title: A96 vs a96_Sample 16

description: dye-swap


title: a60 vs a36-2_Sample 11

status: Public on Jun 06 2011

type: RNA

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

country: USA

institute: Yale University

description: dye-swap

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers (53°C water bath). After hybridization, slides were washed sequentially

scan_protocol: Hybridized microarrays were scanned and gridded with a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA)

data_processing: Normalized by background-subtracted mean-by-mean normalization of well measured spots, and statistically analyzed using a Bayesian analysis of gene expression levels with BAGEL software.

molecule: total RNA

organism: Neurospora crassa

source_name: myceilia

label_protocol: 2 µg of mRNA were primed with .5 µl of 10 µM MTP or Oligo-d(T) primer at 70°C for 10min, then reversed transcribed at 42°C for 2h in the presence of 40 U SuperScript II RTase (Invitrogen), and .8ul Amino-allyl dUTP/dNTP made from Sigma in mg aliquotes and dissolved in 20µl H2O-(DEPC) and mixed with 30µl of 100mM dATP, dTTP, dGTP, dCTP and 12µl 100mM dTTP;  25 µM Cy3/Cy5-label

growth_protocol: Bird media, room temperature

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

treatment_protocol: constant light

tag: strain

value: mat-a FGSC 4200

tag: developmental stage (culture time)


title: Digestive_gland_Dec/Nov_rep3

city: Alessandria

first: Francesco

last: Dondero

address: Via Michel 11

department: Department of Environmental and Life Sciences

country: Italy

institute: University of Piemonte Orientale "Amedeo Avogadro"

description: loop design representing month n+1 / month n (example, Feb/Jan, Mar/Feb, April/March, etc.)

hyb_protocol: 43°C, 16/20 h, hybridization buffer Northern Max (Ambion). Pre-hybridization for 1h in same conditions.

scan_protocol: Scanned on Chip Reader (Bio-rad Laboratories) at 5 µm resolution

data_processing: Offset background subtracted, loess normalized. Data obtained from log2 of processed Ch1 signal / processed Ch2 signal. LIMMA software was used

organism: Mytilus galloprovincialis

source_name: digestive gland tissue, individual sampled on December 2007, Bizerta Lagoon, Tunisia

label_protocol: 15 µg of total RNA were primed with 0.5 µg oligodT(19)VN primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U ReverseAid MuLV H minus  RTase (Fermentas), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labeled dCTP or Cy5-label dCTP

extract_protocol: Total RNA extracted a the digestive gland of a single individual mussel using Trizol following manufacturer's instructions

tag: gender

value: female

tag: tissue

value: digestive gland

tag: date

tag: geographical location

value: Bizerta Lagoon, Tunisia

source_name: digestive gland tissue, individual sampled on November 2007, Bizerta Lagoon, Tunisia


title: Digestive_gland_Feb/Jan_rep3

source_name: digestive gland tissue, individual sampled on February 2008, Bizerta Lagoon, Tunisia

source_name: digestive gland tissue, individual sampled on January 2008, Bizerta Lagoon, Tunisia


title: Digestive_gland_Feb/Jan_rep4


title: Digestive_gland_Feb/Jan_rep1


title: a60 vs a36_Sample 9

description: dye-swap


title: A96 vs A36_Sample 6

description: dye-swap

value: mat A FGSC 2489


title: Digestive_gland_Feb/Jan_rep2


title: A60 vs A36_Sample 7

description: dye-swap


title: A36 vs A96_Sample 5

description: dye-swap


title: a36 vs a96_Sample 1

description: dye-swap


title: A36 vs A60_Sample 8

description: dye-swap


title: A36 vs a36_Sample 3

description: dye-swap


title: a36 vs A36_Sample 4

description: dye-swap


title: a96 vs a36_Sample 2

description: dye-swap


title: PolyA+ RNA from Skeletal Muscle_sense

status: Public on Jun 05 2011

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

institute: University of Ferrara

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: polyA RNA

organism: Homo sapiens

source_name: control Skeletal Muscle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: not applicable; three commercial poly A+ RNAs from normal human brain, heart and skeletal muscle tissues were utilised (Ambion).

tag: tissue type

value: Skeletal Muscle

tag: condition

value: normal tissue


title: PolyA+ RNA from Brain_sense

source_name: control Brain

value: Brain


title: PolyA+ RNA from Skin_sense

source_name: control Skin

value: Skin


title: PolyA+ RNA from Heart_sense

source_name: control Heart

value: Heart


title: Plus A3-Resting cells+IFN+Rv exosomes_rep1

city: Notre Dame

first: Erliang

last: Zeng

state: IN

address: 384 Fitzpatrick Hall

institute: University of Notre Dame

description:
Resting cells+IFN+Rv exosomes
This sample is of resting cells treated with Rv exosomes followed by IFN-γ. It is the first of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: 4 μg of Cy3-labeled cDNA from each group was hybridized onto Musmusculus 4672 Nimblegen microarray using Nimblegen Hybridization system 4 according to manufacturer’s instructions (Roche).

scan_protocol: Arrays were scanned and chip images were collected on a Nimblegen MS200 station running Nimblegen 1.0 software.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.).

organism: Mus musculus

source_name: Plus A3- Resting cells+IFN+Rv exosomes

label_protocol: Double stranded cDNA was synthesized using the Invitrogen Superscript Double-Stranded cDNA synthesis kit and was subsequently labeled using Nimblegen one color DNA labeling kit (Roche Nimblegen Inc. WI).

growth_protocol: Bone marrow derived macrophages (BMMØ) were isolated from 6–8 weeks old female C57BL6 mice and cultured in vitro as previously described [Roach et al. InfectImmun 70: 3040–3052]. The mouse macrophage cell line RAW 264.7 was maintained in RPMI supplemented with 10% fetal bovine serum, 10 mM sodium pyruvate and 25 mM HEPES. wild-type and the LspA-deficient H37Rv (kindly provided by Joel Ernst, NYU, New York) were each grown in Middlebrook 7H9 broth supplemented with OADC until mid logarithmic growth phase and frozen down as stocks in growth media plus 15% glycerol.

extract_protocol: Cells were harvested and RNA was isolated using RNeasy columns (Qiagen). Double stranded cDNA was synthesized using the Invitrogen Superscript Double-Stranded cDNA synthesis kit.

treatment_protocol: BMMØ were seeded in six well tissue culture plates and allowed to adhere for 24 hours. The cells were treated with exosomes isolated from uninfected and infected RAW cells at 10 μg/well for 18 hours. The media was removed and replenished with fresh media +/- recombinant mouse IFN-γ (eBioscience Inc. San Diego, CA) at 200 U for an additional  18 hours.

tag: cell type

value: Bone marrow derived macrophages (BMMØ)

tag: treatment

value: Rv exosomes

tag: agent

value: IFN-γ


title: Plus A4- Resting cells+IFN+H37Rv infection_rep1

description:
Resting cells+IFN+H37Rv infection
This sample is of resting cells infected with M.tb H37Rv followed by IFN-γ. It is the first of three biological replicates used in this experiment, each from separate cultures.

value: infected with M.tb H37Rv


title: Plus A4- Resting cells+IFN+H37Rv infection_rep3

description:
Resting cells+IFN+H37Rv infection
This sample is of resting cells infected with M.tb H37Rv followed by IFN-γ. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Plus A3-Resting cells+IFN+Rv exosomes_rep3

description:
Resting cells+IFN+Rv exosomes
This sample is of resting cells treated with Rv exosomes followed by IFN-γ. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Plus A4- Resting cells+IFN+H37Rv infection_rep2

description:
Resting cells+IFN+H37Rv infection
This sample is of resting cells infected with M.tb H37Rv followed by IFN-γ. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Plus A3-Resting cells+IFN+Rv exosomes_rep2

description:
Resting cells+IFN+Rv exosomes
This sample is of resting cells treated with Rv exosomes followed by IFN-γ. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Plus A2- Resting cells+IFN+Uninfected exosomes_rep3

description:
Resting cells+IFN+Uninfected exosomes
This sample is of resting cells treated with uninfected exosomes followed by IFN-γ. It is the third of three biological replicates used in this experiment, each from separate cultures.

value: uninfected exosomes


title: Plus A2- Resting cells+IFN+Uninfected exosomes_rep1

description:
Resting cells+IFN+Uninfected exosomes
This sample is of resting cells treated with uninfected exosomes followed by IFN-γ. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Plus A2- Resting cells+IFN+Uninfected exosomes_rep2

description:
Resting cells+IFN+Uninfected exosomes
This sample is of resting cells treated with uninfected exosomes followed by IFN-γ. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: DNA methylation of CpG island in HMEC

type: genomic

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

hyb_protocol: Labeled DNA mixed with cot-1 DNA and Agilent blocking solution was hybridized to microarray for 40 hours at 67℃ and 10 rpm rotation. Microarrays was washed according to Agilent protocol.

scan_protocol: The microarray was scanned with an Agilent G2565BA microarray scanner (Agilent Technologies).

data_processing: Scanned data was analyzed with Feature Extraction Ver.9.1 and normalized (Background subtraction) using Agilent G4477AA ChIP Analytics 1.3 software. Our original parameter, Me value was calculated using normalized log ratio and P[Xbar]. The Me value linearly correlates with the fraction of methylated DNA molecules in CpG islands in samples with various overall DNA methylation levels.

molecule: genomic DNA

source_name: Sonicated HMEC (lot. 0000092969) genomic DNA (WCE)

label_protocol: One μg of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).

extract_protocol: DNA lysis buffer plus proteinase K. Phenol/Chloroform extraction. Ethanol precipitation. RNase treatment.

tag: cell line

value: Normal human mammary epithelial cells, HMEC (lot. 0000092969)

tag: cell fraction

value: WCE

source_name: Sonicated HMEC (lot. 0000092969) genomic DNA (IP)

label_protocol: Five μg of genomic DNA was sonicated by a VP-5s homogenizer (TAITEC, Saitama, Japan). After heat denaturation, DNA was incubated with antibody against 5-methyl cytidine (Diagnode, Liége, Belgium) in 1 x IP buffer [10 mM Na-phosphate, pH 7.0, 140 mM NaCl, 0.05 % (w/v) Triton X-100] at 4ºC overnight. Immuno-complexes were collected with Dynabeads Protein A (Invitrogen Dynal AS, Oslo, Norway), washed with 1 x IP buffer four times, treated with Proteinase K treatment, and purified by phenol extraction and ethanol precipitation. 4.33 μg of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).

tag: antibody

value: 5-methyl cytidine

value: IP

tag: antibody catalog #

tag: antibody lot #


title: MM_#10353

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: Multiple myeloma

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Affymetrix Genotyping Console 4.0 for processing SNPs, detecting copy number abnormalities with default parameters and 270 HapMap reference samples.

label: Biotin

source_name: Bone marrow

label_protocol: According to manufacturer protocol

extract_protocol: DNA was extracted using the DNA AllPrep DNA/RNA MiniKit (Qiagen, Valencia, CA). DNA quality and quantity were assessed using the Nanodrop Spectrophotometer (NanoDrop Technologies, Inc. Wilmington, DE).

tag: patient id

tag: tumor

value: multiple myeloma

value: bone marrow

value: purified CD138+ plasma cells


title: DNA methylation of CpG island in PrEC

description: To recover methylated DNA with anti-5-methyl cytidine antibody, Dynabeads protein A (Dynal) was used.

source_name: Sonicated PrEC genomic DNA (WCE)

value: Prostate cancer cell line, PrEC

source_name: Sonicated PrEC genomic DNA (IP)


title: Plus A1- Resting cells +IFN_rep3

description:
Resting cells +IFN
This sample is of resting cells left untreated followed by IFN-γ. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Plus A1- Resting cells +IFN

tag: strain

value: untreated


title: Plus A1- Resting cells +IFN_rep2

description:
Resting cells +IFN
This sample is of resting cells left untreated followed by IFN-γ. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: MM_#09402

description: Multiple myeloma


title: PolyA+ RNA from Skeletal Muscle_antisense

value: Skeletal Muscle

value: normal tissue


title: DNA methylation of CpG island in MDA-PCa-2b

source_name: Sonicated MDA-PCa-2b genomic DNA (WCE)

value: Prostate cancer cell line, MDA-PCa-2b

source_name: Sonicated MDA-PCa-2b genomic DNA (IP)


title: Minus A1- Resting cells_rep3

description:
Resting cells
This sample is of resting cells. It is the third of three resting cells biological replicates used in this experiment, each from separate cultures.

source_name: Minus A1- Resting cells

value: Bone marrow derived macrophages (BMMØ)


title: DNA methylation of CpG island in BT474

hyb_protocol: Labelled DNA mixed with cot-1 DNA and Agilent blocking solution was hybridized to microarray for 40 hours at 67℃ and 10 rpm rotation. Microarrays was washed according to Agilent protocol.

source_name: Sonicated BT474 genomic DNA (WCE)

value: Breast cancer cell line, BT474

source_name: Sonicated BT474 genomic DNA (IP)


title: DNA methylation of CpG island in MDA-MB-231

source_name: Sonicated MDA-MB-231 genomic DNA (WCE)

value: Breast cancer cell line, MDA-MB-231

source_name: Sonicated MDA-MB-231 genomic DNA (IP)


title: MM_#11762

description: Multiple myeloma


title: MM_#06415

description: Multiple myeloma


title: Plus A1- Resting cells +IFN_rep1

description:
Resting cells +IFN
This sample is of resting cells left untreated followed by IFN-γ. It is the first of three biological replicates used in this experiment, each from separate cultures.

value: IFN-γ


title: MM_#10389

description: Multiple myeloma


title: MM_#08186

description: Multiple myeloma


title: Minus A3- Resting cells + Rv exosomes_rep1

description:
Resting cells + Rv exosomes
This sample is of resting cells treated with Rv exosomes. It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: Minus A3- Resting cells + Rv exosomes

value: Rv exosomes


title: Minus A4- Resting cells +H37Rv infection_rep3

description:
Resting cells +H37Rv infection
This sample is of resting cells infected with M.tb H37Rv. It is the third of three biological replicates used in this experiment, each from separate cultures.

value: infected with M.tb H37Rv


title: MM_#07545

description: Multiple myeloma


title: PolyA+ RNA from Brain_antisense

source_name: control Brain

value: Brain


title: Minus A3- Resting cells + Rv exosomes_rep2

description:
Resting cells + Rv exosomes
This sample is of resting cells treated with Rv exosomes. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Minus A4- Resting cells +H37Rv infection_rep2

description:
Resting cells +H37Rv infection
This sample is of resting cells infected with M.tb H37Rv. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: MM_#10217

description: Multiple myeloma


title: MM_#08209

description: Multiple myeloma


title: MM_#06358

description: Multiple myeloma


title: Minus A1- Resting cells_rep2

description:
Resting cells
This sample is of resting cells. It is the second of three resting cells biological replicates used in this experiment, each from separate cultures.


title: PolyA+ RNA from Skin_antisense

source_name: control Skin

value: Skin


title: Minus A3- Resting cells + Rv exosomes_rep3

description:
Resting cells + Rv exosomes
This sample is of resting cells treated with Rv exosomes. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Minus A2- Resting cells +Uninfected exosomes_rep2

description:
Resting cells +Uninfected exosomes
This sample is of resting cells treated with uninfected exosomes. It is the second of three biological replicates used in this experiment, each from separate cultures.

value: uninfected exosomes


title: Minus A2- Resting cells +Uninfected exosomes_rep3

description:
Resting cells +Uninfected exosomes
This sample is of resting cells treated with uninfected exosomes. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Minus A4- Resting cells +H37Rv infection_rep1

description:
Resting cells +H37Rv infection
This sample is of resting cells infected with M.tb H37Rv. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: HepG2_medip_medip_20081112, rep1

status: Public on Jun 04 2011

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

description: MeDIP-chip of HepG2 cells.

hyb_protocol: All of the steps of hybridization and washing were performed following the Agilent protocol for ChIP-on-ChIP analysis.

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B.

data_processing: The value is log intensity minus log background intensity which is then quantile normalized using the preProcessCore package in R/BioConductor.

source_name: HepG2 MeDIP

label_protocol: After immunoprecipitation with anti-5-methylcytosine antibody, the input and bound fractions were labeled with green and red fluorescent dyes (Cy3-dUTP and Cy5-dUTP, Perkin Elmer), respectively, using the CGH labeling kit (Invitrogen) according to the manufacturer's instructions.  The anti-5-methylcytosine antibody used was from Calbiochem, Cat. # NA81, Lot: D00048001.

extract_protocol: Immunoprecipitation for methylated DNA was performed according to a protocol developed by Cedar's group (Keshet et al., 2006 (PMID 16444255)). Briefly, DNA was extracted by the phenol/chlorofom standard method after tissue homogenization. 2ug of DNA were sonicated to generate a range of fragments between 200bp and 600bp, denatured by boiling for 10 min and incubated overnight at 4C with 10 ug of anti-5-methylcytosine antibodies (Calbiochem, Cat. NA81). 60 ul of sonicated and denatured DNA was maintained for measuring the amount of input DNA. To separate the antibody-bound fraction from the rest of the DNA, the samples were incubated with 5 mg of protein A Sepharose beads (GE Healthcare) for 2 hours at 4C. Following 10 washes of the bound fraction, the DNA from the input, unbound and bound fractions was extracted by phenol/chloroform and precipitated with ethanol (2V/V). 6 ul of the input and bound DNA fractions were amplified using the Whole Genome Amplification kit (Sigma) and subjected to labelling and hybridization to microarrays.

value: hepatocellular carcinoma cells

tag: medip antibody

value: anti-5-methylcytosine antibody

tag: antibody vendor

value: Calbiochem

tag: antibody catalog number

tag: antibody lot number

source_name: HepG2 input


title: PolyA+ RNA from Heart_antisense

source_name: control Heart

tag: tissue type

value: Heart


title: 6_normal_medip_medip_20090306

description: MeDIP-chip of normal cells.

source_name: normal MeDIP

tag: tissue

value: normal liver

tag: patient

source_name: normal, input


title: Minus A1- Resting cells_rep1

description:
Resting cells
This sample is of resting cells. It is the first of three resting cells biological replicates used in this experiment, each from separate cultures.

tag: cell type

tag: treatment

value: untreated


title: Minus A2- Resting cells +Uninfected exosomes_rep1

description:
Resting cells +Uninfected exosomes
This sample is of resting cells treated with uninfected exosomes. It is the first of three biological replicates used in this experiment, each from separate cultures.

tag: agent


title: HepG2_medip_medip_20081112, rep3

description: MeDIP-chip of HepG2 cells.

tag: cell line


title: HepG2_medip_medip_20081112, rep2

description: MeDIP-chip of HepG2 cells.


title: 4_normal_medip_medip_20090227

description: MeDIP-chip of normal cells.


title: 1_cancer_medip_medip_20090227

description: MeDIP-chip of cancer cells.

source_name: cancer MeDIP

value: hepatic cellular carcinoma (HCC)

source_name: cancer, input


title: 9_normal_medip_medip_20090206

description: MeDIP-chip of normal cells.


title: Hep_medip_medip_20081112, rep3

description: MeDIP-chip of NorHep cells.

source_name: Hep MeDIP

value: untransformed normal hepatocytes

source_name: Hep, input


title: Hep_medip_medip_20081112, rep2

description: MeDIP-chip of NorHep cells.


title: 10_normal_medip_medip_20090206

description: MeDIP-chip of normal cells.


title: 9_cancer_medip_medip_20090130

description: MeDIP-chip of cancer cells.


title: 11_cancer_medip_medip_20090206

description: MeDIP-chip of cancer cells.


title: 11_normal_medip_medip_20090206

description: MeDIP-chip of normal cells.


title: 13_cancer_medip_medip_20090213

description: MeDIP-chip of cancer cells.


title: 8_normal_medip_medip_20090130

description: MeDIP-chip of normal cells.


title: untreated_wt_vs_lpdA_03

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate 1_3 of 1_3

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software

data_processing: Spot intensities were quantified using DigitalGENOME (molecularware) spot-finding software. Intensities were then normalized by 75th percentile scaling before building signal ratios.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

label_protocol: For synthesis of cDNA, total RNA was first annealed with N6 random hexamers at 70°C for 10 min and allowed to cool on ice. The cDNA was synthesized in a reaction containing a nucleotide mix with a 2:3 ration of aminoallyl-dUTP:dTTP (Sigma-Aldrich, St. Louis, MO), Super Script- II reverse transcriptase (Invitrogen) and 50 μg total RNA incubated at 42°C overnight. Residual RNA was hydrolyzed in a final concentration of 0.3M NaOH and 0.125M EDTA at 65°C for 10 min, then neutralized with 1M Tris-HCL pH8.0. Unincorporated nucleotides were removed using a Qiaquick PCR purification kit with modified wash buffer: 5mM KPO4 pH8.0 and 80% ethanol. Aminoallyl-labled cDNA was eluted from the columns in water and concentrated on a SpeedVac. Cy5 and Cy3 dyes were coupled to the aminoallyl-labeled cDNA by resuspending the dried cDNA in 0.1M sodium carbonate (pH9.3) with either Cy5 or Cy3 dyes (GE HealthCare)dissolved in DMSO for 1 hr at room temperature. The reaction was neutralized by theaddition of 3M sodium acetate (pH5.2) and excess dye removed by purification on a Qiaquick PCR column using the manufacturer’s wash buffer.

growth_protocol: Overnight cultures were diluted 1:100 in fresh BHI medium, incubated at 37°C with constant agitation, and allowed to reach an OD600 of 1.0.

extract_protocol: RNA from 1 mL culture aliquots of treated and untreated cells was stabilized by the addition of 5 ml RNAProtect (Qiagen). Total RNA was isolated using the Qiagen RNeasy midi kit according to the manufacturer’s guidelines.

treatment_protocol: Experimental cultures were treated with the NO- donor SperNO (1mM) for 15 min.

tag: developmental stage

value: late log


title: wt_untreated_vs_NO_03

description: biological replicate 2_3 of 2_3

value: late log after 15 min treatment with 1mM NO


title: untreated_wt_vs_lpdA_02_dyeswapped

description: biological replicate 1_2 of 1_3, dye swapped


title: 8_cancer_medip_medip_20090130

description: MeDIP-chip of cancer cells.


title: 4_cancer_medip_medip_20090227

description: MeDIP-chip of cancer cells.


title: 1_normal_medip_medip_20090227

description: MeDIP-chip of normal cells.


title: 10_cancer_medip_medip_20090206

description: MeDIP-chip of cancer cells.


title: wt_untreated_vs_NO_02_dyeswapped

description: biological replicate 2_2 of 2_3, dye swapped


title: Hep_medip_medip_20081112, rep1

description: MeDIP-chip of NorHep cells.


title: 14_normal_medip_medip_20090220

description: MeDIP-chip of normal cells.


title: 15_normal_medip_medip_20090220

description: MeDIP-chip of normal cells.


title: 6_cancer_medip_medip_20090306

description: MeDIP-chip of cancer cells.


title: 5_cancer_medip_medip_20090306

description: MeDIP-chip of cancer cells.


title: 12_cancer_medip_medip_20090213

description: MeDIP-chip of cancer cells.


title: 12_normal_medip_medip_20090213

description: MeDIP-chip of normal cells.


title: 13_normal_medip_medip_20090220

description: MeDIP-chip of normal cells.


title: untreated_wt_vs_lpdA_03_dyeswapped

description: biological replicate 1_3 of 1_3, dye swapped


title: Creb3l3 KO mouse liver-2

city: Boston

first: Ann-Hwee

last: Lee

state: MA

address: 651 Huntington Ave, FXB/205

institute: Harvard School of public health

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: After scanning the probe arrays, the resulting images were analyzed using the BeadStudio software (V3, Illumina, Inc., San Diego, CA).

label: biotin

source_name: liver

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

extract_protocol: Total RNA was extracted in Trizol and purified using Qiagen RNeasy MiniElute kit according to manufacturer's instructions.

tag: genetic background

tag: gender

value: male

value: 24 hour fast

tag: diet

value: normal chow

tag: genotype

value: Creb3l3 KO

value: liver


title: 14_cancer_medip_medip_20090220

description: MeDIP-chip of cancer cells.


title: 5_normal_medip_medip_20090306

description: MeDIP-chip of normal cells.


title: 15_cancer_medip_medip_20090220

description: MeDIP-chip of cancer cells.


title: A4-C4

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ

description: Specific peroxidated metabolite issued from LC 3PUFA (4-hydroxyhexenal or 4-HHE) were measured by GC/MS/MS and transcription profiling was conducted in liver

hyb_protocol: The fluorescently labelled cRNA was hybridized using the Agilent gene expression hybridization kit (5188-5242-A) following the manufacturer’s instructions. Briefly, 825 ng cyanine 3-labelled, linearly amplified cRNA were mixed with 825 ng cyanine 5-labelled, linearly amplified cRNA. The mix was loaded onto the Agilent Rabbit Gene Expression Microarrays (4x44k) following a loop design and hybridization proceeded in a hybridization oven set to 65°C for 17 hours. Then, the slides were washed in solutions I, II and III (Agilent Technologies) and air-dried.

scan_protocol: Slides were scanned immediately after washing using the Agilent DNA Microarray Scanner (G2565AA/G2565BA), at photomultiplier tube voltages red and green. Spot identification and quantification were performed using Agilent Feature Extraction Software 7.0.

data_processing: Differentially expressed genes were identified using Bioconductor (Moderated p<0.05, Fold Change>1.20) and clustered into pathways (Ingenuity Pathway Analysis 7.0).

organism: Oryctolagus cuniculus

source_name: Subject A4

label_protocol: RNA samples were labelled using the Agilent Quick-Amp Labelling kit (5190-0424) according to the manufacturer’s instructions. Briefly, 500 ng of purified total RNA from each sample was amplified and reverse transcribed in vitro to cDNA using the T7-polymerase, which was subsequently labelled with either cyanine 3-CTP or cyanine 5-CTP dyes (5188-1170-P, Agilent Technologies, Wilmington, USA). The Nanodrop ND-1000 was used to monitor the yield of amplification and the dye incorporation; all samples had a yield > 825ng cRNA and a specific activity > 8.0 pmol Cy3 or Cy5 per ug cRNA.

growth_protocol:
New-Zealand white rabbits were fed (7 wk) a high cholesterol diet and received by daily oral gavages either oleic acid rich oil or a mixture of oils providing 0.1% (Group 1), 0.5% (Group 2) or 1% (Group 3) of energy as docosahexaenoic acid.
The diet abbreviations T, A, B, C used in the sample records refer to the following :
T : cholesterol rich diet + oleic acid rich oil
A : cholesterol rich diet + mix of oleic acid rich oil and tuna oil providing 0.1% of energy as DHA
B : cholesterol rich diet + mix of oleic acid rich oil and tuna oil providing 0.5% of energy as DHA
C : cholesterol rich diet + mix of oleic acid rich oil and tuna oil providing 1% of energy as DHA
Diets fed for 7 weeks.

extract_protocol: Total RNA from liver tissue was isolated using the Norgen RNA Purification kit (Norgen Bioteck Corporation, Ontario, Canada) according to the manufacturer’s instruction. RNA was quantified with a Nanodrop ND-1000 spectrophotometer (nanoDrop Technologies, Wilmington, Del., USA), and RNA integrity assessed with a RNA 6000 Nano Labchip kit using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, Calif., USA). Only total RNA with an OD 260/230 ratio > 1.7 and a RNA integrity number > 8 was used for microarray hybridization.

tag: strain

value: New Zealand white rabbit

tag: age

value: 12 weeks

tag: mean weight

source_name: Subject C4


title: WT mouse liver-2

value: wild type


title: WT mouse liver-3


title: T4-B3

source_name: Subject T4

treatment_protocol: T : cholesterol rich diet + oleic acid rich oil

source_name: Subject B3

treatment_protocol: B : cholesterol rich diet + mix of oleic acid rich oil and tuna oil providing 0.5% of energy as DHA


title: T6-C5

source_name: Subject T6

source_name: Subject C5

treatment_protocol: C : cholesterol rich diet + mix of oleic acid rich oil and tuna oil providing 1% of energy as DHA


title: B6-T5

source_name: Subject B6

source_name: Subject T5


title: C6-A6

source_name: Subject C6

source_name: Subject A6

treatment_protocol: A : cholesterol rich diet + mix of oleic acid rich oil and tuna oil providing 0.1% of energy as DHA


title: B4-A3

source_name: Subject B4

source_name: Subject A3


title: A5-B5

source_name: Subject A5

source_name: Subject B5


title: untreated_wt_vs_lpdA_02

description: biological replicate 1_2 of 1_3


title: Creb3l3 KO mouse liver-3


title: wt_untreated_vs_NO_02

description: biological replicate 2_2 of 2_3


title: C3-T3

source_name: Subject C3

source_name: Subject T3


title: B2-T2

source_name: Subject B2

source_name: Subject T2


title: C2-B1

source_name: Subject C2


title: 5_normal

description: Gene expression data from normal hepatocytes.

hyb_protocol: Samples were hybridized to HG-U133 Plus 2.0 high-density oligonucleotide arrays (Affymetrix). Hybridization and washing were performed according to the manufacturer's instructions (One-Cycle Target Labeling Assay, Affymetrix).

scan_protocol: The microarrays were scanned according to the manufacturer's instructions (One-Cycle Target Labeling Assay, Affymetrix).

data_processing: The data were RMA normalized using the affy package in R/BioConductor.

source_name: Normal liver tissue

label_protocol: 1 ug RNA served as template for cDNA synthesis using reverse transcriptase.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol.

value: microdissected normal liver

tag: portal vein infiltration

value: normal tissue


title: A2-C1

source_name: Subject A2

source_name: Subject C1


title: Creb3l3 KO mouse liver-1

source_name: liver


title: WT mouse liver-1


title: T1-A1

source_name: Subject T1

source_name: Subject A1


title: subcutaneous fat_male_obese_rep5

city: Darlinghurst

first: Mark

last: Cowley

state: NSW

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

country: Australia

institute: Garvan Institute of Medical Research

description: pre-pubertal subcutaneous fat sample from an obese, male subject, replicate 5

hyb_protocol: Affymetrix GeneChip Human Gene 1.0 ST arrays were hybridized with 11 μg of labeled sense DNA, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007).

scan_protocol: Array images were acquired using an Affymetrix GeneChip 3000 7G scanner

data_processing: Raw CEL files were normalised using RMA, via the Affymetrix Power Tools, v 1.8.5

source_name: subcutaneous fat

label_protocol: 1 μg of total RNA was amplified and labelled using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol without rRNA reduction.

extract_protocol: Total RNA was extracted from adipose tissue samples using TRIzol reagent (Invitrogen, Carlsbad, CA). The integrity and concentration of RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Inc. Headquarter, Palo Alto, CA).

treatment_protocol: We collected fasting abdominal subcutaneous and, where possible, omental fat biopsies from otherwise healthy children having elective surgery at The Children’s Hospital at Westmead and the Institute of Weight Control, Baulkham Hills (Sydney, Australia). Participants were older than 6 months of age, lacked intercurrent illness (notably inflammatory disease) and were having an elective procedure where abdominal fat could be obtained. Surgical adipose tissue biopsies were immediately frozen in liquid nitrogen and stored at -80ºC until gene expression analysis.

value: subcutaneous adipose tissue

tag: weight

value: obese

tag: array batch


title: visceral fat_female_obese_rep2

description: pre-pubertal visceral fat sample from an obese, female subject, replicate 2

source_name: visceral fat

tag: tissue

value: visceral adipose tissue

value: female


title: visceral fat_female_obese_rep1

description: pre-pubertal visceral fat sample from an obese, female subject, replicate 1


title: A38-5 vs. normal spleen

city: Baltimore

first: AUDREY

last: VINCENT

state: MD

address: 1550 Orleans Street, CRBII

department: Pathology

institute: Johns Hopkins University

hyb_protocol: standard Agilent protocol

scan_protocol: Arrays were scanned by using Agilent G2505B scanner

data_processing: Data were extracted with Agilent Feature Extraction 9.1 software. Methylation-specific sites were called with Agilent Genomic Workbench Standard Edition 5.0.14 software for methylation (CH3) analysis, which calculates the normalized log2-signal ratios (NLR) and combined Z-scores for each probe.

source_name: A38-5 pancreatic adenocarcinoma cell line

label_protocol: 2ug of MCA amplicons were labeled with either Cy3-dUTP or Cy5-dUTP (Perkin Elmer) by using the Bioprime DNA Labeling System (invitrogen)

extract_protocol: 5ug of DNA extracted from pancreatic adenocarcinoma cell lines or normal pancreatic tissues were digested by SmaI and XmaI, ligated to RMCA adapters and PCR amplified.

tag: disease state

value: Adenocarcinoma

tag: restriction enzyme digest

value: SmaI and XmaI digested DNA

source_name: Match normal spleen

value: Spleen

value: Normal


title: 9_normal

tag: patient


title: 9_cancer

description: Gene expression data from cancerous hepatocytes.

source_name: HCC tissue

value: microdissected hepatic cellular carcinoma (HCC)

value: non-infiltration


title: 8_normal


title: A32-1 vs. lymphocyte

source_name: A32-1 pancreatic adenocarcinoma cell line

source_name: Matched peripheral blood lymphocytes

tag: cell type

value: Lymphocytes


title: wt_untreated_vs_NO_03_dyeswapped

description: biological replicate 2_3 of 2_3, dye swapped

value: late log

value: late log after 15 min treatment with 1mM NO


title: 8_cancer


title: 5_cancer

value: portal vein infiltration


title: primary human trabecular meshwork cells T2h

city: Genoa

first: Alberto

last: Izzotti

address: A. Pastore, 1

department: Dept. of Health Sciences

institute: University of Genoa

description: Channel 2 in raw file slt2data.txt

hyb_protocol: Probes were lyophilized, diluted in 4 ul of EDTA 10 mM and  incubated at 95°C for 10 min. Hybridization solution (18 ul) was added and labelled probe mixed together to a final volume of 44 ul. Mixture was then transferred onto microarrays which were then  covered with a coverslip and  hybridized overnight at 50°C in a Hybridization Cassette (Life Technologies, Carlsbad, CA, USA). After 16 hours the microarrays were washed twice in a low stringency wash buffer (2X SSC, 0.5% SDS) and twice in a high stringency wash buffer (0.5X SSC, 0,5% SDS). Microarray were dried in centrifuge

scan_protocol: Scanned on laser scanner (ScanArray, PerkinElmer, Waltham, MA,USA). Images were quantified using QuantArray 3.0.0.0, Packard BioScience

data_processing: Data analysis was performed subtracting for each microarray the local spot background from raw spot intensity (data in sample tables), log transformation, normalization per chip and per array (GeneSpring software version 7.2, Agilent Technologies, Santa Clara, CA) (data in Series supplementary file).

label_protocol: Purified RNA underwent reverse transcription and amplification using quantitative real-time PCR (qPCR) prior to probe synthesis for array hybridization. A particular retrotranscription protocol (SuperSMART, Clontech, Palo Alto, CA, USA) aimed at the introduction of a target sequence at 3′ and 5′ of the cDNA library was applied as follows: RNA was incubated with a mix of a target sequence-oligo(dT)-linked primer and a target sequence-oligo(dG)-linked at 72°C for 5 minutes then a master-mix solution was added containing reverse transcriptase and dNTPs mix. Samples were then incubated at 42°C for 90 minutes. Reaction was terminated by adding ethylenediaminetetraacetic acid, mixture diluted in phosphate buffer and synthesized cDNA purified by column chromatography using a commercially available purification kit (QIAquick PCR purification kit, Qiagen, Chatsworth, CA, USA). A PCR mix, including the specific primer for the target sequences and the fluorescent tracers SYBR GREEN, was added to the purified cDNA. The PCR reaction was performed at 95°C x 1 minute, 50 amplification cycles at 95°C x 15 s, 65°C x 30 s and 68°C x 3 minutes. The amplification curve was observed in real time by recording fluorescence and the pre-plateau amplification cycle was identified for each sample. A second set of sample was amplified to the identified pre-plateau cycle using the same conditions without the fluorescent tracer. This procedure was applied to all samples in order to standardize the amplification process thus allowing reliable comparisons of microarray data among different samples. PCR reactions were performed in a thermocycler equipped with microvial rotating support (Rotorgene, Corbett Research, Mortlake, Australia).   2 ug of amplified cDNA, as purified by column chromatography, were converted in aminomodified probes performing a three cycle PCR using a PCR mix containing N-18 random primers, aminomodified dNTPs and Taq polymerase. The reaction was performed at 95°C x 5minutes, 94°C x 1 minute, 25°C x 90 s, 50°C x 10 minutes and 68°C x 5 minutes. Synthesized amino-modified oligo-nucleotides were purified by column chromatography and alcohol precipitation then labelled with fluorescent tracers Cy3 or Cy5 by incubation at room temperature in the dark for 90 minutes. Fluorescent oligonucleotides were precipitated by cold ethanol and sodium acetate, and then purified by column chromatography. The efficacy of the procedure was checked by spectrophotometric analysis measuring abosorbance at 550 (Cy3) and 650 (Cy5).

growth_protocol: Cultured in fibroblast medium (FM, ScienCell), 2% fetal bovine serum (FBS, ScienCell), fibroblast growth supplement (FGS, 1%, ScienCell) and penicillin/streptomycin solution (P/S, 1%, ScienCell) using poly-L-lysine-coated flasks having a 6 mm diameter. Cell were growth to semi confluence accounting for approximately 1x105 cell per well.

treatment_protocol: When reaching semi-confluence cells underwent SLT treatment: TM cells underwent SLT under similar conditions usually adopted for human subjects using a SLT laser system (Laserex Tango Ellex Medical Pty Ltd – Australia). Specific treatment conditions were Q-swithched frequency doubled with Nd:YAG laser at 532 nm. TM cells underwent SLT under similar conditions usually adopted for human subjects using a SLT laser system (Laserex Tango Ellex Medical Pty Ltd – Australia). Specific treatment conditions were Q-swithched frequency doubled with Nd:YAG laser at 532 nm.  Wavelength, energy settings at 0.5 mJ single pulse, pulse duration 3 nsec, and treatment spot size of 400 micron.   After treatment cells were immediately restored in incubator and then collected by scraping after 2 hours

value: primary human trabecular meshwork cells


title: subcutaneous fat_male_obese_rep4

description: pre-pubertal subcutaneous fat sample from an obese, male subject, replicate 4

value: male


title: 4_normal

value: microdissected normal liver

value: normal tissue


title: subcutaneous fat_male_obese_rep1

description: pre-pubertal subcutaneous fat sample from an obese, male subject, replicate 1

value: subcutaneous adipose tissue

value: obese


title: Panc215 vs. lymphocyte

source_name: Panc215 pancreatic adenocarcinoma cell line

tag: cell line


title: 4_cancer


title: 15_normal


title: A32-1 vs. normal pancreas

source_name: Pooled laser-captured microdissected normal pancreatic duct tissues

value: pancreatic duct tissues


title: subcutaneous fat_male_obese_rep3

description: pre-pubertal subcutaneous fat sample from an obese, male subject, replicate 3


title: primary human trabecular meshwork cells T6h

description: Channel 1 in raw file slt2data.txt

treatment_protocol: When reaching semi-confluence cells underwent SLT treatment: TM cells underwent SLT under similar conditions usually adopted for human subjects using a SLT laser system (Laserex Tango Ellex Medical Pty Ltd – Australia). Specific treatment conditions were Q-swithched frequency doubled with Nd:YAG laser at 532 nm. TM cells underwent SLT under similar conditions usually adopted for human subjects using a SLT laser system (Laserex Tango Ellex Medical Pty Ltd – Australia). Specific treatment conditions were Q-swithched frequency doubled with Nd:YAG laser at 532 nm.  Wavelength, energy settings at 0.5 mJ single pulse, pulse duration 3 nsec, and treatment spot size of 400 micron.   After treatment cells were immediately restored in incubator and then collected by scraping after 6 hours


title: primary human trabecular meshwork cells T0,5h

description: Channel 1 in raw file slt1data.txt

treatment_protocol: When reaching semi-confluence cells underwent SLT treatment: TM cells underwent SLT under similar conditions usually adopted for human subjects using a SLT laser system (Laserex Tango Ellex Medical Pty Ltd – Australia). Specific treatment conditions were Q-swithched frequency doubled with Nd:YAG laser at 532 nm. TM cells underwent SLT under similar conditions usually adopted for human subjects using a SLT laser system (Laserex Tango Ellex Medical Pty Ltd – Australia). Specific treatment conditions were Q-swithched frequency doubled with Nd:YAG laser at 532 nm.  Wavelength, energy settings at 0.5 mJ single pulse, pulse duration 3 nsec, and treatment spot size of 400 micron.   After treatment cells were immediately restored in incubator and then collected by scraping after 0.5 hours


title: primary human trabecular meshwork cells CONTROL

description: Channel 2 in raw file slt1data.txt

treatment_protocol: When reaching semi-confluence were stored in incubator in absence of SLT


title: Panc2.5 vs. normal pancreas

source_name: Panc2.5 pancreatic adenocarcinoma cell line

value: Adenocarcinoma


title: subcutaneous fat_female_obese_rep1

description: pre-pubertal subcutaneous fat sample from an obese, female subject, replicate 1

value: female


title: 1_normal


title: 15_cancer


title: subcutaneous fat_female_obese_rep2

description: pre-pubertal subcutaneous fat sample from an obese, female subject, replicate 2


title: visceral fat_male_obese_rep1

description: pre-pubertal visceral fat sample from an obese, male subject, replicate 1

value: visceral adipose tissue


title: 14_normal


title: subcutaneous fat_male_obese_rep2

description: pre-pubertal subcutaneous fat sample from an obese, male subject, replicate 2


title: Panc215 vs. normal pancreas

value: SmaI and XmaI digested DNA

value: Normal


title: Panc3.014 vs. normal pancreas

source_name: Panc3.014 pancreatic adenocarcinoma cell line


title: 14_cancer

value: microdissected hepatic cellular carcinoma (HCC)

value: non-infiltration


title: 1_cancer


title: visceral fat_male_lean_rep1

description: pre-pubertal visceral fat sample from an lean, male subject, replicate 1

value: lean


title: 11_normal

source_name: Normal liver tissue


title: Panc2.8 vs. normal pancreas

source_name: Panc2.8 pancreatic adenocarcinoma cell line


title: visceral fat_female_lean_rep1

description: pre-pubertal visceral fat sample from an lean, female subject, replicate 1


title: 12_normal


title: A38-5 vs. normal pancreas


title: MiaPaca2 vs. normal pancreas

source_name: MiaPaca2 pancreatic adenocarcinoma cell line

source_name: Normal pancreatic tissue

value: Pancreas


title: 12_cancer


title: 10_normal


title: subcutaneous fat_male_lean_rep3

description: pre-pubertal subcutaneous fat sample from an lean, male subject, replicate 3


title: subcutaneous fat_male_lean_rep2

description: pre-pubertal subcutaneous fat sample from an lean, male subject, replicate 2


title: subcutaneous fat_male_lean_rep4

description: pre-pubertal subcutaneous fat sample from an lean, male subject, replicate 4


title: 10_cancer


title: Heat Killed E coli #1

first: Read

last: Pukkila-Worley

address: 55 Fruit Street

department: Molecular Biology and Medicine

institute: Massachusetts General Hospital

hyb_protocol: Affymetrix standard scan protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Data were analyzed using Resolver Gene Expression Data Analysis System, version 5.1 (Rosetta Inpharmatics).  Three biologic replicates per condition were normalized using the Resolver intensity error model for single color chips.  Conditions were compared using Resolver to determine the fold-change between conditions for each probe set and to generate a P value using a modified t-test.  Probe sets were considered differentially expressed if the fold change was 2-fold or greater (P<0.01).

organism: Caenorhabditis elegans

source_name: Heat Killed E coli #1

label_protocol: RNA samples were prepared and hybridized to Affymetrix full-genome GeneChips for C. elegans at the Harvard Medical School Biopolymer Facility following previously described protocols and instructions from Affymetrix.

growth_protocol: N2 animals were synchronized by hypochlorite treatment.  Arrested L1s were plated on 10-cm NGM plates seeded with E. coli OP50 and grown at 20°C until they were young adults.

extract_protocol: RNA was extracted using TRI Reagent (Molecular Research Center) according to the manufactures instructions and purified using an RNeasy column (Qiagen).

treatment_protocol: Young adult C. elegans were added to 10-cm plates containing 20-mL of BHI agar (with 45 μg of kanamycin/ ml) and live C. albicans, heat-killed C. albicans or heat-killed E. coli.  Three separate biological replicates of nematodes were exposed to these conditions for 4 hours at 25°C.

tag: infection

value: Heat Killed E coli


title: Heat Killed E coli #2

source_name: Heat Killed E coli #2


title: AsPC1 vs. HPDE

source_name: AsPC1 pancreatic adenocarcinoma cell line

source_name: Immortalized human pancreatic ductal epithelial cells HPDE


title: 11_cancer


title: subcutaneous fat_male_lean_rep1

description: pre-pubertal subcutaneous fat sample from an lean, male subject, replicate 1

source_name: subcutaneous fat


title: subcutaneous fat_female_lean_rep2

description: pre-pubertal subcutaneous fat sample from an lean, female subject, replicate 2


title: HT29_wildtype_100ng_AffyExpress

city: Phoenix

first: Jonathan

middle: J

last: Keats

state: Arizona

address: 445 N. Fifth Street

department: Integrated Cancer Genomics

institute: Translational Genomics Research Institute (TGen)

description: Single sample standard labeling and hybridization

hyb_protocol: Labeled cRNA was hybridized to U133Plus2.0 GeneChips in a GeneChip Hybridization Oven 640 and washed using a GeneChip Fluidics Station 450 as per the manufacturers protocol

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 following the recommendations of the manufacturer

data_processing: Signal estimates were generated in R/Bioconductor using the GCRMA package with default settings

source_name: HT29 Wildtype RNA

label_protocol: 3 ug of Total RNA was labeled using the One-Cycle Target Labeling kit and 100 ng of Total RNA was labeled using the 3' IVT Express kit from Affymetrix as per the manufacturers suggestion

growth_protocol: HT-29 cells (American Type Culture Collection, Manassas, VA) were cultured in 37°C incubators with 5% CO2, using McCoy’s 5a with L-glutamine and supplemented with 10% fetal bovine serum (FBS), 2.2g/l sodium bicarbonate, 100 units/ml penicillin, 100 units/ml streptomycin and 1.5g/l D-glucose.

extract_protocol: RNA was extracted from cells using TRIzol (Invitrogen) in combination with PureLink Micro-to-Midi RNA columns (Invitrogen) using the manufacturers protocol. RNA samples were tested for purity and concentration on a Nanodrop spectrophotometer and quality checked on an Agilent Bioanalyzer

treatment_protocol: HT-29 cells were cultured with continuous presence of bortezomib by stepwise increases in concentration (20 nM to 300 nM) over 7 months. Clonal isolates were derived by 2 separate limiting dilution analysis in 96-well plates under constant bortezomib exposure of 100 nM or 300 nM for an additional 4 months.

tag: cell variant

value: wild type

tag: treatment


title: Heat Killed C. albicans #1

source_name: Heat Killed C. albicans #1

value: Heat Killed C. albicans


title: Heat Killed E coli #3

source_name: Heat Killed E coli #3


title: C. albicans alive #2

source_name: C. albicans alive #2

value: C. albicans alive


title: subcutaneous fat_female_lean_rep1

description: pre-pubertal subcutaneous fat sample from an lean, female subject, replicate 1

tag: gender


title: Heat Killed C. albicans #2

source_name: Heat Killed C. albicans #2


title: HT29_wildtype_3ug_AffyOneStep


title: Capan2 vs. normal pancreas

source_name: Capan2 pancreatic adenocarcinoma cell line


title: subcutaneous fat_female_lean_rep4

description: pre-pubertal subcutaneous fat sample from an lean, female subject, replicate 4


title: wt_untreated_vs_NO_01

description: biological replicate 2_1 of 2_3

tag: developmental stage

value: late log after 15 min treatment with 1mM NO

value: late log


title: C. albicans alive #1

source_name: C. albicans alive #1


title: HT29_BR200_3ug_AffyOneStep

source_name: HT29 BR200 RNA


title: HT29_BR200_100ng_AffyExpress


title: C. albicans alive #3

source_name: C. albicans alive #3


title: NCI-H2228 xenograft_CH5424802_20mg/kg_rep2

status: Public on Jun 03 2011

city: Kamakura

first: Hiroshi

last: Sakamoto

address: Kajiwara 200

institute: Chugai Pharmaceutical co. ltd.

hyb_protocol: The cRNA products were fragmented, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: Scanning was carried out using the GeneChip Scanner and image analysis was performed using GeneChip Operating Software.

data_processing: GCRMA; data processing software is R version 2.10.0.

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's instructions (Affymetrix Expression Analysis Technical Manual, Rev. 4).

growth_protocol: NCI-H2228 cell line (ATCC) was cultured using the medium recommended by ATCC, and cells are grown as s.c. tumors in SCID mice

extract_protocol: Total RNA was isolated with RNeasy kits (Qiagen) according to the manufacturers' instructions.

treatment_protocol: Mice bearing NCI-H2228 cells were orally administered at dose of 0 (vehicle), 4 or 20 mg/kg of CH5424802, and the tumors were collected and lysed at 6 hours post-dose.

value: NCI-H2228 xenograft tumor

tag: agent

tag: dose


title: HT29_BR100_3ug_AffyOneStep

source_name: HT29 BR100 RNA


title: untreated_wt_vs_lpdA_01

description: biological replicate 1_1 of 1_3

tag: strain


title: NCI-H2228 xenograft_CH5424802_4mg/kg_rep2


title: HT29_BR100_100ng_AffyExpress


title: NCI-H2228 xenograft_CH5424802_20mg/kg_rep1


title: NCI-H2228 xenograft_CH5424802_4mg/kg_rep1


title: NCI-H2228 xenograft_Vehicle_rep2

source_name: NCI-H2228 xenograft_Vehicle_rep2

value: Vehicle


title: NCI-H2228 xenograft_Vehicle_rep1

source_name: NCI-H2228 xenograft_Vehicle_rep1


title: Adjacent non-tumor colorectal tissue 17800

city: Los Angeles

first: Toshinori

last: Hinoue

address: 1450 Biggy Street, NRT G511

institute: USC Epigenome Center

description: Paired with tumor 17774

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27k Beadchip using standard Illumina protocol.

scan_protocol: Beadchips were imaged using Illumina BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Mean non-background corrected signal intensities of the methylated (M) and unmethylated (U) for each CpG locus were extracted using the Illumina BeadStudio software v3.2. We masked data point as “NA” for the following conditions; 1) Probes containing single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Beta values with detection P value greater than 0.05 were also replaced as "NA". Furthermore, probes containing at least one “NA” across the tumor sample set were masked as “NA”. Beta values were normalized to eliminate the batch effects. Briefly, the batch means of beta values were brought closer to the overall mean while retaining the original range of DNA methylation data (0 to 1). We used only the tumor samples to calculate the batch means and overall mean in estimating the scaling factor for each batch.
Beta value was calculated as M/(M+U). Detection P values were obtained using the Z-score formula as previously described (Noushmehr et al., 2010, Cancer Cell). Detection P values that are less than 1.11e-16 are represented as 0.

label: Cy5 and Cy3

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17800

label_protocol: standard Illumina label protocol

extract_protocol: Genomic DNA was extracted using Trizol reagent according to the manufacturer’s protocol.

tag: sample type

value: Fresh Frozen tissue

value: Normal adjacent to colorectal adenocarcinoma

value: Female

tag: tissue source site

value: The Groene Hart Hospital,The Neterlands

tag: batch

value: Batch 2


title: Adjacent non-tumor colorectal tissue 17808

description: Paired with tumor 14838

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17808

value: Male

value: The ontario tumor bank network,Canada


title: Adjacent non-tumor colorectal tissue 17803

description: Paired with tumor 17777

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17803


title: Adjacent non-tumor colorectal tissue 17805

description: Paired with tumor 14805

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17805


title: Adjacent non-tumor colorectal tissue 17801

description: Paired with tumor 17775

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17801


title: Adjacent non-tumor colorectal tissue 17806

description: Paired with tumor 14807

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17806


title: Adjacent non-tumor colorectal tissue 17807

description: Paired with tumor 14809

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17807


title: Adjacent non-tumor colorectal tissue 17804

description: Paired with tumor 17778

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17804


title: Adjacent non-tumor colorectal tissue 17798

description: Paired with tumor 17772

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17798


title: Adjacent non-tumor colorectal tissue 17799

description: Paired with tumor 17773

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17799


title: Adjacent non-tumor colorectal tissue 17795

description: Paired with tumor 17769

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17795


title: Adjacent non-tumor colorectal tissue 17797

description: Paired with tumor 17771

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17797


title: Adjacent non-tumor colorectal tissue 17792

description: Paired with tumor 17766

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17792


title: Adjacent non-tumor colorectal tissue 17793

description: Paired with tumor 17767

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17793


title: Adjacent non-tumor colorectal tissue 17789

description: Paired with tumor 17763

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17789


title: Adjacent non-tumor colorectal tissue 17796

description: Paired with tumor 17770

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17796


title: Adjacent non-tumor colorectal tissue 17794

description: Paired with tumor 17768

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17794


title: Adjacent non-tumor colorectal tissue 17788

description: Paired with tumor 17762

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17788


title: Adjacent non-tumor colorectal tissue 17791

description: Paired with tumor 17765

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17791


title: Adjacent non-tumor colorectal tissue 17802

description: Paired with tumor 17776

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17802


title: Adjacent non-tumor colorectal tissue 17786

description: Paired with tumor 17760

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17786


title: Adjacent non-tumor colorectal tissue 17781

description: Paired with tumor 17755

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17781


title: Adjacent non-tumor colorectal tissue 17782

description: Paired with tumor 17756

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17782


title: Adjacent non-tumor colorectal tissue 17784

description: Paired with tumor 17758

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17784


title: Colorectal Adenocarinoma 17774

description: Paired with normal adjacent tissue17800

source_name: genomic DNA from colorectal adenocarcinoma 17774

value: Adenocarcinoma

tag: tumor subsite

value: Distal


title: Adjacent non-tumor colorectal tissue 17783

description: Paired with tumor 17757

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17783

tag: disease state


title: Adjacent non-tumor colorectal tissue 17787

description: Paired with tumor 17761

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17787


title: Adjacent non-tumor colorectal tissue 17779

description: Paired with tumor 17753

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17779


title: Adjacent non-tumor colorectal tissue 17780

description: Paired with tumor 17754

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17780


title: Colorectal Adenocarinoma 17777

description: Paired with normal adjacent tissue17803

source_name: genomic DNA from colorectal adenocarcinoma 17777

value: Proximal


title: Colorectal Adenocarinoma 17775

description: Paired with normal adjacent tissue17801

source_name: genomic DNA from colorectal adenocarcinoma 17775


title: Colorectal Adenocarinoma 17776

description: Paired with normal adjacent tissue17802

source_name: genomic DNA from colorectal adenocarcinoma 17776


title: Colorectal Adenocarinoma 17778

description: Paired with normal adjacent tissue17804

source_name: genomic DNA from colorectal adenocarcinoma 17778


title: Colorectal Adenocarinoma 17772

description: Paired with normal adjacent tissue17798

source_name: genomic DNA from colorectal adenocarcinoma 17772


title: Heat Killed C. albicans #3

source_name: Heat Killed C. albicans #3


title: HT-29 300 nM bortezomib resistant

description: Competitive Oligo CGH assay, HT-29 BR300 versus HapMap Female Mix

hyb_protocol: hybridizations were carried out as suggested in the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.2 (October 2009)

scan_protocol: scans were carried out as suggested in the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.2 (October 2009) with both PMTs at 100%

data_processing: Raw data was extracted from TIFF image files by  Agilent Feature extraction version 10.5.1.1 using the CGH_105_Dec08 protocol and the 021529_D_F_20081113 grid file

label: Alexa 5

source_name: HT29 BR300 DNA

label_protocol: genomic DNA was digested with DNaseI for 12 min, digested DNA was labeled using the Invitrogen BioPrime Plus Labeling kit, Test HT-29 samples were labeled with Alexa 5 and control DNA from a mixture of nine HapMap female samples were labeled with Alexa 3

extract_protocol: DNA was extracted from 5 million cells using the Purgene kit (Qiagen)

treatment_protocol: HT-29 cells were cultured with continuous presence of bortezomib by stepwise increases in concentration (20 nM to 300 nM) over 7 months.  Clonal isolates were derived by 2 separate limiting dilution analysis in 96-well plates under constant bortezomib exposure of 100 nM or 300 nM for an additional 4 months.

label: Alexa 3

source_name: HapMap Nine Female DNA Mix

tag: reference

value: control DNA


title: subcutaneous fat_female_lean_rep3

description: pre-pubertal subcutaneous fat sample from an lean, female subject, replicate 3

source_name: subcutaneous fat

tag: tissue

value: subcutaneous adipose tissue

value: female

tag: weight

value: lean

tag: array batch


title: Colorectal Adenocarinoma 17773

description: Paired with normal adjacent tissue17799

source_name: genomic DNA from colorectal adenocarcinoma 17773


title: CD8 viremic non-progessor VNP_IC820

city: Charlestown

first: Matthew

last: Woods

address: 149 13th Street

department: Computational Biology Core

institute: The Ragon Institute of MGH, MIT, and Harvard

scan_protocol: Standard Illumina scan protocol

data_processing: Quantile normalized, log2 transformed, present call filtered at p=0.01

source_name: CD8 T cells purified from frozen PBMC from HIV infected individuals

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

extract_protocol: Total RNA was extracted from purified CD8+ T cells using mirVana miRNA isolation kit (Ambion) according to the manufacturer’s protocol for total RNA

tag: disease progression status

value: viremic non-progessor

tag: diseaste state

value: HIV

tag: cell type

value: CD8 T


title: CD8 viremic non-progessor VNP_6309


title: Colorectal Adenocarinoma 17771

description: Paired with normal adjacent tissue17797

source_name: genomic DNA from colorectal adenocarcinoma 17771

value: Fresh Frozen tissue

tag: gender


title: CD8 viremic non-progessor VNP_7852


title: HT-29 100 nM bortezomib resistant

description: Competitive Oligo CGH assay, HT-29 BR100 versus HapMap Female Mix

source_name: HT29 BR100 DNA

tag: cell line

tag: cell variant


title: CD8 rapid progessor RP_IC699

value: rapid progessor


title: CD8 rapid progessor RP_IC654


title: HT-29 Wildtype

description: Competitive Oligo CGH assay, HT-29 wildtype versus HapMap Female Mix

source_name: HT29 Wildtype DNA

value: wildtype


title: Colorectal Adenocarinoma 17767

description: Paired with normal adjacent tissue17793

source_name: genomic DNA from colorectal adenocarcinoma 17767

value: Female

value: The Groene Hart Hospital,The Neterlands


title: Colorectal Adenocarinoma 17770

description: Paired with normal adjacent tissue17796

source_name: genomic DNA from colorectal adenocarcinoma 17770

value: Male

value: Rectum

value: Batch 2


title: CD8 rapid progessor RP_IC720


title: CD8 rapid progessor RP_IC760


title: Colorectal Adenocarinoma 17769

description: Paired with normal adjacent tissue17795

source_name: genomic DNA from colorectal adenocarcinoma 17769

value: Adenocarcinoma

value: Distal


title: Colorectal Adenocarinoma 17766

description: Paired with normal adjacent tissue17792

source_name: genomic DNA from colorectal adenocarcinoma 17766

value: Proximal


title: CD8 rapid progessor RP_IC590


title: CD8 rapid progessor RP_IC519


title: CD8 rapid progessor RP_IC450


title: CD8 rapid progessor RP_IC458


title: CD8 rapid progessor RP_IC527


title: CD8 viremic non-progessor VNP_7843


title: CD8 viremic non-progessor VNP_6109


title: CD8 rapid progessor RP_IC548


title: HT-29 200 nM bortezomib resistant

description: Competitive Oligo CGH assay, HT-29 BR200 versus HapMap Female Mix

source_name: HT29 BR200 DNA

value: control DNA


title: Colorectal Adenocarinoma 17763

description: Paired with normal adjacent tissue17789

source_name: genomic DNA from colorectal adenocarcinoma 17763


title: Colorectal Adenocarinoma 17764

description: Paired with normal adjacent tissue17790

source_name: genomic DNA from colorectal adenocarcinoma 17764


title: Adjacent non-tumor colorectal tissue 17790

description: Paired with tumor 17764

source_name: genomic DNA from adjacent non-tumor colorectal tissue 17790

value: Normal adjacent to colorectal adenocarcinoma


title: Colorectal Adenocarinoma 17762

description: Paired with normal adjacent tissue17788

source_name: genomic DNA from colorectal adenocarcinoma 17762


title: Colorectal Adenocarinoma 17761

description: Paired with normal adjacent tissue17787

source_name: genomic DNA from colorectal adenocarcinoma 17761


title: Colorectal Adenocarinoma 17768

description: Paired with normal adjacent tissue17794

source_name: genomic DNA from colorectal adenocarcinoma 17768


title: Colorectal Adenocarinoma 17765

description: Paired with normal adjacent tissue17791

source_name: genomic DNA from colorectal adenocarcinoma 17765


title: CD8 rapid progessor RP_IC330


title: CD8 rapid progessor RP_HC16


title: CD8 rapid progessor RP_7777


title: CD8 rapid progessor RP_IC436


title: CD8 rapid progessor RP_IC443


title: CD8 rapid progessor RP_IC678


title: CD8 rapid progessor RP_HC13


title: Colorectal Adenocarinoma 17757

description: Paired with normal adjacent tissue17783

source_name: genomic DNA from colorectal adenocarcinoma 17757


title: CD8 rapid progessor RP_7781

source_name: CD8 T cells purified from frozen PBMC from HIV infected individuals


title: CD8 rapid progessor RP_5619


title: CD8 rapid progessor RP_3997


title: Colorectal Adenocarinoma 17756

description: Paired with normal adjacent tissue17782

source_name: genomic DNA from colorectal adenocarcinoma 17756


title: Colorectal Adenocarinoma 17758

description: Paired with normal adjacent tissue17784

source_name: genomic DNA from colorectal adenocarcinoma 17758


title: Colorectal Adenocarinoma 17760

description: Paired with normal adjacent tissue17786

source_name: genomic DNA from colorectal adenocarcinoma 17760


title: CD8 rapid progessor RP_7783


title: CD8 rapid progessor RP_5685


title: CD8 rapid progessor RP_5506


title: CD8 rapid progessor RP_5643


title: CD8 elite/viremic controller EC_5563

value: elite/viremic controller


title: Colorectal Adenocarinoma 17755

description: Paired with normal adjacent tissue17781

source_name: genomic DNA from colorectal adenocarcinoma 17755


title: CD4 viremic non-progessor VNP_7852

source_name: CD4 T cells purified from frozen PBMC from HIV infected individuals

extract_protocol: Total RNA was extracted from purified CD4+ T cells using mirVana miRNA isolation kit (Ambion) according to the manufacturer’s protocol for total RNA

value: viremic non-progessor

value: CD4 T


title: CD4 viremic non-progessor VNP_6109

value: HIV


title: CD8 elite/viremic controller EC_5683

value: CD8 T


title: Colorectal Adenocarinoma 17754

description: Paired with normal adjacent tissue17780

source_name: genomic DNA from colorectal adenocarcinoma 17754

value: Fresh Frozen tissue


title: CD8 elite/viremic controller EC_5681


title: CD8 elite/viremic controller EC_5647


title: Colorectal Adenocarinoma 14908

source_name: genomic DNA from colorectal adenocarcinoma 14908

value: The ontario tumor bank network,Canada

value: Batch 1


title: CD4 viremic non-progessor VNP_IC820


title: Colorectal Adenocarinoma 14907

source_name: genomic DNA from colorectal adenocarcinoma 14907


title: Colorectal Adenocarinoma 14906

source_name: genomic DNA from colorectal adenocarcinoma 14906

value: Female


title: Colorectal Adenocarinoma 17753

description: Paired with normal adjacent tissue17779

source_name: genomic DNA from colorectal adenocarcinoma 17753

value: The Groene Hart Hospital,The Neterlands


title: CD8 rapid progessor RP_3079

value: rapid progessor


title: CD8 elite/viremic controller EC_3336


title: CD8 elite/viremic controller EC_3984


title: CD4 viremic non-progessor VNP_6309


title: CD4 viremic non-progessor VNP_7843


title: CD8 elite/viremic controller EC_3713


title: CD4 rapid progessor RP_IC760


title: CD8 elite/viremic controller EC_5627


title: CD4 rapid progessor RP_IC654


title: CD4 rapid progessor RP_IC720


title: CD4 rapid progessor RP_IC590


title: Colorectal Adenocarinoma 14903

source_name: genomic DNA from colorectal adenocarcinoma 14903

value: Male


title: Colorectal Adenocarinoma 14905

source_name: genomic DNA from colorectal adenocarcinoma 14905

value: Adenocarcinoma

value: Rectum


title: CD4 rapid progessor RP_IC699


title: CD4 rapid progessor RP_IC678


title: CD4 rapid progessor RP_IC548


title: Colorectal Adenocarinoma 14904

source_name: genomic DNA from colorectal adenocarcinoma 14904

value: Distal


title: Colorectal Adenocarinoma 14899

source_name: genomic DNA from colorectal adenocarcinoma 14899


title: Colorectal Adenocarinoma 14900

source_name: genomic DNA from colorectal adenocarcinoma 14900

value: Proximal


title: Colorectal Adenocarinoma 14901

source_name: genomic DNA from colorectal adenocarcinoma 14901


title: CD4 rapid progessor RP_IC458


title: CD4 rapid progessor RP_IC330


title: Colorectal Adenocarinoma 14896

source_name: genomic DNA from colorectal adenocarcinoma 14896


title: Colorectal Adenocarinoma 14893

source_name: genomic DNA from colorectal adenocarcinoma 14893


title: CD4 rapid progessor RP_7783


title: CD4 rapid progessor RP_7781


title: Colorectal Adenocarinoma 14897

source_name: genomic DNA from colorectal adenocarcinoma 14897


title: CD4 rapid progessor RP_5643


title: Colorectal Adenocarinoma 14894

source_name: genomic DNA from colorectal adenocarcinoma 14894


title: Colorectal Adenocarinoma 14891

source_name: genomic DNA from colorectal adenocarcinoma 14891


title: CD4 rapid progessor RP_7777

source_name: CD4 T cells purified from frozen PBMC from HIV infected individuals


title: CD4 rapid progessor RP_5619


title: Colorectal Adenocarinoma 14895

source_name: genomic DNA from colorectal adenocarcinoma 14895


title: CD4 rapid progessor RP_IC443


title: CD4 rapid progessor RP_5506


title: CD4 rapid progessor RP_5484


title: Colorectal Adenocarinoma 14902

source_name: genomic DNA from colorectal adenocarcinoma 14902


title: Colorectal Adenocarinoma 14892

source_name: genomic DNA from colorectal adenocarcinoma 14892


title: CD4 rapid progessor RP_HC13


title: CD4 rapid progessor RP_5537


title: CD4 rapid progessor RP_IC450


title: CD4 rapid progessor RP_HC16


title: CD4 rapid progessor RP_IC527


title: CD4 rapid progessor RP_IC436


title: CD4 rapid progessor RP_IC519


title: Colorectal Adenocarinoma 14889

source_name: genomic DNA from colorectal adenocarcinoma 14889


title: CD4 elite/viremic controller EC_5683


title: Colorectal Adenocarinoma 14887

source_name: genomic DNA from colorectal adenocarcinoma 14887


title: Colorectal Adenocarinoma 14888

source_name: genomic DNA from colorectal adenocarcinoma 14888


title: CD4 rapid progessor RP_3997


title: Colorectal Adenocarinoma 14886

source_name: genomic DNA from colorectal adenocarcinoma 14886


title: CD4 rapid progessor RP_3079


title: Colorectal Adenocarinoma 14890

source_name: genomic DNA from colorectal adenocarcinoma 14890


title: Colorectal Adenocarinoma 14885

source_name: genomic DNA from colorectal adenocarcinoma 14885


title: Colorectal Adenocarinoma 14882

source_name: genomic DNA from colorectal adenocarcinoma 14882

value: Transverse


title: CD4 rapid progessor RP_5685


title: Colorectal Adenocarinoma 14877

source_name: genomic DNA from colorectal adenocarcinoma 14877


title: Colorectal Adenocarinoma 14881

source_name: genomic DNA from colorectal adenocarcinoma 14881


title: CD4 elite/viremic controller EC_5681

value: elite/viremic controller


title: CD4 elite/viremic controller EC_3984


title: Colorectal Adenocarinoma 14884

source_name: genomic DNA from colorectal adenocarcinoma 14884


title: CD4 elite/viremic controller EC_3713


title: CD4 elite/viremic controller EC_5647


title: Colorectal Adenocarinoma 14879

source_name: genomic DNA from colorectal adenocarcinoma 14879


title: CD4 elite/viremic controller EC_5563


title: CD4 elite/viremic controller EC_5627


title: CD4 elite/viremic controller EC_3336


title: SW480-LY294002-3

city: Berlin

first: Markus

last: Morkel

state: Berlin

address: Ihnestr. 73

department: Developmental Genetics

country: Germany

institute: Max Planck Institute for Molecular Genetics

hyb_protocol: Standard Illumina

scan_protocol: Standard Illumina

data_processing: Illumina Inc. GenomeStudio version 1.1.1, cubic spline normalisation, background substraction

label_protocol: Aminon MessageAMP, according to manufacturer´s suggestions

growth_protocol: subconfluent SW480 cells, DMEM, 10%FCS

extract_protocol: Qiagen RNeasy, according to manufacturer´s suggestions

treatment_protocol: treated for 24h with the following inhibitors or with solvent (DMSO): SU5402 (42uM); U0126 (10uM), SP600125 (20uM), LY294002 (20uM)

value: Colon Cancer

tag: agent

value: small molecular inhibitor LY294002


title: CD4 elite/viremic controller EC_3011

value: HIV

value: CD4 T


title: Colorectal Adenocarinoma 14872

source_name: genomic DNA from colorectal adenocarcinoma 14872

value: Fresh Frozen tissue


title: Colorectal Adenocarinoma 14873

source_name: genomic DNA from colorectal adenocarcinoma 14873

value: The ontario tumor bank network,Canada


title: Colorectal Adenocarinoma 14871

source_name: genomic DNA from colorectal adenocarcinoma 14871

value: Batch 1


title: Colorectal Adenocarinoma 14870

source_name: genomic DNA from colorectal adenocarcinoma 14870

value: Female


title: Colorectal Adenocarinoma 14874

source_name: genomic DNA from colorectal adenocarcinoma 14874


title: SW480-LY294002-2


title: SW480-SP600125-3

value: small molecular inhibitor SP600125


title: 293T_Aza-CR_exp2

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

institute: Tohoku University Graduate School of Medicine

description: Gene expression in 293T cells treated with Aza-CR

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 293T, Aza-CR, experiment 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: A human embryonic kidney cell line 293T was grown in Dulbecco’s modified Eagle’s medium (Sigma) supplemented with 10% fetal bovine serum (Invitrogen).

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 293T cells were seeded on 6-well tissue culture dishes and were treated with 5-aza-cytidine (Aza-CR, 25 uM) for 96 h. Medium was replaced every 24 h.

value: Aza-CR

value: embryonic kidney cell line 293T

tag: age

value: fetus


title: SW480-U0126-3

value: small molecular inhibitor U0126


title: 293T_PBS_exp2

description: Gene expression in 293T cells treated with PBS

source_name: 293T, PBS, experiment 2

treatment_protocol: 293T cells were seeded on 6-well tissue culture dishes and were treated with PBS for 96 h. Medium was replaced every 24 h.

value: control (PBS)


title: Colorectal Adenocarinoma 14880

source_name: genomic DNA from colorectal adenocarcinoma 14880

tag: sample type

value: Adenocarcinoma

value: Male

value: Proximal


title: SW480-SP600125-2

value: Colon Cancer


title: 293T_MeTA_exp2

description: Gene expression in 293T cells transfected with pcDNA6-3xFLAG-NFkB (AD)-MBD

source_name: 293T, MeTA, experiment 2

treatment_protocol: 293T cells were seeded on 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6-3xFLAG-NFkB (AD)-MBD. Transfection was performed using lipofectamine reagents (Invitrogen) according to supplier’s recommendations. The cells were harvested 48 h after transfection.

tag: transfection

value: MeTA


title: SW480-SP600125-1


title: Colorectal Adenocarinoma 14866

source_name: genomic DNA from colorectal adenocarcinoma 14866

value: Distal

tag: tissue source site

tag: batch


title: Colorectal Adenocarinoma 14878

source_name: genomic DNA from colorectal adenocarcinoma 14878

tag: disease state

tag: tumor subsite


title: Colorectal Adenocarinoma 14869

source_name: genomic DNA from colorectal adenocarcinoma 14869


title: SW480-U0126-1


title: SW480-SU5402-3

value: small molecular inhibitor SU5402


title: Colorectal Adenocarinoma 14864

source_name: genomic DNA from colorectal adenocarcinoma 14864

value: Fresh Frozen tissue

value: Rectum


title: Colorectal Adenocarinoma 14868

source_name: genomic DNA from colorectal adenocarcinoma 14868

value: The ontario tumor bank network,Canada

value: Batch 1


title: SW480-SU5402-1


title: 293T_Aza-CR_exp1

source_name: 293T, Aza-CR, experiment 1


title: SW480-DMSO-3

value: solvent (DMSO)


title: SW480-DMSO-1


title: Colorectal Adenocarinoma 14867

source_name: genomic DNA from colorectal adenocarcinoma 14867


title: SW480-SU5402-2


title: 293T_Vec_exp1

description: Gene expression in 293T cells transfected with pcDNA6/myc-His vector

source_name: 293T, Vector, experiment 1

treatment_protocol: 293T cells were seeded on 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6/myc-His vector. Transfection was performed using lipofectamine reagents (Invitrogen) according to supplier’s recommendations. The cells were harvested 48 h after transfection.

value: control (vector)


title: Colorectal Adenocarinoma 14862

source_name: genomic DNA from colorectal adenocarcinoma 14862

value: Female


title: 293T_PBS_exp1

source_name: 293T, PBS, experiment 1

value: embryonic kidney cell line 293T

value: fetus


title: 293T_Vec_exp2

source_name: 293T, Vector, experiment 2


title: SW480-LY294002-1

value: small molecular inhibitor LY294002


title: Colorectal Adenocarinoma 14865

source_name: genomic DNA from colorectal adenocarcinoma 14865

value: Adenocarcinoma


title: Colorectal Adenocarinoma 14861

source_name: genomic DNA from colorectal adenocarcinoma 14861

value: Male


title: Colorectal Adenocarinoma 14863

source_name: genomic DNA from colorectal adenocarcinoma 14863

value: Proximal


title: Adjacent non-tumor colorectal tissue 17803

description: Paired with tumor 17777

hyb_protocol: The biotinylated cRNA was hybridized to the BeadChips per standard Illumina hybridization protocol.

scan_protocol: The hybridized chips were stained and scanned using the Illumina HD BeadArray following the standard Illumina protocol.

data_processing: Scanned image and bead-level data processing were performed using the Illumina BeadStudio software v3.2. The summarized data for each bead type were then processed, log2 transformed and normalized using Robust Spline Normalization (RSN) as implemented in the R-based lumi package.

source_name: total RNA from adjacent non-tumor colorectal tissue 17803

label_protocol: Biotinylated, amplified cRNA was prepared from total RNA using the Illumina TotalPrep RNA Amplification Kit.

extract_protocol: Total RNA was isolated using the Trizol reagent according to the manufacturer’s protocol. The quality of the RNA samples was assessed using the Bio-Rad Experion RNA StdSens analysis kit.

value: Fresh Frozen Tissue

value: Normal adjacent to colorectal adenocarcinoma

tag: tissue pair

value: tumor 17777


title: iPS62 (feeder)-2

city: Sydney

first: Henry

last: Chung

address: High St

department: Clinical Sciences Bld

institute: Prince of Wales Hospital

hyb_protocol: Following fragmentation, cRNA was processed through second-cycle single stranded cDNA. Fragmented and labelled cDNA was then hybridized onto Affymetrix Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay manual).

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

data_processing: Gene array data is processed by Partek GenomeSuite software in which mean probeset signals for all probesets were analysed. A receiver operating curve (ROC) is generated by thresholding the computed value for the probesets. PLIER signals that pass this QC control is used for subsequent analysis.

source_name: iPSC maintained under feeder conditions

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay manual).

extract_protocol: Total RNA was extracted from cell cultures using TRIZOL (Invitrogen) as per manufacturer instructions.

value: iPSC

tag: culture condition

value: feeder


title: iPS65 (feeder-free)-2

source_name: iPSC maintained under feeder-free conditions

value: feeder-free


title: Colorectal Adenocarinoma 14860

source_name: genomic DNA from colorectal adenocarcinoma 14860

value: Fresh Frozen tissue

value: Rectum

value: The ontario tumor bank network,Canada


title: iPS65 (feeder-free)-1


title: Adjacent non-tumor colorectal tissue 17804

description: Paired with tumor 17778

source_name: total RNA from adjacent non-tumor colorectal tissue 17804

value: tumor 17778


title: Adjacent non-tumor colorectal tissue 17801

description: Paired with tumor 17775

source_name: total RNA from adjacent non-tumor colorectal tissue 17801

value: Female

value: tumor 17775


title: Colorectal Adenocarinoma 14859

source_name: genomic DNA from colorectal adenocarcinoma 14859

value: Batch 1


description: Paired with tumor 17776

source_name: total RNA from adjacent non-tumor colorectal tissue 17802

value: tumor 17776


title: Colorectal Adenocarinoma 14857

source_name: genomic DNA from colorectal adenocarcinoma 14856

value: Adenocarcinoma

value: Distal


title: Colorectal Adenocarinoma 14855

source_name: genomic DNA from colorectal adenocarcinoma 14854

value: Proximal


title: Colorectal Adenocarinoma 14853

source_name: genomic DNA from colorectal adenocarcinoma 14853

value: Male


title: E2 (feeder-free)-2

source_name: hESC maintained under feeder-free conditions

value: hESC


title: Adjacent non-tumor colorectal tissue 17797

description: Paired with tumor 17771

source_name: total RNA from adjacent non-tumor colorectal tissue 17797

value: Fresh Frozen Tissue

value: Normal adjacent to colorectal adenocarcinoma

value: tumor 17771


title: Adjacent non-tumor colorectal tissue 17799

description: Paired with tumor 17773

source_name: total RNA from adjacent non-tumor colorectal tissue 17799

value: tumor 17773


title: Colorectal Adenocarinoma 14852

source_name: genomic DNA from colorectal adenocarcinoma 14852

value: Fresh Frozen tissue

value: Transverse


title: Adjacent non-tumor colorectal tissue 17800

description: Paired with tumor 17774

source_name: total RNA from adjacent non-tumor colorectal tissue 17800

value: tumor 17774


title: Adjacent non-tumor colorectal tissue 17798

description: Paired with tumor 17772

source_name: total RNA from adjacent non-tumor colorectal tissue 17798

value: tumor 17772


title: Adjacent non-tumor colorectal tissue 17796

description: Paired with tumor 17770

source_name: total RNA from adjacent non-tumor colorectal tissue 17796

value: tumor 17770


title: Colorectal Adenocarinoma 14850

source_name: genomic DNA from colorectal adenocarcinoma 14850

value: Female

value: The ontario tumor bank network,Canada


title: E2 (feeder-free)-1

value: feeder-free


title: Colorectal Adenocarinoma 14856

source_name: genomic DNA from colorectal adenocarcinoma 14855

value: Adenocarcinoma

value: Rectum

value: Batch 1


title: E1 (feeder-free)-1


title: E2 (feeder-free)-3


title: iPS60 (feeder-free)-3

source_name: iPSC derived under feeder-free conditions

value: iPSC


title: Colorectal Adenocarinoma 14851

source_name: genomic DNA from colorectal adenocarcinoma 14851

value: Male

value: Distal


title: Colorectal Adenocarinoma 14849

source_name: genomic DNA from colorectal adenocarcinoma 14849


title: Adjacent non-tumor colorectal tissue 17795

description: Paired with tumor 17769

source_name: total RNA from adjacent non-tumor colorectal tissue 17795

value: Fresh Frozen Tissue

value: Normal adjacent to colorectal adenocarcinoma

value: tumor 17769


title: E1 (feeder-free)-2

value: hESC


title: iPS60 (feeder-free)-2


title: Colorectal Adenocarinoma 14848

source_name: genomic DNA from colorectal adenocarcinoma 14848

value: Fresh Frozen tissue


title: iPS60 (feeder-free)-1


title: Adjacent non-tumor colorectal tissue 17794

description: Paired with tumor 17768

source_name: total RNA from adjacent non-tumor colorectal tissue 17794

value: tumor 17768


title: Adjacent non-tumor colorectal tissue 17792

description: Paired with tumor 17766

source_name: total RNA from adjacent non-tumor colorectal tissue 17792

value: tumor 17766


title: iPS62 (feeder)-1

source_name: iPSC maintained under feeder conditions

value: feeder


title: Colorectal Adenocarinoma 14847

source_name: genomic DNA from colorectal adenocarcinoma 14847

value: Female

value: Proximal


title: iPS52 (feeder)-3

source_name: iPSC derived under feeder conditions


title: iPS52 (feeder)-2


title: Adjacent non-tumor colorectal tissue 17791

description: Paired with tumor 17765

source_name: total RNA from adjacent non-tumor colorectal tissue 17791

value: tumor 17765


description: Paired with tumor 17764

source_name: total RNA from adjacent non-tumor colorectal tissue 17790

value: tumor 17764


title: Colorectal Adenocarinoma 14846

source_name: genomic DNA from colorectal adenocarcinoma 14846

value: Adenocarcinoma

value: The ontario tumor bank network,Canada


title: Adjacent non-tumor colorectal tissue 17789

description: Paired with tumor 17763

source_name: total RNA from adjacent non-tumor colorectal tissue 17789

value: tumor 17763


title: Adjacent non-tumor colorectal tissue 17788

description: Paired with tumor 17762

source_name: total RNA from adjacent non-tumor colorectal tissue 17788

value: tumor 17762


title: iPS52 (feeder)-1

value: iPSC


title: hFF-3

source_name: Parental human fetal fibroblasts

value: fetal fibroblasts


title: Adjacent non-tumor colorectal tissue 17787

description: Paired with tumor 17761

source_name: total RNA from adjacent non-tumor colorectal tissue 17787

value: Fresh Frozen Tissue

value: Normal adjacent to colorectal adenocarcinoma

value: Male

value: tumor 17761


title: hFF-2


title: SW480-DMSO-2

value: Colon Cancer

value: solvent (DMSO)


title: SW480-U0126-2

value: small molecular inhibitor U0126


title: hFF-1


title: Colorectal Adenocarinoma 14843

source_name: genomic DNA from colorectal adenocarcinoma 14843

value: Fresh Frozen tissue

value: Female

value: Distal

value: Batch 1


title: Colorectal Adenocarinoma 14841

source_name: genomic DNA from colorectal adenocarcinoma 14841

value: Adenocarcinoma


title: E2 (feeder)-3

source_name: hESC maintained under feeder conditions

value: hESC

value: feeder


title: Colorectal Adenocarinoma 14844

source_name: genomic DNA from colorectal adenocarcinoma 14844

value: The ontario tumor bank network,Canada


title: Colorectal Adenocarinoma 14845

source_name: genomic DNA from colorectal adenocarcinoma 14845

value: Proximal


title: Colorectal Adenocarinoma 14875

source_name: genomic DNA from colorectal adenocarcinoma 14875


title: Colorectal Adenocarinoma 14842

source_name: genomic DNA from colorectal adenocarcinoma 14842


title: Adjacent non-tumor colorectal tissue 17786

description: Paired with tumor 17760

source_name: total RNA from adjacent non-tumor colorectal tissue 17786

value: tumor 17760


title: Adjacent non-tumor colorectal tissue 17784

description: Paired with tumor 17758

source_name: total RNA from adjacent non-tumor colorectal tissue 17784

value: Fresh Frozen Tissue

value: tumor 17758


title: Adjacent non-tumor colorectal tissue 17785

description: Paired with tumor 17759

source_name: total RNA from adjacent non-tumor colorectal tissue 17785

value: Normal adjacent to colorectal adenocarcinoma

value: Male

value: tumor 17759


title: Adjacent non-tumor colorectal tissue 17782

description: Paired with tumor 17756

source_name: total RNA from adjacent non-tumor colorectal tissue 17782

value: tumor 17756


title: ∆idr1∆idr2 double mutant 60 minutes after addition of iron, replicate 2

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

description:
raw data file 13126.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13127.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3

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

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

data_processing:
AnalyzerDG software for spotfinding. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel such that the 75th percentile in each channel was made equal. See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details.
VERA/SAM normalized log10 ratio (test/reference); see also: Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. 2006. SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics. 7:286.
Each Sample is based on two arrrays (one with dye-swap).

label: cy3, cy5

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium salinarum, iron

label_protocol: 5 ug quality-checked total RNA was direct-labeled with Cy3 and Cy5 dyes according to manufacturer's instructions (Kreatech, Alameda, CA).

growth_protocol: The Δura3 parent, Δidr2 and Δidr1, and Δ idr1Δidr2 mutant strains were grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CDM (Schmid et al., 2009, Mol Sys Biol, 5:282) with all trace metals except iron.

extract_protocol: RNA was prepared the following day using the Absolutely RNA miniprep kit according to manufacturer’s instructions (Agilent Technologies, Santa Clara, CA). RNA quality was measured using an Agilent Bioanalyzer as described (Schmid et al., 2009). Freedom from DNA contamination was determined on 200 ng samples of RNA in 25 cycles of PCR.

treatment_protocol: Cultures were split in half and FeSO4 was added to one half, while the other was continued under iron limitation. 8-mL samples were collected from each culture every 20 minutes for 60 minutes (see also experimental design, Supplementary Figure 1). The zero time point was harvested immediately before the addition of iron. At each time point, samples were removed from the culture, pelleted for 30 seconds at 15 krpm in a microcentrifuge and snap frozen in liquid nitrogen. Pellets were stored at -80°C overnight

tag: strain

tag: iron concentration (um)

tag: time (min)

label: cy5, cy3

source_name: Halobacterium standard reference sample

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6, 37C, 225 rpm) Halobacterium salinarum reference sample.


title: ∆idr1∆idr2 double mutant 60 minutes after addition of iron, replicate 1

description:
raw data file 13124.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13125.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3

treatment_protocol: Standard mid-log phase (OD600 - 0.5-0.6, 37C, 225 rpm) Halobacterium salinarum reference sample.


title: Adjacent non-tumor colorectal tissue 17783

description: Paired with tumor 17757

source_name: total RNA from adjacent non-tumor colorectal tissue 17783

value: tumor 17757


title: Colorectal Adenocarinoma 14838

description: Paired with normal adjacent 17809

source_name: genomic DNA from colorectal adenocarcinoma 14838

value: Fresh Frozen tissue


title: ∆idr1∆idr2 double mutant 40 minutes after addition of iron, replicate 2

description:
raw data file 13118.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13119.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3