title: PHEO_AG_HS_059

description: paraganglioma

value: MAX


title: PHEO_AG_HS_058

status: Public on May 06 2013

type: genomic

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

description: paraganglioma

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing: Standard Illumina protocol. Beta values were exported from Illumina Beadstudio software.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: paraganglioma, benign

label_protocol: Standard Illumina protocol.

extract_protocol: DNA was extracted from frozen tissue samples using a QIAamp DNA mini kit or an AllPrep kit (Qiagen).

tag: tissue

value: paraganglioma

tag: Sex

value: female

tag: malignancy

value: benign


title: R5, T=3

type: RNA

city: london

first: siamak

last: salehi

address: denmark hill

department: liver studies

country: United Kingdom

institute: kings college hospital

description:
23N
RG patient 5
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

hyb_protocol: After labeling, 21.5 ug of RNA was hybridized for 16 hr at 48°C on GeneChip miRNA 1.0 Arrays . GeneChips were washed and stained in the Affymetrix GeneChip Fluidics 450 Station.

scan_protocol: Hybridized samples were scanned using the GeneChip scanner 3000 7G (Affymetrix).

data_processing:
miRNA QC Tool v1.0.33.0.
Algorithm: Default
Settings: Detection (Background detection), Background adjustment (BC-CG Adjustment), Normalization (Quantile), Other Process (Add small constant, CVS tab), Other Processes (Threshhold), Summarization (Median Polish).

label: biotin

molecule: total RNA

source_name: Native liver biopsy, RG

label_protocol: Total RNA containing miRNA was enriched using microcon YM-100 centrifugal filter devices (Millipore Cat no: 42413) according to the manufacturer's protocol. 100 ng of miRNA-enriched RNA was labeled using the Flashtag biotin RNA labeling kit (Genisphere) according to the protocol by Genisphere for labeling RNA for Affymetrix GeneChip arrays.

extract_protocol: The High Pure FFPE RNA Micro Kit (Roche Applied Sciences) was used to extract total RNA from FFPE liver sections or slides according to the manufacturer's instructions.

value: liver

tag: patient identifier

tag: treatment

value: auxiliary liver transplant (ALT)

tag: regeneration status

value: successful

tag: time point


title: PHEO_AG_HS_057

description: paraganglioma

value: male


title: Hypoxia RV Animal 20 Replicate 3

city: Richmond

first: Jennifer

middle: I.

last: Drake

state: Virginia

address: 1220 E. Broad Street, Room 6-003

department: Pulmonary and Critical Care Medicine

country: USA

institute: Virginia Commonwealth University

description: Biological replicate 2 of 6. Technical replicate 3 of 4.

hyb_protocol: 825 ng of each sample were combined and hybridized on Agilent Whole Rat Genome 4x44k microarray slide for 17 hours at 65°C.  Slides were washed sequentially in Agilent Wash Buffer 1 and Water Buffer 2.

scan_protocol: Scanned on Axon GenePix 4100A scanner Images were quantified using GenePix Pro 5.0

data_processing: LOWESS normalized data obtained from log2 of processed Red signal/processed Green signal using marray packed in R.

organism: Rattus norvegicus

source_name: 20 RV RNA

label_protocol: 500 ng of total RNA was amplified and labeled with Cy5 and 500 ng of Stratagene Universal Rat Reference RNA was amplified and labeled with Cy3 using Agilent QuickAmp labeling kit following manufacturer's instructions

growth_protocol: Rats were allowed free access to water and food throughout the study.

extract_protocol: Total RNA was extracted using Qiagen Rneasy following manufacturer's instructions

treatment_protocol:
Hypoxia: 10% O2 for 4 weeks
SuHx: 20mg/kg SU5416, 10% O2 for 4 weeks
SuHx + Carvedilol: 20mg/kg SU5416, 10% O2 for 4 weeks, then 15 mg/kg carvedilol daily for 4 weeks at room air

tag: strain

value: Sprague Dawley

value: Hypoxia 10% O2 for 4 weeks

value: right ventricle

tag: gender

source_name: Stratagene Universal Rat Reference RNA

tag: sample type

value: Pooled from 14 rat cell lines

tag: manufacturer

value: Stratagene


title: Feature Expression in Red tissue at 30 dpb, replicate 2

city: Norwich

first: Andreas

last: Magusin

address: Norwich Research Park

department: Crop Genetics

institute: John Innes Centre

description: 141.05.796 Br2 (02.12.09)

hyb_protocol: Telechem Hybridization Chambers (Corning) were employed for the manual hybridisation of labelled samples

scan_protocol: Scanned on an Agilent GenePix 4000B scanner; at 532 nm and 635 nm; with a resolution of 10 μm and 100% power.

data_processing:
Images were quantified using GenePix Pro 4.1 image analysis software (Axon Instruments/Molecular Devices). Valid spots were defined as having intensity values ≥2-fold the mean background intensity in ≥1 channel.
Normalisation and calculation of differential expression were performed in R (http://cran.r-project.org) using Bioconductor libraries (http://www.bioconductor.org). Within-array normalisation was performed with the aim of making the background-subtracted log-ratios average to zero within each microarray. This was achieved by fitting a LOESS curve to each print tip (with the parameters smoothing filter = 0.4, iterations = 3; and δ = 0.01). The resulting data were then subject to a between-array normalisation step where the average intensity values for each array were transformed such that they followed the same empirical distribution; while leaving the log-ratios unaffected.
Differential expression was calculated by fitting a linear model for each gene across the microarrays[6] (where the contrasts were parameterised as differential gene expression between purple and red sectors, at 8, 30 and 45 days post-breaker respectively); the estimated coefficients were, in turn, computed from the fit; followed by computation of moderated t-scores and log-odds by empirical Bayes shrinkage of the standard errors towards a common constant. Genes exhibiting a fold-change of ≥3 and Benjamini Hochberg-adjusted p-values ≤ 0.05 were selected for further scrutiny.

organism: Solanum lycopersicum

source_name: Stage B_red tissue

label_protocol: RNA amplification and aminoallyl labeling were performed by using the Message Amp™ aRNA kit (Ambion # AM1750)

growth_protocol: The Del/Ros1 N MicroTom was crossed with MoneyMaker tomato to generate globe sized purple tomatoes. After the initial cross, the hybrid line went through self-pollination to the F8 generation (F8DR). Fruits from the F8DR line were used for VIGS (Virus-induced gene silencing) treatment.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: pTRV2-Del/Ros1 was made previously (Plant Physiology vol. 150 no. 3 1122-1134). Fruit were infiltrated at mature green stage. RNA samples were isolated from purple and red sectors at 8, 30 and 45 days after breaker (8 dpb, 30 dpb and 45 dpb)

tag: genetic background

value: Del/Ros1 fruit in the MoneyMaker background

tag: line

tag: fruit stage

value: Stage B

tag: tissue/sector

value: red

value: 30 day after breaker

source_name: common reference

value: pooled total RNA


title: R6, T=2

description:
8N
RG patient 6
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.


title: Feature Expression in purple tissue at 8 dpb, replicate 2

description: 141.05.788 Dp2(08.12.09)

source_name: Stage D_purple tissue

value: Stage D

value: purple

value: 8 day after breaker


title: R7, T=2

description:
10N
RG patient 7
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

value: liver


title: Feature Expression in Red tissue at 8 dpb, replicate 2

description: 141.05.786 Dr2(08.12.09)

source_name: Stage D_red tissue


title: Feature Expression in purple tissue at 8 dpb, replicate 3

description: 141.05.785 Dp3 (08.12.09)


title: R3, T=3

description:
8
RG patient 3
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

value: auxiliary liver transplant (ALT)


title: Feature Expression in purple tissue at 45 dpb, replicate 3

description: 140.89.528 Cp3 (10.12.09)

source_name: Stage C_purple tissue

value: Stage C

value: 45 day after breaker


title: R4, T=2

description:
4
RG pateint 4
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

value: successful


title: Feature Expression in purple tissue at 45 dpb, replicate 2

description: 140.89.526 Cp2 (10.12.09)


title: Hypoxia RV Animal 20 Replicate 1

description: Biological replicate 2 of 6. Technical replicate 1 of 4.

value: Sprague Dawley

value: Hypoxia 10% O2 for 4 weeks

value: male


title: Hypoxia RV Animal 19 Replicate 2

description: Biological replicate 1 of 6. Technical replicate 2 of 2.

source_name: 19 RV RNA

value: right ventricle

value: Pooled from 14 rat cell lines

value: Stratagene


title: R3, T=2

description:
3
RG patient 3
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.


title: PHEO_AG_HS_053

description: paraganglioma

value: paraganglioma

tag: mutation (gene)

tag: mutation (type)

value: somatic

value: benign


title: R6, T=1

description:
5N
RG patient 6
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

tag: tissue


title: Hypoxia RV Animal 20 Replicate 2

description: Biological replicate 2 of 6. Technical replicate 2 of 4.


title: R7, T=3

description:
3N
RG patient 7
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.


title: PHEO_AG_HS_049

description: paraganglioma

source_name: paraganglioma, malignant

tag: Sex

value: malignant


title: PHEO_AG_HS_041

description: paraganglioma

value: female

value: RET

tag: malignancy


title: PHEO_AG_HS_045

description: paraganglioma


title: Hypoxia RV Animal 19 Replicate 1

description: Biological replicate 1 of 6. Technical replicate 1 of 2.


title: PHEO_AG_HS_048

description: paraganglioma

value: SDHD

value: germline


title: PHEO_AG_HS_052

description: paraganglioma


title: PHEO_AG_HS_047

description: paraganglioma


title: Feature Expression in purple tissue at 8 dpb, replicate 1

description: 140.89.525 Dp1 (10.12.09)

value: Del/Ros1 fruit in the MoneyMaker background

value: Stage D

value: purple

value: 8 day after breaker

value: pooled total RNA


title: R1, T=3

description:
3.4
RG patient 1
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

value: liver

tag: patient identifier

value: auxiliary liver transplant (ALT)

value: successful


title: R1, T=2

description:
3.2
RG patient 1
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

tag: treatment


title: PHEO_AG_HS_040

description: paraganglioma

value: syndromic


title: R1, T=1

description:
3.1
RG patient 1
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

tag: regeneration status


title: R4, T=3

description:
1
RG patient 4
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

tag: time point


title: PHEO_AG_HS_033

description: paraganglioma

value: paraganglioma


title: PHEO_AG_HS_036

description: paraganglioma

value: male


title: PHEO_AG_HS_034

description: paraganglioma

value: benign


title: Feature Expression in Red tissue at 45 dpb, replicate 2

description: 140.89.524 Cr2 (10.12.09)

source_name: Stage C_red tissue

value: Stage C

value: red

value: 45 day after breaker


title: PHEO_AG_HS_028

description: paraganglioma

value: female

value: SDHB


title: Time series t2 / t0 replicates d

city: Groningen

first: Maarten

last: Mols

address: Nijenborgh 7

country: Netherlands

institute: University of Groningen

description:
US22502548_251734310045_S01_Bcereus14579_3rdDesign_2_2
plasma treated t2 vs untreated

hyb_protocol: cDNA synthesis, labelling, microarray hybridization and scanning was performed as previously described (Mols et al., 2010).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Agilent Feature Extraction Software (v 8.1.1.1) was used for background subtraction and LOWESS normalization.

organism: Bacillus cereus

growth_protocol: Bacillus cereus ATCC 14579 (type strain) was grown in BHI at 30C, 200 rpm, to OD 0.5 (mid exponential phase)

extract_protocol: The filters were tranferred to tubes containing Tri-reagent, further total RNA extraction was performed as previously described (Mols et al., 2010).

treatment_protocol: The vegetative cells were tranferred onto a celulose nitrate filter by filtration and the filters were placed ontop of nutrient agar plates. The plates, divided into 6 sectors, were exposed to a nitrogen gas assisted low temperature plasma at atmospheric pressure for 0, 1, 2, or 5 minutes per sector.

tag: strain

tag: exposure time

value: plasma treated exposure 6X2 min

value: plasma treated exposure 6X0 min


title: PHEO_AG_HS_031

description: paraganglioma


title: PHEO_AG_HS_032

description: paraganglioma

value: VHL

value: somatic


title: PHEO_AG_HS_035

description: paraganglioma


title: PHEO_AG_HS_029

description: paraganglioma


title: Time series t1 / t0 replicates d

description:
US22502548_251734310045_S01_Bcereus14579_3rdDesign_2_1
plasma treated t1 vs untreated

label_protocol: cDNA synthesis, labelling, microarray hybridization and scanning was performed as previously described (Mols et al., 2010).

value: plasma treated exposure 6X1 min


title: N2 flow control t5 replicates b_2

description:
US22502548_251734310045_S01_Bcereus14579_3rdDesign_2_4
plasma vs N2 flow t5

value: plasma treated exposure 6X5 min

value: nitrogen flow treated exposure 6X5 min


title: Time series t0 / t2 replicates c

description:
US22502548_251734310045_S01_Bcereus14579_3rdDesign_1_2
untreated vs plasma treated t2


title: Time series t0 / t5 replicates c

description:
US22502548_251734310045_S01_Bcereus14579_3rdDesign_1_3
untreated vs plasma treated t5


title: Time series t0 / t1 replicates c

description:
US22502548_251734310045_S01_Bcereus14579_3rdDesign_1_1
untreated vs plasma treated t1


title: N2 flow control t5 replicates b

description:
US22502548_251734310044_S01_Bcereus14579_3rdDesign_2_4
plasma vs N2 flow t5


title: PHEO_AG_HS_020

description: paraganglioma


title: PHEO_AG_HS_191

description: paraganglioma

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol. Illumina Beadstudio software.

label_protocol: standard Illumina protocol

value: Female

value: Germline

value: Benign

tag: pathological diagnosis


title: PHEO_AG_HS_026

description: paraganglioma

value: paraganglioma

value: male

value: SDHD

value: germline


title: N2 flow control t2 replicates b_2

description:
US22502548_251734310045_S01_Bcereus14579_3rdDesign_1_4
plasma vs N2 flow t2

value: nitrogen flow treated exposure 6X2 min


title: PHEO_AG_HS_085

description: paraganglioma

value: Malignant


title: N2 flow control t2 replicates b

description:
US22502548_251734310044_S01_Bcereus14579_3rdDesign_2_3
plasma vs N2 flow t2


title: PHEO_AG_HS_021

description: paraganglioma

value: female

value: benign


title: PHEO_AG_HS_210

description: normal adrenal medulla

value: Male

value: normal adrenal medulla


title: PHEO_AG_HS_019

description: paraganglioma


title: PHEO_AG_HS_186

description: paraganglioma

value: SDHA


title: PHEO_AG_HS_211

description: normal adrenal medulla


title: PHEO_AG_HS_178

description: paraganglioma


title: PHEO_AG_HS_205

description: paraganglioma

value: VHL


title: PHEO_AG_HS_207

description: paraganglioma

value: SDHC


title: PHEO_AG_HS_017

description: paraganglioma

value: somatic


title: Time series t5 / t0 replicates d

description:
US22502548_251734310045_S01_Bcereus14579_3rdDesign_2_3
plasma treated t5 vs untreated

value: plasma treated exposure 6X5 min

value: plasma treated exposure 6X0 min


title: N2 flow control t5 replicates a

description:
US22502548_251734310044_S01_Bcereus14579_3rdDesign_1_4
N2 flow vs plasma t5

value: nitrogen flow treated exposure 6X5 min


title: N2 flow control t0 replicates b

description:
US22502548_251734310044_S01_Bcereus14579_3rdDesign_2_1
untreated vs untreated

value: nitrogen flow treated exposure 6X0 min


title: PHEO_AG_HS_013

description: paraganglioma

value: paraganglioma

value: male


title: PHEO_AG_HS_022

description: paraganglioma

value: germline


title: PHEO_AG_HS_010

description: paraganglioma

value: RET


title: PHEO_AG_HS_011

description: paraganglioma


title: PHEO_AG_HS_009

description: paraganglioma


title: N2 flow control t1 replicates a

description:
US22502548_251734310044_S01_Bcereus14579_3rdDesign_1_2
N2 flow vs plasma t1

value: nitrogen flow treated exposure 6X1 min

value: plasma treated exposure 6X1 min


title: N2 flow control t2 replicates a

description:
US22502548_251734310044_S01_Bcereus14579_3rdDesign_1_3
N2 flow vs plasma t2

value: nitrogen flow treated exposure 6X2 min

value: plasma treated exposure 6X2 min


title: N2 flow control t0 replicates a

description:
US22502548_251734310044_S01_Bcereus14579_3rdDesign_1_1
untreated vs untreated


title: PHEO_AG_HS_008

description: paraganglioma

value: benign


title: PHEO_AG_HS_164

description: paraganglioma

value: Male

value: Benign


title: fertilized vs virgin Sample1 Chip 3

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

hyb_protocol: Labeled products were pooled to serve as a Master Mix for Array set. The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybrization master for a given source and biological replicate

scan_protocol: Image acquisition with Axon GenePix 4200A Professional scanner, 5 micron resolution.

data_processing: Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.

organism: Tribolium castaneum

source_name: Total RNA from fertilized female Tribolium castaneum

label_protocol: Labeled 1 microgram double stranded cDNA with Cy-dye nonamers in triplicate using NimbleGen Dual-Color Labeing kit with recommened user guide. Http://www.nimblegen.com/

extract_protocol: Total RNA extracted using Rneasy Mini Kit (Qiagen) following tissue protocol. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

value: Mated

value: whole eggs

tag: developmental stage

value: 0-24 hour

tag: replicate

value: biological

source_name: Total RNA from virgin female Tribolium castaneum

value: Virgin


title: PHEO_AG_HS_165

description: paraganglioma


title: PHEO_AG_HS_005

description: paraganglioma

value: VHL

value: somatic


title: PHEO_AG_HS_007

description: paraganglioma

value: paraganglioma

value: male


title: PHEO_AG_HS_003

description: paraganglioma


title: fertilized vs virgin Sample3 Chip 3


title: PHEO_AG_HS_002

description: paraganglioma

value: female

value: germline


title: virgin vs fertilized Sample2 Chip 3


title: PHEO_AG_HS_149

description: paraganglioma

value: SDHB

value: Germline

value: Malignant


title: PHEO_AG_HS_001

description: paraganglioma

value: benign


title: PHEO_AG_HS_144

description: paraganglioma

value: Male


title: PHEO_AG_HS_129

description: paraganglioma

value: Female

value: Benign


title: PHEO_AG_HS_082

description: paraganglioma


title: PHEO_AG_HS_060

description: paraganglioma

value: RET

value: Somatic


title: PHEO_AG_HS_045

description: paraganglioma


title: PHEO_AG_HS_132

description: paraganglioma

value: MAX


title: PHEO_AG_HS_021

description: paraganglioma


title: PHEO_AG_HS_083

description: paraganglioma


title: PHEO_AG_HS_168

description: paraganglioma


title: HL-60 untreated

status: Public on May 05 2013

city: Nanjing

first: zhu

last: dihan

address: Hankou 22

country: China

institute: Nanjing university

hyb_protocol: Running TaqMan® Low Density Arrays on 7900HT Real- Time PCR Systems

data_processing:
1. To review the results, transfer the SDS files into an RQ study.
2. View the amplification plots, then review the baseline and
threshold settings. Adjust the baseline and threshold settings for
individual assays if necessary.
3. Review the gene expression plot (for SDS v2.3 software, view
the amplification plots in the Plate, Detector, or Sample view).
Comparative CT uses arithmetic formulas to determine the
change in expression of a target in an experimental sample
relative to the same target in a reference sample. This method is
used for high-throughput measurements of relative gene
expression when there are many genes in many samples.
4. In the well table or results table, review CT values for each well
and for each replicate group. Omit outliers if necessary.
For additional analysis the raw CT and/or ΔCT values can be
exported. If you are using SDS v2.3 software, raw CT values are
exported from the Plate Centric View.
For detailed downstream analysis, Applied Biosystems
recommends software such as Integromics Real-Time
StatMiner™ Software

label: probe TaqMan®

source_name: relative CT value

label_protocol: Using sequence-specific primers and probe on the TaqMan® MicroRNA Array.

extract_protocol:
The starting material is total RNA. To prepare the starting material,
use the mirVana™ miRNA Isolation Kit

tag: cell line

tag: time

value: 12 hours


title: PHEO_AG_HS_088

description: paraganglioma

value: SDHD


title: N2 flow control t1 replicates b

description:
US22502548_251734310044_S01_Bcereus14579_3rdDesign_2_2
plasma vs N2 flow t1

value: plasma treated exposure 6X1 min

value: nitrogen flow treated exposure 6X1 min


title: PHEO_AG_HS_201

description: paraganglioma

value: paraganglioma


title: HL-60 TPA

scan_protocol: Running TaqMan® Low Density Arrays on 7900HT Real- Time PCR Systems

source_name: Relative CT value vs u6

value: TPA


title: HUVEC CTL12-4

city: Stanford

first: Zhen

last: Wang

state: CA

address: Campus Drive

department: Surgery

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58511.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Universal Control aRNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene Universal Control aRNA

source_name: HUVEC - BSA-coating - 12 hours

tag: cell type

value: HUVEC

tag: media

value: BSA


title: AP_whole_hh_rep2

status: Public on May 04 2013

city: Berlin

first: Ansgar

last: Klebes

address: Chausseestr. 117

country: Germany

institute: Humboldt University Berlin

description: comparison of A and P cells from the same imaginal disc

hyb_protocol: Hybridization was done in a DeRisi-style Hyb chamber in a 64.5°C waterbath over-night. To 34ul labeled probe add 6.8ul 20x SSC,//3.5 ul polyA RNA to block,//1 ul 10% SDS,//1.1ul 0.5M Hepes, pH 7.5,//Boil 2 min.,//Spin down and adjust to RT,//Apply to array and hybridize in hyb chamber o/n at 64.5°C in a waterbath.  Using lifter slides in DeRisi style hybridization chamber.  To 34ul labeled probe add 6.8ul 20x SSC,  3.5 ul polyA RNA to block,  1 ul 10% SDS,  1.1ul 0.5M Hepes, pH 7.5,  Boil 2 min.,  Spin down and adjust to RT,  Apply to array and hybridize in hyb chamber o/n at 64.5°C in a waterbath.

scan_protocol: Scanning was performed with a GenePix 4000A Scanner and processed with GenePix software (Molecular Devices)

data_processing: Data was uploaded to the NOMAD data base (http://ucsf-nomad.sourceforge.net/) and global median normalized. The data provided is the raw data as it is provided by the GenePix results file.

organism: Drosophila melanogaster

source_name: A cells, hhGal4

label_protocol: Probes were indirectly labeled with amino-allyl-dUTP and subsequently coupled to Cy3- and Cy5-reactive dyes. Indirect aa-labeling protocol using amplified RNA ////Xul of aRNA,//1ul Ts-Amp (Klebes and Kornberg, 2008) primer (1ug/ul) and 1ul random hexanucleotides (2.5ug/ul),//to a total vol. of 14.5uL with ddH2O,//incubate at 70°C for 10 min., chill on ice,//add 6ul 5x first strand buffer (Invitrogen),//3ul 0.1M DTT (Invitrogen),//2ul 50x aa-dUTP/dNTP mix (10ul each 100mM dATP, dCTP, dGTP + 4 ul 100mM aa-dUTP + 6 ul 100mM dTTP)//1.5ul ddH2O,//1ul Rnasin,//2ul Superscript III (Invitrogen),//Incubate at 50°C for 2 hrs.////aa-aRNA hydrolysis & clean-up //add 10ul 1N NaOH and 10ul 0.5M EDTA,//Incubate at 65°C for 15 min.,//Neutralize with 30ul 1M Tris, pH7.4,//Clean-up with Qiagen PCR purification kit, but elute with water!//Dry in speed vac to 4.5ul.////Coupling and quenching//To 4.5ul aa-aRNA add 4.5ul monofunctional NHS-ester Cy3 or Cy5 (Amersham) that has been resuspended in 0.1M NaBicarbonate pH 9!//Incubate in the dark for 1h,//Add 4.5ul 4M Hydorylamine to quench,//Incubate for 15 min. in the dark.//Combine Cy3 and Cy5 reactions, add 70ul ddH2O,//Clean-up with Qiagen PCR purification kit,//Speed vac to 35 ul in the dark.//Check labeling efficiency of 1ul in nanodrop or similar.

growth_protocol: Wing imaginal discs were isolated from wandering third instar larvae that developed at 25°C.

extract_protocol: Total RNA of each sample was extracted using the Zymo Mini RNA isolation kit (Zymo Research) and subjected to two rounds of T7-based llinear RNA amplification as described in Klebes and Kornberg, 2008 (Methods Mol Biol. 2008;420:303-17. doi: 10.1007/978-1-59745-583-1_19).    PMID:      18641956

treatment_protocol: The A/P compartment border was labeled with UAS-GFP activated either by ptc-Gal4 or hh-Gal4. Individual wing imaginal discs were micro-dissected along the compartment border under UV-light in PBS with fine tungsten needles.

tag: development stage

value: 3rd instar

tag: tissue

value: wing disc

tag: genotype/variation

tag: cell location

value: anterior whole

source_name: P cells, hhGal4

value: posterior whole


title: PHEO_AG_HS_111

description: paraganglioma

tag: Sex

value: Female

value: VHL

value: Germline

tag: malignancy

value: Benign


title: AP_pouch_hh_rep2

source_name: A cells pouch only, hhGal4

value: anterior pouch

source_name: P cells pouch only, hhGal4

value: posterior pouch


title: AP_whole_ptc_rep3

source_name: A cells, ptcGal4

source_name: P cells, ptcGal4


title: PA_pouch_ptc_rep3

source_name: P cells pouch only, ptcGal4

source_name: A cells pouch only, ptcGal4


title: PA_whole_hh_rep1


title: PA_whole_ptc_rep2


title: PHEO_AG_HS_033

description: paraganglioma

value: Somatic


title: AP_whole_ptc_rep1


title: HUVEC Del12-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58513.gif

source_name: HUVEC - Del1-coating - 12 hours


title: HUVEC Del24-4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58522.gif

source_name: HUVEC - Del1-coating - 24 hours


title: HUVEC Del12-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58512.gif


title: HUVEC CTL12-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58509.gif


title: PA_pouch_hh_rep3


title: PA_pouch_ptc_rep2


title: HUVEC CTL24-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58515.gif

source_name: HUVEC - BSA-coating - 24 hours


title: PA_whole_hh_rep3


title: AP_pouch_ptc_rep1


title: HUVEC Del24-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58519.gif


title: HUVEC Del24-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58520.gif


title: HUVEC CTL12-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58510.gif


title: HUVEC CTL24-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58516.gif


title: WT-D0 rep3

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Irf4+/+; Day0, rep3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C. on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained, using an anti-biotin amplification step, in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 according to manufacturer's specifications.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. The resulting data was then normalized and scaled using D-chip (PM-only) model.

organism: Mus musculus

source_name: purified primary B cells from Irf4+/+ mice; stimulated for 0 Days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: RPMI medium + 10% FCS and supplements (Hepes, 2-Me, glutamine, NEAA, Na-Pyruvate, Pen/Strep); isolated primary cells stimulated as indicated at a density of 0.5million/mL.

extract_protocol: Trizol

treatment_protocol: CD40L + IL-2 + IL-4 + IL-5; some samples included 16 or 100ng/mL doxycycline as indicated.

tag: strain/background

tag: genotype

value: resting mature peripheral primary B cells

tag: stimulation duration


title: WT-D3 rep2

description: Irf4+/+; Day3, rep2

source_name: purified primary B cells from Irf4+/+ mice; stimulated for 3 Days


title: HUVEC Del12-4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58514.gif


title: 4KO-zeroD3 rep3

description: Irf4-/-; Day3, zero DOX, rep3

source_name: purified primary B cells from Irf4-inducible mice on the Irf4-/- background; stimulated for 3 Days; 0ng/mL DOX

tag: treatment

value: zero DOX


title: WT-D1 rep1

description: Irf4+/+; Day1, rep1

source_name: purified primary B cells from Irf4+/+ mice; stimulated for 1 Days


title: WT-D3 rep3

description: Irf4+/+; Day3, rep3


title: WT-D0 rep2

description: Irf4+/+; Day0, rep2


title: HUVEC Del24-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58521.gif

source_name: Stratagene Universal Control aRNA


title: 4KO-zeroD0 rep2

description: Irf4-/-; Day0, zero DOX, rep2

source_name: purified primary B cells from Irf4-inducible mice on the Irf4-/- background; stimulated for 0 Days; 0ng/mL DOX


title: WT-D0 rep1

description: Irf4+/+; Day0, rep1


title: 4KO-loD3 rep3

description: Irf4-/-; Day3, low DOX, rep3

source_name: purified primary B cells from Irf4-inducible mice on the Irf4-/- background; stimulated for 3 Days; 16ng/mL DOX

value: low DOX


title: 4KO-zeroD1 rep3

description: Irf4-/-; Day1, zero DOX, rep3

source_name: purified primary B cells from Irf4-inducible mice on the Irf4-/- background; stimulated for 1 Days; 0ng/mL DOX


title: 4KO-loD1 rep2

description: Irf4-/-; Day1, low DOX, rep2

source_name: purified primary B cells from Irf4-inducible mice on the Irf4-/- background; stimulated for 1 Days; 16ng/mL DOX


title: HUVEC CTL24-4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58518.gif

value: Stratagene Universal Control aRNA


title: 4KO-zeroD1 rep2

description: Irf4-/-; Day1, zero DOX, rep2


title: WT-D1 rep2

description: Irf4+/+; Day1, rep2


title: 4KO-hiD1 rep3

description: Irf4-/-; Day1, high DOX, rep3

source_name: purified primary B cells from Irf4-inducible mice on the Irf4-/- background; stimulated for 1 Days; 100ng/mL DOX

value: high DOX


title: 4KO-loD1 rep3

description: Irf4-/-; Day1, low DOX, rep3


title: 4KO-zeroD3 rep2

description: Irf4-/-; Day3, zero DOX, rep2


title: 4KO-zeroD0 rep3

description: Irf4-/-; Day0, zero DOX, rep3


title: 4KO-loD3 rep2

description: Irf4-/-; Day3, low DOX, rep2


title: AP_pouch_hh_rep1

source_name: A cells pouch only, hhGal4

source_name: P cells pouch only, hhGal4


title: 4KO-zeroD1 rep1

description: Irf4-/-; Day1, zero DOX, rep1


title: 4KO-hiD3 rep2

description: Irf4-/-; Day3, high DOX, rep2

source_name: purified primary B cells from Irf4-inducible mice on the Irf4-/- background; stimulated for 3 Days; 100ng/mL DOX


title: WT-D3 rep1

description: Irf4+/+; Day3, rep1


title: 4KO-hiD1 rep2

description: Irf4-/-; Day1, high DOX, rep2


title: 8226R5 PRIMA #2

city: Toronto

first: Hong

last: Chang

address: 200 Elizabeth St.

country: Canada

institute: University Health Network

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol. 750ng of cRNA was hybridised to each microarray chip following manufacturer instructions.

scan_protocol: Standard Illumina scanning protocol. The signals were detected and gathered using BeadArray Reader (Illumina, USA). The data were uploaded to Bead Studio software (Illumina,USA) and after qualitative evaluation, the text file data was extracted and statistically analysed.

data_processing:
We preprocessed the raw data using lumi R package. Background correction was done in Beadstudio, www.illumina.com). The quantile normalization method (Bolstad et al. 2003) implemented in lumi R package was used to normalize the data.
We used LIMMA (linear models for microarray data) to identify differentially expressed genes. Briefly speaking, it star by fitting a linear model for each spot/gene in the data, then an empirical Bayes (EB) method is used to moderate the standard errors for estimating the moderated t-statistics for each spot/gene, which shrinks the standard errors towards a common value. This test is similar to an ANOVA method for each spot/gene except that the residual standard deviations are moderated across genes to ensure more stable inference for each gene. The moderated standard deviations are a compromise between the individual genewise standard deviations and an overall pooled standard deviation. Tvalue: modified t-statistic value; raw_pvalue: unadjusted pvalue ; adjusted_pvalue: adjusted pvalue.

label: Biotin

source_name: Meyloma cell line

label_protocol: Standard Illumina labelling protocol.250 ng total RNA was used to prepare amplified and biotinylated cRNAs using Illumina TotalPrep RNA amplification kit (Life Technologies, USA).

growth_protocol: Multiple myeloma cells (2 x 106) were seeded into 6-well plates in duplicates and allowed to grow for 24 hrs in CO2 incubator prior to treatment with the PRIMA-1Met or DMSO control

extract_protocol: Total RNA was isolated from the cells using Trizol reagent followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality and quantity of the isolated RNA was checked by Nanodrop and Agilent Bioanalyzer, respectively

treatment_protocol: Myeloma cells were treated with 20, 40, and 40 µM PRIMA-1Met, respectively for 8 hrs

tag: p53 status


title: WT-D1 rep3

description: Irf4+/+; Day1, rep3


title: 4KO-zeroD3 rep1

description: Irf4-/-; Day3, zero DOX, rep1


title: 8226R5 PRIMA #1

description: Replicate 1


title: 701700_4°C

city: Berkeley

first: Juliana

last: Durack

address: Barker Hall

department: MCB

institute: University of California

description: WebArray normalized raw data from four replicates

hyb_protocol: Slides were pre-hybridized in a hybridization solution [25 %, v/v, formamide, 5x SSC buffer (0.75 M NaCl, 0.075 M trisodium citrate, pH 7.0), 0.1 % SDS] containing 10 mg BSA ml–1 for 45 min at 42 °C. Slides were then rinsed twice in distilled water and air-dried. Hybridization was performed in a humid hybridization chamber at 42 °C for 16–20 h using a hybridization solution containing 0.42 µg human Cot1 DNA µl–1, 0.62 µg polyA µl–1 and 0.83 µg salmon sperm DNA µl–1. Slides were washed at room temperature in 1x SSC buffer containing 0.2 % SDS for 5 min and again in 0.1x SSC buffer containing 0.2 % SDS for 5 min. The slides were then further washed twice in 0.1x SSC buffer at room temperature for 2 min and then air-dried.

scan_protocol: Scanned using a GenePix 4000A scanner (Axon Instruments)

data_processing: Normalization of raw data and subsequent statistical analysis was performed with the WebArray Online platform described by Xia et al, 2005 (Xia, X., McClelland, M., and Wang, Y., 2005. WebArray: an online platform for microarray data analysis. BMC Bioinformatics 6, 306). Within-array normalization used the global LOESS procedure. Between each array quantile normalization was used to insure intensities had the same empirical distribution across arrays and across channels. The significance of differential expression was analysed using linear modal statistical analysis following the method of Smyth, 2004 (Smyth, G.K., 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3). Oligonucleotides that showed negligible or no hybridization when compared with background hybridization were excluded from analyses.

organism: Listeria monocytogenes

source_name: BHI broth+0% NaCl at 25°C

label_protocol: RNA was converted to cDNA and post-labelled with Cy5 (red) and Cy3 (green) fluorescent dyes using the SuperScript Indirect cDNA Labelling System (Invitrogen).

growth_protocol: Controls grown to exponential growth phase (at 25°C) in brain-heart infusion broth (Oxoid). Flasks shaken inwatherbath at 100 rpm per minute.

extract_protocol: All cultures were pelleted at 4000 rpm for 10 min and then suspended in 3 ml Bacterial RNA Protect reagent (Qiagen) for 15 min with constant agitation followed by centrifugation and storage at -80 C. Cells were defrosted and underwent a 2–3 h (25 °C) enzymic treatment in TE buffer (10 mM Tris/HCl, 1 mM disodium EDTA, pH 7.5) containing 20 mg lysozyme ml–1 and 10 mg proteinase K ml–1. Cells were fully lysed by bead beating using 0.1 mm zirconium-silica sand in RNAeasy MIDI RNA extraction kit (Qiagen) lysis buffer containing 0.1 % β-mercaptoethanol. RNA was then extracted and purified using the RNAeasy kit and subsequently stored at –80 °C. RNA quality and quantity was assessed with the Agilent Technologies bioanalyser 2100 and RNA LabChip.

treatment_protocol: Hyperosmotic stress cultures grown to exponential growth phase (at  25°C) in brain-heart infusion broth (Oxoid), suplimented with additional 8%, 10% or 12% NaCl was added to . Cold stress cultures were grown to exponential growth phase (at  4°C) in brain-heart infusion broth (Oxoid). Flasks shaken in a watherbath at 100 rpm per minute.

tag: strain

value: control BHI broth + 0 pct. NaCl at 25 C

source_name: BHI broth+0% NaCl at 4°C

value: BHI broth+0% NaCl at 4°C


title: HUVEC CTL24-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58517.gif

source_name: HUVEC - BSA-coating - 24 hours

value: HUVEC

value: BSA


title: ScottA_4°C

value: ScottA


title: 4KO-hiD3 rep3

description: Irf4-/-; Day3, high DOX, rep3


title: U266 Control #2

description: Replicate 2

tag: cell line

value: Mutant


title: MM.1S PRIMA #1

description: Replicate 1

value: Wild type


title: 8226R5 Control #1

description: Replicate 1


title: 4KO-hiD1 rep1

description: Irf4-/-; Day1, high DOX, rep1


title: 8226R5 Control #2

description: Replicate 2


title: U266 PRIMA #2

description: Replicate 2


title: MM.1S Control #1

description: Replicate 1


title: ScottA_12%NaCl

source_name: BHI broth+12% NaCl at 25°C

value: BHI broth+12% NaCl at 25°C


title: 701700_8%NaCl

source_name: BHI broth+8% NaCl at 25°C

value: BHI broth+8% NaCl at 25°C


title: ATCC19115_4°C


title: 4KO-zeroD0 rep1

description: Irf4-/-; Day0, zero DOX, rep1


title: 4KO-loD3 rep1

description: Irf4-/-; Day3, low DOX, rep1


title: MM.1S PRIMA #2

description: Replicate 2


title: U266 Control #1

description: Replicate 1


title: 4KO-hiD3 rep1

description: Irf4-/-; Day3, high DOX, rep1


title: Mef2 ChIP ZT14

status: Public on May 03 2013

city: Waltham

first: Anna

last: Sivachenko

state: MA

address: 415 South St

institute: Brandeis University

description:
chIP: AS-MC-m14.CEL
chIP: AS-MC-I14.CEL

hyb_protocol: ChIP samples were hybridized to Drosophila 2.0 Tiling Arrays exactly as described in manufacturers instructions.  See www.affymetrix.com/support/.../chromatin_immun_ChIP.pdf

scan_protocol: Drosophila 2.0 Tiling Arrays were scanned via a Gene CHIP Scanner 3000 (Affymetrix) and the GeneCHIP Operating Software version 1.4.

data_processing: To identify significant peaks of Mef2 binding throughout the genome Affymetrix .CEL files for both input and IP samples were analyzed using MAT (Johnson et al. 2006).

source_name: ZT14 Mef2 ChIP DNA from yw flies

label_protocol: ChIP samples were labeled exactly as described in manufacturers instructions.  See www.affymetrix.com/support/.../chromatin_immun_ChIP.pdf

growth_protocol: Drosophila were entrained for 3-4 days in 12:12 light:dark conditions.  Flies were harvested at the appropriate time (see above).

extract_protocol: Chromatin was prepared from adult fly heads of yw flies entrained for 3 days in12:12 light:dark cycles and then harvested every 4 hours for a total of 6 timepoints. ChIP with anti-Mef2 antibody (Sandmann et al., 2007) was performed as described (Abruzzi et al., 2011; Menet et al., 2010)  with the exception that 3ul of anti-Mef2 antibody was used per 125 µl chromatin.  Briefly, nuclei were isolated from 1ml of fly heads for each time point, 25 µl of sonicated chromatin was removed for the input sample, and the remaining 125µl of chromatin was incubated with 3µl of anti-Mef2 antibody and purified with Protein G-Sepharose beads (Zymed).  To control for non-specific binding, rabbit IgG (Sigma) was incubated with chromatin instead of Mef2 antibody. DNA was isolated with using a PCR purification kit (Qiagen).

treatment_protocol: Flies were frozen on dry ice and heads isolated.

value: yw

value: head

source_name: ZT14 Input DNA from yw flies


title: Mef2 ChIP ZT22

description:
chIP: AS-MC-M22.CEL
chIP: AS-MC-I22.CEL

source_name: ZT22 Mef2 ChIP DNA from yw flies

source_name: ZT22 Input DNA from yw flies


title: Mef2 ChIP ZT18

description:
chIP: AS-MC-m18.CEL
chIP: AS-MC-I18.CEL

source_name: ZT18 Mef2 ChIP DNA from yw flies

source_name: ZT18 Input DNA from yw flies


title: Mef2 ChIP ZT2

description:
Input: AS-MC-I2.CEL
chIP: AS-MC-I2.CEL

source_name: ZT2 Mef2 ChIP DNA from yw flies

source_name: ZT2 Input DNA from yw flies


title: ATCC19115_10%NaCl

source_name: BHI broth+10% NaCl at 25°C

value: BHI broth+10% NaCl at 25°C


title: U266 PRIMA #1

description: Replicate 1


title: 4KO-loD1 rep1

description: Irf4-/-; Day1, low DOX, rep1

source_name: purified primary B cells from Irf4-inducible mice on the Irf4-/- background; stimulated for 1 Days; 16ng/mL DOX

value: resting mature peripheral primary B cells


title: Mef2 ChIP ZT6

description:
chIP: AS-MC-m6.CEL
chIP: AS-MC-I6.CEL

source_name: ZT6 Mef2 ChIP DNA from yw flies

source_name: ZT6 Input DNA from yw flies


title: Mef2 ChIP ZT10

description:
chIP: AS-MC-M10.CEL
chIP: AS-MC-In10.CEL

source_name: ZT10 Mef2 ChIP DNA from yw flies

source_name: ZT10 Input DNA from yw flies


title: control Guichao2

city: Shanghai

first: Xianxin

last: dong

address: 220 Handan Road

department: School of Life Sciences, Fudan University

institute: State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Science Research

description: Gene expression data from leaf tissues of 6-week-old seedlings (10 plants each).

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).

organism: Oryza sativa

source_name: 6-week-old control Guichao2

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: OsEBS transgenic rice and control Guichao2 were grown in greenhouse under a 14/10 h (light/dark) photoperiod at 28°C.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

treatment_protocol: No treatment

value: leaf

tag: genetic background

value: wild type

tag: age


title: OsEBS-transgenic rice B10301

source_name: 6-week-old OsEBS-transgenic rice B10301

value: OsEBS transgenic Guichao2


title: OsEBS-transgenic rice B10201

source_name: 6-week-old OsEBS-transgenic rice B10201


title: T1682 attach

city: Pisa

first: Iacopo

last: Petrini

address: Via Roma 67

country: Italy

institute: Pisa University

description:
Thymoma B1 cell line
Platform GPL4093 is based on NCBI Build 35, and Platform GPL10123 is based on NCBI Build 36.

hyb_protocol: According to ULS labeling kit protocol version 3 November 2008

data_processing:
Data were extracted and normalized using the linear method by Feature Extraction v10.5 (Agilent).
Copy number call thresholds were defined: high gain +0.8, gain +0.3, loss -0.3 and big loss -0.8
Data were further Centralized.  For complete details, please see readme.txt supplementary file on the Series record.  Centralized data files are available as Sample supplementary files.

source_name: Thymoma B1 cell line

label_protocol: The labeling procedure was conducted using the Genomic DNA Enzymatic Labeling Kit (Agilent) for 7 samples and using the Genomic DNA ULS labeling kit (Agilent) for the remaining 52 samples

growth_protocol: All cell lines were cultured in RPMI 1640 containing 200 mM L-Glutamine (Gibco, Invitrogen, Grand Island, NY), 50 U/mL penicillin, 50 U/mL streptomycin (Invitrogen) and 10% heat-inactivated calf serum (Invitrogen) and grown in a 37 oC incubator with humidified 5% CO2 atmosphere. Media was supplemented with 25nM Hepes for T1889 and T1682.

extract_protocol: FFPE tumor specimens were assessed for quality and adequacy of fixation and storage. A Hematoxylin & Eosin stained slide was prepared for each sample. A pathologist verified the presence of tumor tissue and marked the areas with more than 80% cancer cells on the paraffin blocks. Five cores of tissue were punched from the marked area on FFPE blocks using a 0.6-mm tissue microarray needle, to a depth of approximately 1 mm. The DNA was extracted using DNeasy kit (Qiagen, Inc., Valencia, CA) according to Genomic DNA ULS labeling kit protocol (Agilent Technologies, Inc., Palo Alto, CA)

value: Thymoma B1 cell line

tag: who histotype

tag: labeling kit

value: ULS labeling kit

source_name: Promega Genomic DNA

tag: sex

value: Male


title: I-Thy 132A

description:
Thymic epithelial tumor FFPE
Platform GPL4093 is based on NCBI Build 35, and Platform GPL10123 is based on NCBI Build 36.

scan_protocol: According to ULS labeling kit protocol version 3 November 2008

source_name: Thymic epithelial tumor FFPE

tag: tissue

value: Thymic epithelial tumor FFPE

tag: gender

value: M


title: I-Thy 122

value: C


title: I-Thy 129

value: AB


title: I-Thy 105

value: A

value: F


title: MM.1S Control #2

description: Replicate 2

source_name: Meyloma cell line

value: Wild type


title: T1889

description:
Thymic carcioma cell line
Platform GPL4093 is based on NCBI Build 35, and Platform GPL10123 is based on NCBI Build 36.

source_name: Thymic carcinoma cell line

value: Thymic carcinoma cell line


title: I-Thy 120


title: I-Thy 107


title: I-Thy 084


title: I-Thy 091A


title: TY-82


title: I-Thy 056


title: I-Thy 057


title: I-Thy 053


title: I-Thy 065


title: I-Thy 124


title: I-Thy 051C


title: I-Thy 113


title: I-Thy 101


title: I-Thy 088A


title: I-Thy 060


title: I-Thy 073


title: I-Thy 072


title: I-Thy 100


title: I-Thy 058


title: I-Thy 082


title: I-Thy 076


title: I-Thy 077


title: I-Thy 063


title: I-Thy 050A


title: I-Thy 043


title: Bladder cancer BT148

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description: Bladder cancer BT148

hyb_protocol: Fluorescence signals corresponding to C or T nucleotides were measured and the data were used to assign a quantitative measure of methylation level (β value).

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: Each methylation data point represents the fluorescent signal from the methylated (M) and unmethylated (U) allele. Background intensity was computed from a set of negative controls and subtracted from each analytical data point. The ratio of the fluorescent signals from the two alleles was then computed. The β value is a quantitative measure of DNA methylation levels of specific CpGs and ranges from 0 for completely unmethylated to 1 for completely methylated. Data processing were performed on Illumina BeadStudio software.

source_name: non-muscle invasive bladder cancer

label_protocol: Bisulfite conversion of genomic DNA was performed using the EZ DNA Methylation Kit (Zymo Research, Orange, CA) according to the Manufacturer's instructions.

extract_protocol: Genomic DNA for the Infinium methylation assay was extracted by standard methods using the Wizard Genomic DNA Purification System (Promega, Madison, WI).

value: non-muscle invasive bladder cancer

tag: tnm stage

tag: grade

value: LOW

tag: overall survival (1

value: survival, 2:death):1

tag: survival time (month)


title: I-Thy 029


title: I-Thy 022


title: I-Thy 023


title: Bladder cancer BT126

description: Bladder cancer BT126

value: survival, 2:death):2


title: Bladder cancer BT149

description: Bladder cancer BT149


title: I-Thy 021


title: Bladder cancer BT191

description: Bladder cancer BT191

value: HIGH


title: Bladder cancer BT211

description: Bladder cancer BT211


title: I-Thy 010


title: Bladder cancer BT213

description: Bladder cancer BT213


title: Bladder cancer BT252

description: Bladder cancer BT252


title: Bladder cancer BT110

description: Bladder cancer BT110


title: I-Thy 016B


title: Bladder cancer BT91

description: Bladder cancer BT91


title: I-Thy 009


title: Bladder cancer BT256

description: Bladder cancer BT256


title: I-Thy 006


title: I-Thy 017A


title: Bladder cancer BT177

description: Bladder cancer BT177


title: Bladder cancer BT210

description: Bladder cancer BT210


title: Bladder cancer BT127

description: Bladder cancer BT127


title: Bladder cancer BT143

description: Bladder cancer BT143


title: Bladder cancer BT279

description: Bladder cancer BT279


title: Bladder cancer BT222

description: Bladder cancer BT222


title: I-Thy 008


title: I-Thy 049


title: I-Thy 034B


title: Control bladder C51

description: Control bladder C51

source_name: control bladder

value: Control bladder tissue


title: Control bladder C29

description: Control bladder C29


title: Control bladder C40

description: Control bladder C40


title: Bladder cancer BT144

description: Bladder cancer BT144


title: Control bladder C41

description: Control bladder C41


title: D-Glutamate-1

city: Atlanta

first: CHun-Kai

last: Yang

state: GA

address: 166 Jesse Hill Jr. Dr.

institute: Georgia state University

description: Pseudomonas aeruginosa PAO1 with amino acids.

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1 at log phase, D-Glutamate

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

growth_protocol: Pseudomonas aeruginosa PAO1 cells were grown in minimal medium P supplemented with 20mM L-glu at 37°C with vigorous shaking in flasks. Overnight cultures were diluted 100-fold in fresh pre-warmed medium with different amino acids and samples were collected at indicated time points.

extract_protocol: Total RNA was extracted by method provided by Qiagen and Qiagen RNeasy kit was used for total RNA extraction.

treatment_protocol: Cells were centrifuged at 1,3000rpm and pellets were kept at -80C for further extraction.

tag: Stage

tag: amino acid

value: D-Glutamate


title: Control bladder C45

description: Control bladder C45


title: L-Arginine-2

source_name: Pseudomonas aeruginosa PAO1 at log phase, L-Arginine

value: L-Arginine


title: D-Glutamate-2


title: L-Glutamate-1

source_name: Pseudomonas aeruginosa PAO1 at log phase, L-Glutamate

value: L-Glutamate


title: Control bladder C17

description: Control bladder C17


title: L-Arginine-1


title: L-Glutamate-2


title: SCC23/MET/Scrsh

city: Los angeles

first: Xiangming

last: Ding

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

description: Gene expression data in SCC23/MET infected with control virus

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix human Genome 133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Bioconductor and R language were used for pre-processing the two hybridizations. The robust multi-array analysis(RMA) was used for bacjground adjustment,normalization and log2 transformation of the signal intensity

source_name: Scramble shRNA control

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

growth_protocol: Cells were grown in humidified 5% CO2 incubator in DMEM supplemented with 10% FBS

extract_protocol: Rneasy kit (Qiagen) extraction of total RNA was performed according to the manufacture's protocol

tag: knockdown

value: scramble shRNA


title: SCC23/MET/KDM4Ash

description: Gene expression data in SCC23/MET infected with KDM4A knockdown virus

source_name: KDM4A knockdown

value: KDM4A shRNA


title: T-cell- h-H2O2 -H

city: Anderlecht

first: Maxime

last: Tarabichi

state: Bruxelles

address: Route de Lennik 808

country: Belgium

institute: IRIBHM

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: R/Bioconductor : RMA (Irizarry et al., 2003).

source_name: T-cells, high H2O2, H

label_protocol: Standard Affymetrix protocol.

growth_protocol:
Thyrocytes and matched T-cells were obtained from people undergoing total or partial thyroidectomy for non-cancerous thyroid pathologies. Protocols complied with the ethical rules of the Université Libre de Bruxelles and received approval from the institutional ethics committee.
Human primary thyroid cells were prepared and incubated as previously described (Roger et al. 1988). They were extracted from the 'healthy' thyroid tissue of people undergoing total or partial thyroidectomy for non-cancerous thyroid pathologies. The cells were used 5 days after isolation and cultured in specially adapted medium (half Dulbecco's Modified Eagle Medium (Gibco, Invitrogen, Merelbeke, Belgium), one quarter F-12 Nutrient Mixture (Ham) (Gibco) and one quarter MCDB 104 medium (Gibco) with an added 1 mM sodium pyruvate (Gibco), 5.625 µg insulin/ml (Sigma-Aldrich, St. Louis, MO, USA), 40 µg ascorbic acid/ml (Sigma-Aldrich), 2.5 µg Amphotericin B/ml (Gibco) and 100 U penicillin and 100 µg streptomycin/ml (Gibco)). All thyroid cell experiments were performed in this medium and at 50.000 – 250.000 cells/ml.
Human primary T-cells were prepared from the fresh blood of healthy volunteers and of people undergoing total or partial thyroidectomy for non-cancerous thyroid pathologies. A detailed protocol for T-cell isolation can be found in the Supplementary Information of the manuscript. In brief, the blood was submitted to a Lymphoprep (Axis Shield, Oslo, Norway) gradient in order to isolate the peripheral mononuclear cells. T-cells were isolated by negative selection with a Pan T-cell Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Propidium iodide (Sigma-Aldrich) and FITC anti-human CD3 (BD Pharmingen, BD Biosciences, Erembodegem, Belgium) staining confirmed a viability and purity of approximately 95%. The cells were used immediately after isolation and cultured in specially adapted medium (RPMI 1640 25mM HEPES with an added 10% decomplemented Fetal Bovine Serum, 0.05 mg gentamycin/ml, 0.05 mM 2-mercaptoethanol, 1 mM sodium pyruvate and 2 mM glutamine (all from Gibco)). All T-cell experiments were performed in this medium and at 1x10^6 cells/ml.

extract_protocol: Total RNA was extracted and purified from primary thyroid and T-cells, 4 hours after treatment with radiation or H2O2, by use of the TRI Reagent (Ambion, Austin, TX, USA) and the RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol:
H2O2: H2O2 (Merck Chemicals, Nottingham, UK) dilutions were prepared in culture medium immediately before use. Cells were incubated with H2O2 (0.0025–0.3mM) for 15 minutes.
Irradiation: Cells were exposed to a single dose of γ-irradiation from a Cesium137 source at a dose rate of 2 Gy/min. DL-Buthionine-[S,R]-sulfoximine. Cells were pre-incubated overnight with DL-Buthionine-[S,R]-sulfoximine (Sigma-Aldrich).

tag: patient id

value: H

tag: cells type

value: primary T-cells

tag: treatment

value: high H2O2

tag: Sex

tag: age (years)

tag: pathology

value: isolated cold nodule

tag: date of blood test (dmy)

tag: comet

tag: experiment

tag: purity

tag: cell count

tag: anti-tpo

tag: anti-tg

tag: tsi


title: T-cell- rad -H

source_name: T-cells, radiation, H

value: radiation

value: F


title: Thyroid- h-H2O2 -H

source_name: thyroid cells, high H2O2, H

value: primary thyroid cells


title: T-cell- l-H2O2 -H

source_name: T-cells, low H2O2, H

value: low H2O2


title: Thyroid- ctl -H

source_name: thyroid cells, control, H


title: Thyroid- rad -H

source_name: thyroid cells, radiation, H


title: T-cell- rad -G

source_name: T-cells, radiation, G

value: G

value: multinodular goiter


title: Thyroid- l-H2O2 -H

source_name: thyroid cells, low H2O2, H


title: T-cell- ctl -H

source_name: T-cells, control, H


title: T-cell- h-H2O2 -G

source_name: T-cells, high H2O2, G


title: T-cell- ctl -G

source_name: T-cells, control, G


title: Thyroid- h-H2O2 -G

source_name: thyroid cells, high H2O2, G


title: Bladder cancer BT172

description: Bladder cancer BT172

source_name: non-muscle invasive bladder cancer

tag: tissue

value: non-muscle invasive bladder cancer

tag: tnm stage

tag: grade

value: LOW

tag: overall survival (1

value: survival, 2:death):1

tag: survival time (month)


title: Thyroid- rad -G

source_name: thyroid cells, radiation, G

tag: patient id

tag: cells type

tag: treatment


title: Thyroid- ctl -G

source_name: thyroid cells, control, G

tag: Sex

tag: age (years)

tag: pathology


title: T-cell- rad -F

source_name: T-cells, radiation, F

value: Graves' disease

tag: date of blood test (dmy)

tag: comet

tag: experiment


title: Thyroid- l-H2O2 -G

source_name: thyroid cells, low H2O2, G

tag: purity

tag: cell count

tag: anti-tpo


title: T-cell- l-H2O2 -G

source_name: T-cells, low H2O2, G

tag: anti-tg

tag: tsi


title: T-cell- l-H2O2 -F

source_name: T-cells, low H2O2, F


title: Thyroid- rad -F

source_name: thyroid cells, radiation, F


title: T-cell- ctl -F

source_name: T-cells, control, F


title: T-cell- h-H2O2 -F

source_name: T-cells, high H2O2, F


title: T-cell- rad -E

source_name: T-cells, radiation, E

value: E

value: M

value: Isolated cold nodule


title: Thyroid- l-H2O2 -F

source_name: thyroid cells, low H2O2, F


title: Thyroid- ctl -F

source_name: thyroid cells, control, F


title: T-cell- l-H2O2 -E

source_name: T-cells, low H2O2, E


title: Thyroid- h-H2O2 -E

source_name: thyroid cells, high H2O2, E


title: T-cell- h-H2O2 -E

source_name: T-cells, high H2O2, E


title: T-cell- h-H2O2 -D

source_name: T-cells, high H2O2, D

value: D


title: T-cell- ctl -E

source_name: T-cells, control, E

value: primary T-cells


title: Thyroid- h-H2O2 -F

source_name: thyroid cells, high H2O2, F

value: high H2O2


title: Thyroid- ctl -E

source_name: thyroid cells, control, E


title: T-cell- rad -C

source_name: T-cells, radiation, C

value: C

value: multinodular thyroid


title: T-cell- h-H2O2 -C

source_name: T-cells, high H2O2, C

value: F


title: Thyroid- rad -C

source_name: thyroid cells, radiation, C

value: primary thyroid cells

value: radiation


title: T-cell- ctl -C

source_name: T-cells, control, C


title: T-cell- l-H2O2 -C

source_name: T-cells, low H2O2, C

value: low H2O2


title: Thyroid- l-H2O2 -C

source_name: thyroid cells, low H2O2, C


title: T-cell- l-H2O2 -D

source_name: T-cells, low H2O2, D

value: multinodular goiter


title: Thyroid- ctl -C

source_name: thyroid cells, control, C


title: Thyroid- h-H2O2 -D

source_name: thyroid cells, high H2O2, D


title: T-cell- ctl -D

source_name: T-cells, control, D


title: Thyroid- l-H2O2 -D

source_name: thyroid cells, low H2O2, D


title: Thyroid- rad -E

source_name: thyroid cells, radiation, E


title: T-cell- rad -D

source_name: T-cells, radiation, D


title: Thyroid- l-H2O2 -E

source_name: thyroid cells, low H2O2, E


title: Thyroid- h-H2O2 -C

source_name: thyroid cells, high H2O2, C


title: Thyroid- ctl -D

source_name: thyroid cells, control, D


title: T-cell- rad -B

source_name: T-cells, radiation, B

value: B


title: Thyroid- rad -D

source_name: thyroid cells, radiation, D


title: T-cell- ctl -B

source_name: T-cells, control, B


title: T-cell- l-H2O2 -B

source_name: T-cells, low H2O2, B


title: Thyroid- rad -B

source_name: thyroid cells, radiation, B


title: T-cell- h-H2O2 -B

source_name: T-cells, high H2O2, B


title: T-cell- rad -A

source_name: T-cells, radiation, A

value: A


title: Thyroid- l-H2O2 -B

source_name: thyroid cells, low H2O2, B


title: T-cell- h-H2O2 -A

source_name: T-cells, high H2O2, A


title: Thyroid- h-H2O2 -A

source_name: thyroid cells, high H2O2, A


title: Thyroid- h-H2O2 -B

source_name: thyroid cells, high H2O2, B


title: T-cell- l-H2O2 -A

source_name: T-cells, low H2O2, A


title: replication set 118

city: Boston

first: Jong-Min

last: Lee

department: CHGR

institute: MGH

description:
R6-7_E04.9798.32.M
Gene expression data from embryonic stem cells without Hdh

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: gcRMA

source_name: Human lymphoblastoid cell line

label_protocol: Affymetrix protocol

growth_protocol: Standard growth condition for human lymphoblastoid cell lines

extract_protocol: Trizol extraction and Qiagen Rneasy mini coulmn clean up

tag: gender

value: male

tag: htt cag repeat length (longer allele)

tag: batch


title: replication set 111

description:
R6-19_B02.1730.47.F.O45
Gene expression data from embryonic stem cells without Hdh

value: female


title: T-cell- ctl -A

source_name: T-cells, control, A

tag: patient id

value: Graves' disease


title: replication set 112

description:
R6-2_E20.2930.55.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 120

description:
R6-9_B06.8138.39.F.O67
Gene expression data from embryonic stem cells without Hdh


title: replication set 119

description:
R6-8_E19.2916.23.M
Gene expression data from embryonic stem cells without Hdh


title: Thyroid- ctl -B

source_name: thyroid cells, control, B

tag: cells type

value: M


title: replication set 113

description:
R6-20_A11.10928.20.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 104

description:
R6-12_A10.10438.29.F
Gene expression data from embryonic stem cells without Hdh


title: Thyroid- rad -A

source_name: thyroid cells, radiation, A

tag: treatment


title: replication set 107

description:
R6-15_C22.21453.46.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 102

description:
R6-10_B01.334.41.M.O62
Gene expression data from embryonic stem cells without Hdh


title: replication set 114

description:
R6-3_E23.7498.43.M
Gene expression data from embryonic stem cells without Hdh


title: Thyroid- ctl -A

source_name: thyroid cells, control, A

tag: Sex


title: Thyroid- l-H2O2 -A

source_name: thyroid cells, low H2O2, A

tag: age (years)


title: replication set 110

description:
R6-18_C06.11321.42.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 116

description:
R6-5_E10.25436.38.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 103

description:
R6-11_D02.1188.46.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 106

description:
R6-14_D03.1154.48.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 109

description:
R6-17_A19.1714.53.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 105

description:
R6-13_B12.17300.51.F.Y25
Gene expression data from embryonic stem cells without Hdh


title: replication set 115

description:
R6-4_A07.21250.34.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 117

description:
R6-6_E17.25510.26.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 108

description:
R6-16_E18.1298.45.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 101

description:
R6-1_A08.21521.36.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 100

description:
R5-9_B06.8138.39.F.O67
Gene expression data from embryonic stem cells without Hdh


title: replication set 97

description:
R5-6_E17.25510.26.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 96

description:
R5-5_E10.25436.38.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 99

description:
R5-8_E19.2916.23.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 98

description:
R5-7_E04.9798.32.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 94

description:
R5-3_E23.7498.43.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 93

description:
R5-20_A11.10928.20.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 95

description:
R5-4_A07.21250.34.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 90

description:
R5-18_C06.11321.42.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 80

description:
R4-9_B06.8138.39.F.O67
Gene expression data from embryonic stem cells without Hdh


title: replication set 82

description:
R5-10_B01.334.41.M.O62
Gene expression data from embryonic stem cells without Hdh


title: replication set 79

description:
R4-8_E19.2916.23.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 83

description:
R5-11_D02.1188.46.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 81

description:
R5-1_A08.21521.36.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 84

description:
R5-12_A10.10438.29.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 71

description:
R4-19_B02.1730.47.F.O45
Gene expression data from embryonic stem cells without Hdh


title: replication set 88

description:
R5-16_E18.1298.45.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 85

description:
R5-13_B12.17300.51.F.Y25
Gene expression data from embryonic stem cells without Hdh


title: replication set 89

description:
R5-17_A19.1714.53.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 87

description:
R5-15_C22.21453.46.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 86

description:
R5-14_D03.1154.48.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 91

description:
R5-19_B02.1730.47.F.O45
Gene expression data from embryonic stem cells without Hdh


title: replication set 75

description:
R4-4_A07.21250.34.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 77

description:
R4-6_E17.25510.26.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 92

description:
R5-2_E20.2930.55.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 78

description:
R4-7_E04.9798.32.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 74

description:
R4-3_E23.7498.43.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 76

description:
R4-5_E10.25436.38.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 73

description:
R4-20_A11.10928.20.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 68

description:
R4-16_E18.1298.45.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 72

description:
R4-2_E20.2930.55.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 70

description:
R4-18_C06.11321.42.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 69

description:
R4-17_A19.1714.53.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 59

description:
R3-8_E19.2916.23.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 67

description:
R4-15_C22.21453.46.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 64

description:
R4-12_A10.10438.29.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 62

description:
R4-10_B01.334.41.M.O62
Gene expression data from embryonic stem cells without Hdh


title: replication set 65

description:
R4-13_B12.17300.51.F.Y25
Gene expression data from embryonic stem cells without Hdh


title: replication set 66

description:
R4-14_D03.1154.48.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 61

description:
R4-1_A08.21521.36.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 63

description:
R4-11_D02.1188.46.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 51

description:
R3-19_B02.1730.47.F.O45
Gene expression data from embryonic stem cells without Hdh


title: replication set 60

description:
R3-9_B06.8138.39.F.O67
Gene expression data from embryonic stem cells without Hdh


title: replication set 57

description:
R3-6_E17.25510.26.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 54

description:
R3-3_E23.7498.43.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 47

description:
R3-15_C22.21453.46.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 55

description:
R3-4_A07.21250.34.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 56

description:
R3-5_E10.25436.38.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 53

description:
R3-20_A11.10928.20.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 43

description:
R3-11_D02.1188.46.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 42

description:
R3-10_B01.334.41.M.O62
Gene expression data from embryonic stem cells without Hdh


title: replication set 45

description:
R3-13_B12.17300.51.F.Y25
Gene expression data from embryonic stem cells without Hdh


title: replication set 39

description:
R2-8_E19.2916.23.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 46

description:
R3-14_D03.1154.48.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 52

description:
R3-2_E20.2930.55.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 48

description:
R3-16_E18.1298.45.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 49

description:
R3-17_A19.1714.53.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 44

description:
R3-12_A10.10438.29.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 58

description:
R3-7_E04.9798.32.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 41

description:
R3-1_A08.21521.36.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 50

description:
R3-18_C06.11321.42.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 40

description:
R2-9_B06.8138.39.F.O67
Gene expression data from embryonic stem cells without Hdh


title: replication set 38

description:
R2-7_E04.9798.32.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 37

description:
R2-6_E17.25510.26.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 33

description:
R2-20_A11.10928.20.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 29

description:
R2-17_A19.1714.53.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 32

description:
R2-2_E20.2930.55.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 31

description:
R2-19_B02.1730.47.F.O45
Gene expression data from embryonic stem cells without Hdh


title: replication set 30

description:
R2-18_C06.11321.42.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 28

description:
R2-16_E18.1298.45.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 25

description:
R2-13_B12.17300.51.F.Y25
Gene expression data from embryonic stem cells without Hdh


title: replication set 35

description:
R2-4_A07.21250.34.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 34

description:
R2-3_E23.7498.43.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 22

description:
R2-10_B01.334.41.M.O62
Gene expression data from embryonic stem cells without Hdh


title: ECL001_EMC_3hr_3

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: US93503719_251485073373_S01_GE1_107_Sep09_1_3.txt

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.
Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages (R v.2.12.2 (2011-02-25)). Replicate probes were mean summarized, and all probes were required to pass Agilent QC flags for all replicates of at least one infected time point.

growth_protocol: Calu-3 2B4 cells, a clonal population of Calu-3 cells sorted for ACE2 expression, were grown in MEM (Gibco) supplemented with 20% fetal bovine serum (Hyclone) and 1% antibiotic antimycotic (Gibco). Viral titrations and propagation HCoV-EMC were performed in VeroE6 cells using standard methods.   Human Coronavirus EMC 2012 (HCoV-EMC) was received from Bart L. Haagmans, Erasmus Medical Center, Rotterdam, Netherlands via MTA. Experiments with SARS-CoV were previously performed in the same conditions using the same cells.

extract_protocol: At indicated time points, triplicate wells of mock-infected or virus-infected Calu-3 2B4 monolayers were washed with 5 ml cold phosphate buffered saline (PBS) and lysed directly with 1 ml of TRIzol (Invitrogen) according to the manufacturer’s recommendation, and resulting lysates were stored at -80°C until further processing.  All Trizol lysates were processed simultaneously:  they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for quantitative real-time PCR (qPCR) and microarray analyses.

treatment_protocol: For RNA isolation, Calu-3 2B4 cells were seeded in 6-well plates (1 x 10^6 cells/well) two days prior to infection.  Immediately preceding infection, monolayers were washed three times with fresh media and inoculated with virus at an MOI of 5 in PBS for 40 minutes at 37°C.  Mock-infected controls were inoculated with PBS only.

tag: cell type

value: Calu-3 2B4 cells

tag: infected with

value: Human Coronavirus EMC 2012 (HCoV-EMC)

tag: time point

value: 3 hpi

tag: biological replicate


title: ECL001_EMC_7hr_1

description: US93503719_251485073373_S01_GE1_107_Sep09_1_2.txt

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

value: 7 hpi


title: replication set 26

description:
R2-14_D03.1154.48.M
Gene expression data from embryonic stem cells without Hdh


title: ECL001_Mock_7hr_1

description: US93503719_251485073371_S01_GE1_107_Sep09_1_4.txt

value: Mock


title: replication set 23

description:
R2-11_D02.1188.46.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 17

description:
R1-6_E17.25510.26.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 24

description:
R2-12_A10.10438.29.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 20

description:
R1-9_B06.8138.39.F.O67
Gene expression data from embryonic stem cells without Hdh


title: replication set 21

description:
R2-1_A08.21521.36.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 27

description:
R2-15_C22.21453.46.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 19

description:
R1-8_E19.2916.23.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 18

description:
R1-7_E04.9798.32.M
Gene expression data from embryonic stem cells without Hdh


title: ECL001_EMC_18hr_1

description: US93503719_251485073373_S01_GE1_107_Sep09_1_1.txt

value: 18 hpi


title: ECL001_Mock_3hr_3

description: US93503719_251485073372_S01_GE1_107_Sep09_1_3.txt


title: replication set 16

description:
R1-5_E10.25436.38.M
Gene expression data from embryonic stem cells without Hdh


title: ECL001_EMC_7hr_3

description: US93503719_251485073371_S01_GE1_107_Sep09_1_2.txt


title: ECL001_EMC_18hr_2

description: US93503719_251485073371_S01_GE1_107_Sep09_1_3.txt


title: replication set 13

description:
R1-20_A11.10928.20.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 15

description:
R1-4_A07.21250.34.M
Gene expression data from embryonic stem cells without Hdh


title: ECL001_Mock_12hr_2

description: US93503719_251485073370_S01_GE1_107_Sep09_1_4.txt

value: 12 hpi


title: replication set 10

description:
R1-18_C06.11321.42.F
Gene expression data from embryonic stem cells without Hdh


title: ECL001_Mock_3hr_1

description: US93503719_251485073372_S01_GE1_107_Sep09_1_2.txt


title: replication set 9

description:
R1-17_A19.1714.53.M
Gene expression data from embryonic stem cells without Hdh


title: replication set 12

description:
R1-2_E20.2930.55.F
Gene expression data from embryonic stem cells without Hdh


title: ECL001_EMC_18hr_3

description: US93503719_251485073370_S01_GE1_107_Sep09_1_3.txt


title: replication set 11

description:
R1-19_B02.1730.47.F.O45
Gene expression data from embryonic stem cells without Hdh


title: replication set 8

description:
R1-16_E18.1298.45.F
Gene expression data from embryonic stem cells without Hdh


title: ECL001_Mock_0hr_1

description: US93503719_251485073370_S01_GE1_107_Sep09_1_2.txt

value: 0 hpi


title: replication set 14

description:
R1-3_E23.7498.43.M
Gene expression data from embryonic stem cells without Hdh


title: ECL001_EMC_24hr_1

description: US93503719_251485073369_S01_GE1_107_Sep09_1_1.txt

value: 24 hpi


title: replication set 7

description:
R1-15_C22.21453.46.F
Gene expression data from embryonic stem cells without Hdh


title: replication set 6

description:
R1-14_D03.1154.48.M
Gene expression data from embryonic stem cells without Hdh


title: ECL001_EMC_12hr_3

description: US93503719_251485073368_S01_GE1_107_Sep09_1_2.txt


title: ECL001_EMC_0hr_1

description: US93503719_251485073369_S01_GE1_107_Sep09_1_3.txt


title: ECL001_EMC_12hr_2

description: US93503719_251485073369_S01_GE1_107_Sep09_1_2.txt


title: ECL001_Mock_0hr_3

description: US93503719_251485073371_S01_GE1_107_Sep09_1_1.txt


title: ECL001_Mock_7hr_3

description: US93503719_251485073368_S01_GE1_107_Sep09_1_3.txt


title: ECL001_Mock_24hr_1

description: US93503719_251485073368_S01_GE1_107_Sep09_1_1.txt


title: replication set 5

description:
R1-13_B12.17300.51.F.Y25
Gene expression data from embryonic stem cells without Hdh


title: FOXP1 ChIP-on-chip in OCI-Ly1 cells, replicate 2

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra

description: ChIP-on-chip performed in OCI-Ly1 cells with anti-FOXP1 antibody (ab 16645)

hyb_protocol: standard NimbleGen protocol

scan_protocol: standard NimbleGen protocol

data_processing: Take all the probes in promoter regions and perform Log2 transformation of the ratio ChIP/INPUT (Cy5/Cy3). Then use the maximal summary of three connected probes as the bound intensity of the promoter. The detailed analysis method (script) was published in Ci et al. Blood, 2009 May 28;113(22):5536-48 (PMID 19307668).

source_name: OCI-Ly1 Diffuse large B-cell lymphoma cell line

label_protocol: standard NimbleGen protocol

growth_protocol: Cells were cultured in IMDM (Iscove's Modified Dulbecco's Medium) medium supplemented with 10% human serum and 1% penicillin-streptomycin

extract_protocol: Input: sonicated genomic DNA, and then purified by Qiagen column. ChIP: chromatin IP products corresponding to genomic regions bound by FOXP1, and then purified by Qiagen column.

treatment_protocol: Not treatment

tag: sample type

value: FOXP1 OCI-Ly1 ChIP

tag: cell line

tag: chip antibody

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #

value: Input


title: replication set 3

description:
R1-11_D02.1188.46.M
Gene expression data from embryonic stem cells without Hdh

tag: gender


title: replication set 1

description:
R1-1_A08.21521.36.M
Gene expression data from embryonic stem cells without Hdh

tag: htt cag repeat length (longer allele)


title: replication set 4

description:
R1-12_A10.10438.29.F
Gene expression data from embryonic stem cells without Hdh

tag: batch


title: ECL001_Mock_7hr_2

description: US93503719_251485073367_S01_GE1_107_Sep09_1_3.txt


title: discovery set 107

description:
E24.9484.30.M
Gene expression data from embryonic stem cells without Hdh

value: E


title: ECL001_EMC_3hr_1

description: US93503719_251485073367_S01_GE1_107_Sep09_1_1.txt


title: ECL001_Mock_12hr_3

description: US93503719_251485073367_S01_GE1_107_Sep09_1_2.txt


title: replication set 2

description:
R1-10_B01.334.41.M.O62
Gene expression data from embryonic stem cells without Hdh

value: male


title: ECL001_Mock_24hr_3

description: US93503719_251485073366_S01_GE1_107_Sep09_1_4.txt


title: discovery set 106

description:
E23.7498.43.M
Gene expression data from embryonic stem cells without Hdh


title: ECL001_Mock_24hr_2

description: US93503719_251485073367_S01_GE1_107_Sep09_1_4.txt


title: FOXP1 ChIP-on-chip in OCI-Ly1 cells, replicate 3


title: discovery set 104

description:
E21.1308.46.F
Gene expression data from embryonic stem cells without Hdh

value: female


title: ECL001_EMC_24hr_3

description: US93503719_251485073366_S01_GE1_107_Sep09_1_3.txt


title: ECL001_EMC_3hr_2

description: US93503719_251485073365_S01_GE1_107_Sep09_1_4.txt


title: discovery set 102

description:
E19.2916.23.M
Gene expression data from embryonic stem cells without Hdh


title: ECL001_EMC_0hr_2

description: US93503719_251485073365_S01_GE1_107_Sep09_1_2.txt


title: ECL001_Mock_3hr_2

description: US93503719_251485073365_S01_GE1_107_Sep09_1_3.txt


title: ECL001_EMC_7hr_2

description: US93503719_251485073366_S01_GE1_107_Sep09_1_2.txt


title: FOXP1 ChIP-on-chip in OCI-Ly1 cells, replicate 1

description: ChIP-on-chip performed in OCI-Ly1 cells with anti-FOXP1 antibody (ab 16645)


title: replication set 36

description:
R2-5_E10.25436.38.M
Gene expression data from embryonic stem cells without Hdh


title: ECL001_EMC_24hr_2

description: US93503719_251485073364_S01_GE1_107_Sep09_1_4.txt


title: ECL001_Mock_0hr_2

description: US93503719_251485073365_S01_GE1_107_Sep09_1_1.txt


title: ECL001_EMC_0hr_3

description: US93503719_251485073364_S01_GE1_107_Sep09_1_2.txt


title: discovery set 103

description:
E20.2930.55.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 99

description:
E16.17483.25.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 100

description:
E17.25510.26.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 97

description:
E14.1235.22.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 101

description:
E18.1298.45.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 105

description:
E22.2920.46.F
Gene expression data from embryonic stem cells without Hdh


title: ECL001_Mock_12hr_1

description: US93503719_251485073364_S01_GE1_107_Sep09_1_1.txt


title: discovery set 98

description:
E15.4017.59.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 95

description:
E12.5164.50.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 93

description:
E10.25436.38.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 96

description:
E13.9664.29.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 94

description:
E11.25540.17.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 91

description:
E08.2998.21.M
Gene expression data from embryonic stem cells without Hdh


title: ß-catenin null Eα, biological rep 3

city: Vancouver

first: Annaick

last: Carles

state: BC

address: 2125 East Mall

institute: University of British Columbia

description:
b-cat -/-_Ea_3
Gene expression data from embryonic stem cells devoid of b-catenin stably expressing an E-cadherin-a-catenin fusion construct

hyb_protocol: Hybridization was performed for 17h at 45C in Affymetrix genechip hybridization oven 640. Chips were washed and stained in the Affymetrix Fluidics Station FS450

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000 7G

data_processing:
CEL files were generated by AGCC 1.0 (Command Console) from Affymetrix. Processing and data analysis was done in R programming environment using Bioconductor.
R version is 2.15.0 and Bioconductor version is 2.10. The R package 'oligo' was used for RMA normalization: oligo_1.20.4 (oligoClasses_1.18.0).

source_name: ß-catenin null embryonic stem cells stably transfected with an E-cadherin-α-catenin fusion protein

label_protocol: Samples were processed according to the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay, Biotin Labeling

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates under standard conditions (DMEM supplemented with 15% FCS and 1000 U/ml LIF).

extract_protocol: Total RNA was prepared using the Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells were cultured to sub-confluence and collected by centrifugation prior to RNA extraction.

tag: strain background

value: a mixed background S129S6-C57BL/6

value: mouse embryonic stem cells

tag: genotype

value: Deletion of both ß-catenin alleles, expression of an E-cadherin-α-catenin construct


title: ß-catenin null Eα, biological rep 1

description:
b-cat -/-_Ea_1
Gene expression data from embryonic stem cells devoid of b-catenin stably expressing an E-cadherin-a-catenin fusion construct


title: ß-catenin null, biological rep 3

description:
b-cat -/-_3
Gene expression data from embryonic stem cells devoid of b-catenin

source_name: ß-catenin null embryonic stem cells

value: Deletion of both ß-catenin alleles


title: ß-catenin null, biological rep 2

description:
b-cat -/-_2
Gene expression data from embryonic stem cells devoid of b-catenin


title: discovery set 92

description:
E09.11383.18.F
Gene expression data from embryonic stem cells without Hdh


title: ß-catenin null Eα, biological rep 2

description:
b-cat -/-_Ea_2
Gene expression data from embryonic stem cells devoid of b-catenin stably expressing an E-cadherin-a-catenin fusion construct


title: ß-catenin null, biological rep 1

description:
b-cat -/-_1
Gene expression data from embryonic stem cells devoid of b-catenin


title: discovery set 89

description:
E06.15233.65.M
Gene expression data from embryonic stem cells without Hdh


title: ß-catenin flox/-, biological rep 1

description:
b-cat flox/-_1
Gene expression data from b-catenin flox/- embryonic stem cells (Control cells)

source_name: ß-catenin flox/- embryonic stem cells

value: Deletion of one allele of ß-catenin, the other allele is floxed


title: Colon_heme_pool_day7

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

source_name: pool of colon RNA of n=4 heme fed mice at timepoint 7 days (after a run in of 1 week on control diet (40en% fat))

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: C57BL/6J mice were purchased from Harlan (Horst, the Netherlands), and housed in a light and temperature-controlled animal facility of Wageningen University (12:12 h light/dark cycle, 20±2 °C). Mice had free access to feed and water.

extract_protocol: Total RNA was prepared from colonic scapings using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For array analysis, RNA of 3-4 mice per group was subsequently pooled.

treatment_protocol: Mice were put on a run in control diet (40en% fat) for 1 week. After that, mice received the diet with or without heme for 0, 2, 4, 7, or 14 days. There were 4 mice per group, except for the control group at day 2 in which 1 mouse died. Mice were sacrificed, colons removed and cleaned from any mesenteric fat that was present. Next colons were cut open longitudinally, washed in PBS, and epithelial cells were scraped off.

tag: backgroud

tag: age

value: 9-11 weeks

tag: tissue

value: colon

tag: diet

value: control diet (40en% fat) with heme

tag: timepoint

value: 7 days


title: Colon_heme_pool_day4

source_name: pool of colon RNA of n=4 heme fed mice at timepoint 4 days (after a run in of 1 week on control diet (40en% fat))

value: 4 days


title: ß-catenin flox/-, biological rep 2

description:
b-cat flox/-_2
Gene expression data from b-catenin flox/- embryonic stem cells (Control cells)

tag: cell type


title: discovery set 85

description:
E02.15457.67.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 88

description:
E05.7526.27.F
Gene expression data from embryonic stem cells without Hdh


title: Colon_heme_pool_day14

source_name: pool of colon RNA of n=4 heme fed mice at timepoint 14 days (after a run in of 1 week on control diet (40en% fat))

value: 14 days


title: discovery set 90

description:
E07.1069.15.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 87

description:
E04.9798.32.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 86

description:
E03.1194.47.M
Gene expression data from embryonic stem cells without Hdh


title: Colon_control_pool_day4

source_name: pool of colon RNA of n=4 control mice at timepoint 4 days (after a run in of 1 week on control diet (40en% fat))

value: control diet (40en% fat) without heme


title: Colon_control_pool_day2

source_name: pool of colon RNA of n=3 control mice at timepoint 2 days (after a run in of 1 week on control diet (40en% fat))

value: 2 days


title: Colon_control_pool_day7

source_name: pool of colon RNA of n=4 control mice at timepoint 7 days (after a run in of 1 week on control diet (40en% fat))


title: Colon_control_pool_day14

source_name: pool of colon RNA of n=4 control mice at timepoint 14 days (after a run in of 1 week on control diet (40en% fat))


title: discovery set 83

description:
D24.176.48.F
Gene expression data from embryonic stem cells without Hdh

source_name: Human lymphoblastoid cell line

value: D


title: discovery set 80

description:
D20.636.43.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 82

description:
D23.1103.29.F
Gene expression data from embryonic stem cells without Hdh


title: Colon_heme_pool_day2

source_name: pool of colon RNA of n=4 heme fed mice at timepoint 2 days (after a run in of 1 week on control diet (40en% fat))


title: discovery set 84

description:
E01.2018.38.M
Gene expression data from embryonic stem cells without Hdh

value: E


title: discovery set 81

description:
D22.634.15.F
Gene expression data from embryonic stem cells without Hdh


title: ß-catenin flox/-, biological rep 3

description:
b-cat flox/-_3
Gene expression data from b-catenin flox/- embryonic stem cells (Control cells)


title: Colon_control_pool_day0

source_name: pool of colon RNA of n=4 control mice at timepoint 0 (after a run in of 1 week on control diet (40en% fat))

value: male


title: Id2fl/fl LckCre+ Repl3

city: Parkville

first: Moshe

last: Olshansky

state: Victoria

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter & Eliza Hall Institute of Medical Research

description: SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was background corrected, quantile normalised and log2 transformed (with shift = 16) using neqc function from limma package (v.3.14.4) in R /Bioconductor (v.2.15.2).

source_name: Id2fl/flLckCre+ DbNP366-specific CD8+ T cells

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

extract_protocol: RNA was extracted using a Qiagen RNeasy Mini Kit followed by DNase treatment. Quality control was performed with Agilent Bioanalyser.

tag: genotype/variation

value: Id2fl/fl LckCre+

value: Spleen

value: Db-NP366 specific CD8+ T cells


title: Id2fl/fl LckCre+ Repl2

description: SAMPLE 5


title: Id2fl/fl LckCre+ Repl1

description: SAMPLE 4


title: discovery set 79

description:
D19.21330.38.F
Gene expression data from embryonic stem cells without Hdh

value: female


title: Wild-type Repl3

description: SAMPLE 3

source_name: Wild-type DbNP366-specific CD8+ T cells

value: B6.SJL-Ptprca Pepcb/BoyJ

value: Wild-type


title: Id2-GFPhigh Repl2

description: SAMPLE 5

source_name: Purified Id2-GFPhigh DbNP366-specific CD8+ T cells

extract_protocol: RNA was extracted using a Qiagen RNeasy Mini Kit followed by DNase treatment . Quality control was performed with Agilent Bioanalyser.

tag: levels of gfp

value: high


title: discovery set 76

description:
D16.1121.17.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 77

description:
D17.148.20.F
Gene expression data from embryonic stem cells without Hdh