.M3


title: CGH: FN0131633.06.01.M4_v_M92-220

source_name: DNA from soybean line FN0131633.06.01.M4


title: CD15+ neutrophils from peripheral blood (ND51)


title: Fruit_M20_100daa Replicate 1


title: CGH: FN0123694.01.M3_v_M92-220

source_name: DNA from soybean line FN0123694.01.M3


title: Flower_M74 Replicate 1

source_name: Wild type M74 Whole flower

value: whole flower


title: 63.gpr

description: Biological replicate

value: male (XY)


title: 62.gpr

description: Biological replicate

source_name: Total RNA from D. melanogaster exposed to DEHP for 48 hours.


title: 64.gpr

description: Biological replicate


title: CD14+ monocytes from peripheral blood (ND53)

description: Gene expression data of purified CD14+ monocytes from peripheral blood of a healthy donor

value: sorted CD14+ monocytes population


title: Flower_M74 Replicate 2

value: Hybrid M74


title: CD8+ T-cells from peripheral blood (ND53)

description: Gene expression data of purified CD8+ T-cells from peripheral blood of a healthy donor

value: sorted CD3+ and CD8+ T-cell population


title: CD14+ monocytes from peripheral blood (ND51)

source_name: purified CD14+ monocytes from peripheral blood of a healthy donor


title: CGH: FN0123016.02.M3_v_M92-220

source_name: DNA from soybean line FN0123016.02.M3

source_name: DNA from soybean line M92-220


title: Fruit_M74_100daa Replicate 2

source_name: Wild type M74 fruit


title: CGH: FN0123016.07.M3_v_M92-220

source_name: DNA from soybean line FN0123016.07.M3


title: Mesothelial_cell line2

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

description: Cell line

hyb_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1_v5_95_Feb07 and Grid: 014879_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: Normal peritoneal mesothelial cells, Fischer 344

growth_protocol: Cells were grown in an RPMI-1640 medium (Sigma-Aldrich) containing 10% fetal bovine serum at 37°C under a 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted using RNeasy Mini(QIAGEN).

value: normal peritoneal mesothelial cells


title: 61.gpr

description: Biological replicate

value: 2 days old, unmated

source_name: Total RNA from D. melanogaster control.


title: Leaf_M14 Replicate 1

source_name: Wild type M14 leaf

value: whole leaf


title: CD14+ monocytes from peripheral blood (ND52)


title: Fruit_M74_100daa Replicate 1


title: Mesothelial_cell line1

description: Cell line

scan_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008).


title: CD8+ T-cells from peripheral blood (ND51)

source_name: purified CD8+ T-cells from peripheral blood of a healthy donor


title: CGH: FN0122914.12.01.02.M5_v_M92-220

source_name: DNA from soybean line FN0122914.12.01.02.M5


title: CGH: FN0121155.04.02.M4_v_M92-220

source_name: DNA from soybean line FN0121155.04.02.M4


title: Flower_M67 Replicate 2

source_name: Wild type M67 Whole flower

value: Hybrid M67


title: Flower_M67 Replicate 1


title: CD4+ T-cells from peripheral blood (ND53)

description: Gene expression data of purified CD4+ T-cells from peripheral blood of a healthy donor

value: sorted CD3+ and CD4+ T-cell population


title: Mesothelial_tissue2

description: Tissue

source_name: Normal peritoneal mesothelial cells, Brown Norway

label_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008).


title: Mesothelial_tissue1

description: Tissue


title: Malignant Mesothelioma_Cro8_EM

description: Tissue

source_name: Malignant Mesothelioma, Fischer 344 / Brown Norway F1 hybrid

value: malignant mesothelioma


title: CD8+ T-cells from peripheral blood (ND52)


title: CD4+ T-cells from peripheral blood (ND51)

source_name: purified CD4+ T-cells from peripheral blood of a healthy donor


title: Gb7 glioma stem cells infected with YFP lentivirus

city: MOntpellier

first: jean-philippe

last: hugnot

state: languedoc

address: IGF INSERM UM 141 rue de la cardonille

institute: inserm inm u1191

description: Gb7 control

hyb_protocol: Targets were prepared with 5.5µg of labelled DNA, and hybrized onto Affymetrix Human Gene ST 1.1 array plates using Affymetrix GeneTitan systems. The GeneTitan performed automatically hybridization, washes, stainings, and scanning of arrays.

scan_protocol: The arrays were scanned according to Affymetrix recommendations and GeneTitan robotic procedures.

data_processing: Raw data were controlled using Affymetrix software such as AGCC and Expression Console (www.affymetrix.com). Primary analysis was performed with an external MAQC A sample to validate robustness of data, regarding Affymetrix recommendations and following Institut Curie's genomic platform (Paris, France). Probeset mean, RLE means, AUC were in agreement with Affymetrix recommendations.

source_name: Gb7 glioma cancer stem cells, YFP lentivirus

label_protocol: 100ng of total RNA was amplified according to the Affymetrix GeneChip® Whole Transcript (WT) Expression assay using the Ambion® WT Expression Kit and Affymetrix labelling kit, which generate sense and labeled DNA.

growth_protocol: Glioma cancer stem cells isolated from glioblastoma were grown as neurospheres in defined medium.

extract_protocol: Total RNA were extracted with Qiagen RNeasy kits. Quality checks (RIN>8.7) were performed on an Agilent Bioanalyzer.

treatment_protocol: Cells were infected with lentiviruses expressing YFP or YFP-IRES-NICD (activated form of Notch receptor). After 48h, RNA were extracted.

value: Gb7 glioma cancer stem cells

value: YFP


title: Malignant Mesothelioma_Cro5_SM

description: Tissue


title: Gb7 glioma stem cells infected with YFP-NICD lentivirus

description: Gb7 NICD

source_name: Gb7 glioma cancer stem cells, YFP-NICD lentivirus

value: YFP-NICD


title: CGH: FN0122569.03.03.M4_v_M92-220

source_name: DNA from soybean line FN0122569.03.03.M4


title: Gb4 glioma stem cells infected with YFP-NICD lentivirus

description: Gb4 NICD

source_name: Gb4 glioma cancer stem cells, YFP-NICD lentivirus

value: Gb4 glioma cancer stem cells


title: Malignant Mesothelioma_Cro4_SM

description: Tissue


title: Malignant Mesothelioma_Cro6_EM

description: Tissue


title: Malignant Mesothelioma_Cro7_SM

description: Tissue


title: U87 cell line infected with YFP-NICD lentivirus

description: U87 NICD

source_name: U87 high-grade glioma cell line, YFP-NICD lentivirus

growth_protocol: U87 high-grade glioma cell line (from ATCC) was grown in 10% serum.

value: glioma cell line


title: CGH: FN0120712.10.01.M4_v_M92-220

source_name: DNA from soybean line FN0120712.10.01.M4

value: single plant leaf

source_name: DNA from soybean line M92-220


title: CGH: FN0121131.10.04.M4_v_M92-220

source_name: DNA from soybean line FN0121131.10.04.M4


title: Malignant Mesothelioma_Cro2_EM

description: Tissue


title: CD4+ T-cells from peripheral blood (ND52)


title: Malignant Mesothelioma_Cro1_EM

description: Tissue


title: Human neural stem cell infected with YFP-NICD lentivirus

description: HNP NICD

source_name: Embryonic human neural stem cells, YFP-NICD lentivirus

growth_protocol: Embryonic human neural stem cells obtained from Lonza company were grown as neurospheres in defined media.

value: embryonic human neural stem cells


title: Malignant Mesothelioma_Cro3_SM

description: Tissue


title: U87 cell line infected with YFP lentivirus

description: U87 control

source_name: U87 high-grade glioma cell line, YFP lentivirus


title: Human neural stem cell infected with YFP lentivirus

description: HNP control

source_name: Embryonic human neural stem cells, YFP lentivirus


title: CGH: FN0120687.03.02.M4_v_M92-220

source_name: DNA from soybean line FN0120687.03.02.M4


title: CGH: FN0175255.01.04.10.M5_v_M92-220

source_name: DNA from soybean line FN0175255.01.04.10.M5


title: Malignant Mesothelioma_Chr8_SM

description: Tissue


title: CGH: FN0120247.02.01.M4_v_M92-220

source_name: DNA from soybean line FN0120247.02.01.M4


title: CGH: FN0121037.04.02.M4_v_M92-220

source_name: DNA from soybean line FN0121037.04.02.M4


title: N488T4

first: Richard

last: Lo-Man

address: 25-28 Rue du Docteur Roux

institute: Institut Pasteur

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1) was used to read out and process the microarray image files.

source_name: Cord blood_#488_CD4 Tcell_CCR4

label_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Culture for 24h in RPMI with 10%FCS

extract_protocol: Cell samples were lysed using SuperAmp Lysis Buffer following manufacturer’s instructions. SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol: Activaiton with antiCD3+antiCD28

tag: donor id

value: male

value: cord blood

value: CD4 T cells

tag: cell subset


title: CGH: FN0120105.03.01.M4_v_M92-220

source_name: DNA from soybean line FN0120105.03.01.M4

tag: tissue


title: Malignant Mesothelioma_Chr7_EM

description: Tissue

source_name: Malignant Mesothelioma, Fischer 344 / Brown Norway F1 hybrid


title: N488T5

source_name: Cord blood_#488_CD4 Tcell_CCR6

tag: gender


title: Gb4 glioma stem cells infected with YFP lentivirus

description: Gb4 control

source_name: Gb4 glioma cancer stem cells, YFP lentivirus


title: N488T3

source_name: Cord blood_#488_CD4 Tcell_CXCR3


title: CGH: FN0120166.06.03.M4_v_M92-220

source_name: DNA from soybean line FN0120166.06.03.M4

tag: genotype

tag: strain


title: CGH: FN0141075.03.04.10.M5_v_M92-220

source_name: DNA from soybean line FN0141075.03.04.10.M5


title: Malignant Mesothelioma_Chr5_SM

description: Tissue


title: N488T1

source_name: Cord blood_#488_CD4 Tcell_CCRNEg

value: CCRNEg


title: Malignant Mesothelioma_Chr6_BM

description: Tissue


title: N488T2

source_name: Cord blood_#488_CD4 Tcell_NAIVE

value: NAIVE


title: N487T5

source_name: Cord blood_#487_CD4 Tcell_CCR6


title: CGH: FN0151221.01.10.M4_v_M92-220

source_name: DNA from soybean line FN0151221.01.10.M4

source_name: DNA from soybean line M92-220


title: Malignant Mesothelioma_Chr4_SM

description: Tissue


title: Malignant Mesothelioma_Chr3_EM

description: Tissue


title: CGH: FN0141693.05.01.02.06.10.M7_v_M92-220


title: CGH: FN0141693.07.01.03.10.M6_v_M92-220

source_name: DNA from soybean line FN0141693.07.01.03.10.M6


title: N487T3

source_name: Cord blood_#487_CD4 Tcell_CXCR3


title: CGH: FN0172932.xx.xx.xx.xx.xx.06.M8_v_M92-220

source_name: DNA from soybean line FN0172932.xx.xx.xx.xx.xx.06.M8


title: CGH: FN0143022.01.03.06.10.M6_v_M92-220

source_name: DNA from soybean line FN0143022.01.03.06.10.M6


title: Malignant Mesothelioma_Chr2_BM

description: Tissue


title: N487T2

source_name: Cord blood_#487_CD4 Tcell_NAIVE


title: N487T1

source_name: Cord blood_#487_CD4 Tcell_CCRNEg


title: Malignant Mesothelioma_Chr1_EM

description: Tissue

source_name: Malignant Mesothelioma, Fischer 344 / Brown Norway F1 hybrid


title: Malignant Mesothelioma_Amo8_EM

description: Tissue


title: Malignant Mesothelioma_Amo7_SM

description: Tissue


title: CGH: FN0141075.03.02.10.M5_v_M92-220

source_name: DNA from soybean line FN0141075.03.02.10.M5


title: CGH: FN0173217.xx.xx.xx.xx.xx.02.M8_v_M92-220

source_name: DNA from soybean line FN0173217.xx.xx.xx.xx.xx.02.M8


title: CGH: FN0190008.02.xx.xx.10.M6_v_M92-220

source_name: DNA from soybean line FN0190008.02.xx.xx.10.M6


title: N487T4

source_name: Cord blood_#487_CD4 Tcell_CCR4


title: Malignant Mesothelioma_Amo4_SM

description: Tissue


title: Malignant Mesothelioma_Amo5_EM

description: Tissue


title: Malignant Mesothelioma_Amo6_SM

description: Tissue


title: N480T3

source_name: Cord blood_#480_CD4 Tcell_CXCR3


title: CGH: FN0173117.xx.xx.xx.xx.xx.06.M8_v_M92-220

source_name: DNA from soybean line FN0173117.xx.xx.xx.xx.xx.06.M8


title: CGH: FN0173217.xx.xx.xx.xx.xx.06.M8_v_M92-220

source_name: DNA from soybean line FN0173217.xx.xx.xx.xx.xx.06.M8


title: N480T2

source_name: Cord blood_#480_CD4 Tcell_NAIVE


title: N480T1

source_name: Cord blood_#480_CD4 Tcell_CCRNEg


title: Malignant Mesothelioma_Amo3_BM

description: Tissue


title: N480T4

source_name: Cord blood_#480_CD4 Tcell_CCR4


title: Malignant Mesothelioma_Amo1_SM

description: Tissue


title: N480T5

source_name: Cord blood_#480_CD4 Tcell_CCR6


title: Malignant Mesothelioma_Amo2_SM

description: Tissue


title: CGH: FN0173217.xx.xx.xx.xx.xx.01.M8_v_M92-220

source_name: DNA from soybean line FN0173217.xx.xx.xx.xx.xx.01.M8

source_name: DNA from soybean line M92-220


title: CGH: FN0172932.xx.xx.xx.xx.xx.02.M8_v_M92-220

source_name: DNA from soybean line FN0172932.xx.xx.xx.xx.xx.02.M8


title: CGH: FN0172932.xx.xx.xx.xx.xx.10.M8_v_M92-220

source_name: DNA from soybean line FN0172932.xx.xx.xx.xx.xx.10.M8


title: CGH: FN0170144.xx.xx.xx.xx.xx.01.M8_v_M92-220

source_name: DNA from soybean line FN0170144.xx.xx.xx.xx.xx.01.M8


title: CGH: FN0172932.xx.xx.xx.xx.xx.04.M8_v_M92-220

source_name: DNA from soybean line FN0172932.xx.xx.xx.xx.xx.04.M8


title: CGH: FN0173117.xx.xx.xx.xx.xx.02.M8_v_M92-220

source_name: DNA from soybean line FN0173117.xx.xx.xx.xx.xx.02.M8


title: CGH: FN0176028.xx.xx.xx.xx.xx.02.M8_v_M92-220

source_name: DNA from soybean line FN0176028.xx.xx.xx.xx.xx.02.M8


title: CGH: FN0176028.xx.xx.xx.xx.xx.09.M8_v_M92-220

source_name: DNA from soybean line FN0176028.xx.xx.xx.xx.xx.09.M8


title: CGH: FN0172932.xx.xx.xx.xx.xx.03.M8_v_M92-220

source_name: DNA from soybean line FN0172932.xx.xx.xx.xx.xx.03.M8


title: CGH: FN0173117.xx.xx.xx.xx.xx.04.M8_v_M92-220

source_name: DNA from soybean line FN0173117.xx.xx.xx.xx.xx.04.M8


title: SmoWT-MB_GDC-0449_2

city: Stanford

first: Yujie

last: Tang

address: 265 Campus Dr SIM1 G3055

department: Neurology

institute: Stanford University School of Medicine

description: Sample 6.AVG_Signal

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Rank-invariant normalized data was generated using GenomeStudio v1.9.0 and converted to .gct file format, which was then collapsed to gene symbols using the GSEA desktop application (http://www.broadinstitute.org/gsea/index.jsp).

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

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: SmoWT-MB

value: Ptch-deficient mouse medulloblastoma cell line

tag: treated with

value: SMOi GDC-0449 for 6hrs


title: CGH: FN0176028.xx.xx.xx.xx.xx.07.M8_v_M92-220

source_name: DNA from soybean line FN0176028.xx.xx.xx.xx.xx.07.M8


title: CGH: FN0170144.xx.xx.xx.xx.xx.10.M8_v_M92-220

source_name: DNA from soybean line FN0170144.xx.xx.xx.xx.xx.10.M8


title: SmoWT-MB_JQ1_2

description: Sample 5.AVG_Signal

tag: cell type

value: BETi JQ1 for 6hrs


title: CGH: FN0174958.xx.xx.xx.xx.xx.01.M8_v_M92-220

source_name: DNA from soybean line FN0174958.xx.xx.xx.xx.xx.01.M8