title: subcutaneous adipose tissue needle biopsy Participant 3 exercise group baseline visit


title: subcutaneous adipose tissue needle biopsy Participant 2 diet group 6 month visit

status: Public on Jan 15 2013

type: RNA

city: Seattle

first: Karen

middle: Weber

last: Makar

state: WA

address: 1100 Fairview Ave N Po box 19024

country: USA

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background subtracted and quantile normalized in GenomeStudio (V2011.1, Gene Expression Module v1.9.0).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: adipose tissue_diet_6 month

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

extract_protocol: Qiagen adipose tissue Rneasy kit

tag: gender

value: female

tag: tissue

tag: sample group

value: diet

tag: time point

value: 6 month


title: JB6_HLF_B

city: Richland

first: Katrina

middle: M

last: Waters

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

description: Gene expression data from JB6 cells exposed to ionizing radiation

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

organism: Mus musculus

source_name: JB6 cells, HLF over-expression, replicate2

label_protocol: Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: Maintained in MEM + 5% fetal bovine serum + antibiotics and glutamax at preconfluence and passaged by trypsonation.  Stable RNA transfection was achieved using Phoenix retroviral packing cell system and puromycin selection.  Western blot and in situ hybridization used to confirm ectopic expression of HLF protein.

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: Normal growth media, randomly cycling, preconfluent cells were harvested for RNA extraction.  Three replicates were collected.

tag: cell line

tag: transfection

value: retroviral vector containing human HLF gene


title: CPCs passage 15 rep2

city: Tehran

first: SeyedAhmad

last: Mousavi

state: Tehran

address: Bani hashem st - Resalat hw

department: Molecular systems biology

country: Iran

institute: Royan institute

hyb_protocol: 750 ng of each cRNA sample was hybridized into Illumina’s Sentrix HumanHT-12 v4 Expression Bead Chips at 58 °C overnight according to Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (part # 11322355, rev.A).

scan_protocol: Chips were scanned with Illumina Bead Array Reader (Factor=1.5, PMT=552, Filter=100%)

data_processing: The data were normalised using Robust Spline Normalization normalisation with lumi in R

source_name: human heart biopsies isolated cardiac precursor cells (CPCs) passage 15

label_protocol: From 200 ng total RNA, generation of biotin-labeled cRNA was done using Illumina® TotalPrep™ RNA amplification Kit (Applied Biosystems, AMIL1791).

growth_protocol: cardiac precursor cells isolated from human heart right atria and ventricle were cultured in qrowth medium IMDM, 15% FBS, 1% l-glutamine and 1% peniciline/streptomycine supplemented with 10g/ml bFGF.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer instructions. Briefly, cells were dissolved in 1ml TRIzol reagent. Then they were lysed by vortexing and incubation for 5-10 min, after that 200 µl chloroform was added per 1 ml TRIzol and mixed by inversion. The sample was centrifuged at 12000×g for 15 min at 4°C. The upper layer was carefully removed and stored for RNA isolation. RNA was precipitated by adding 0.5 ml Isopropyl alcohol per 1 ml TRIzol reagent used for the initial homogenization. Samples were incubated at room temperature for 10 minutes and centrifuged at no more than 12,000 x g for 10 minutes at 4°C. Supernatant was carefully removed and the RNA pellet was washed once with 75% ethanol. The sample was vortexed and centrifuged at no more than 7,500 x g for 5 minutes at 4°C. After brief air drying, the RNA pellet was dissolved in RNase-free water and incubated for 10 min at 55°C. The quantity and quality of isolated RNA was evaluated by spectrophotometry.

value: heart tissue

tag: cell type

value: cardiac precursor cells

tag: passage


title: JB6_HLF_A

description: Gene expression data from JB6 cells transfected with containing human HLF gene

source_name: JB6 cells, HLF over-expression, replicate1


title: JB6_vector_C

description: Gene expression data from JB6 cells transfected with retroviral vector only

source_name: JB6 cells, vector only, replicate3

value: retroviral vector only


title: JB6_vector_B

source_name: JB6 cells, vector only, replicate2


title: SI E18_5 WT1_3

city: Irvine

first: Denise

last: Stephens

state: CA

address: 250 Sprague Hall

department: Biological Chemistry

institute: University of California, Irvine

description: Mouse proximal small intestine, embryonic day 18.5

hyb_protocol: 2ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0ST array.  The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing: The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).  The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

label: Biotin

label_protocol: The Ambion WT expression kit (Life Technologies, Carlsbad, CA) was used to prepare RNA samples for whole transcriptome microarray analysis.  Briefly, random hexamers that are tagged with a T7 promoter are used in first strand synthesis of cDNA.   Then using the T7 promoter, second strand synthesis is performed and the double stranded cDNA is subsequently used as a template in an in vitro transcription reaction to generate many copies of antisense cRNA.  10ug of antisense cRNA is input into a second cycle cDNA reaction using reverse transcriptase and random hexamers to produce single stranded DNA in the sense orientation.  The single-stranded DNA is fragmented to an average length of 70 bases and then labeled using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent that is covalently linked to biotin.

growth_protocol: Tissues from mice were collected at respective ages.

extract_protocol: Tissues were homogenized and total RNA extracted with Trizol.  RNA samples were cleaned up with Invitrogen Pure Link kit.

value: proximal small intestine

tag: genotype

value: wildtype CB6 mice


title: subcutaneous adipose tissue needle biopsy Participant 1 control group 6 month visit (technical rep1)

description:
technical replicate 1
071065-702

source_name: adipose tissue_control_6 month

value: control


title: Eso E18_5 WT4

description: Mouse esophagus, embryonic day 18.5

source_name: Mouse esophagus, embryonic day 18.5

value: esophagus


title: CPCs passage 12 rep2

source_name: human heart biopsies isolated cardiac precursor cells (CPCs) passage 12


title: Eso E18_5 WT2

description: Mouse esophagus, embryonic day 18.5


title: JB6_vector_A

source_name: JB6 cells, vector only, replicate1


title: CPCs passage 12 rep1


title: Eso E18_5 WT1

description: Mouse esophagus, embryonic day 18.5


title: JB6_HLF_C

source_name: JB6 cells, HLF over-expression, replicate3


title: E18.5 Get1 +/- Bladder 2-5

description: Bladder from Get1 +/- mouse, embryonic day 18.5

value: bladder

value: Get1 +/-  mice


title: C01-958

city: Houston

first: Keda

last: Yu

address: 6565 Fannin Street

institute: The Methodist Hospital Cancer Center, Houston, Texas

description: Gene expression data from TNBC

hyb_protocol: From each sample, 5 ug of labeled cRNA was hybridized onto an Affymetrix U133 Plus2 GeneChip

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

data_processing: The data analyzed by the software dChip, with the cutoff of P<0.01 and log2(fold-change)>1.1.

source_name: TNBC patient with residual disease

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

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

tag: disease state

value: Triple-negative breast cancer (TNBC)

value: breast

tag: prognosis

value: recurrence

tag: age (years)

tag: menopausal status

value: PRE


title: subcutaneous adipose tissue needle biopsy Participant 1 control group baseline visit (technical rep1)

description:
technical replicate 1
071116-702

source_name: adipose tissue_control_baseline

value: female

value: baseline


title: C01-824

description: Gene expression data from TNBC


title: C01-854

description: Gene expression data from TNBC


title: Liver_G20_4

city: Tokyo

first: Takashi

last: Kohda

address: 1-5-45 Yushima, Bunko-ku

department: Medical Research Institute

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression of neonatal liver from cumulus cell derived 20th generation clone mouse.

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 Mouse Genome Oligo Microarrays (G4112A) 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 (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% and 10% (XDR)).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v1_91-BETA and Grid: 014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.
Signals below background in the process of normalization and analysis.  Thus removed values were indicated as null. Omitted null data from the normalized data  leaving 34,140 probes. Signal for duplicated probes were represented by the mean value of them.

source_name: Somatic cell clones of 20 generations G20-1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 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).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Trizol kit (Lifetech) following the manufacturer's recommendations. Total RNA was then clean-up by RNAeasy column purification (QIAGEN). RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: liver

tag: age

value: neonate

tag: genetic background


title: CPCs passage 9 rep1

source_name: human heart biopsies isolated cardiac precursor cells (CPCs) passage 9

value: heart tissue


title: P0_Ovary_AMH_biological rep2

city: Pullman

first: Michael

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

description: Gene expression data from rat P0 Ovary incubated in the presence of 50 ng/ml AMH for 24 hours

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the   Affymetrix Fluidics Station 4500.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.

data_processing: The data were analyzed with Partek Genomic Suite 6.5 beta software  (Partek Inc., St. Louis, MO) uing RMA, GC-content adjusted algorithm background correction, quantile normalization, median polish methos for probesets summarization, and log values of probes signals using base 2.

organism: Rattus norvegicus

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: Zero-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously [Dole, G., et al., 2008].

extract_protocol: RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.

treatment_protocol: For each ovary sample from which RNA was collected for microarrays, 2-3 ovaries per well were cultured for 24 hours in the absence  (controls) or presence (treated) of either Amh (human Anti-Mülerian hormone)(50ng/mL), CTGF (connective tissue growth factor )(500 ng/mL), progesterone (P4) (10E-6 M),  estradiol (E2) (10E-6 M), TNF (tumor necrosis factor ) (1ng/mL), FGF2 (fibroblast growth factor 2) (50 ng/mL), Inhba (inhibin, beta A) (10 ng/mL).   Two or three ovaries from the same culture well (from different rat pups out of the same litter) and receiving the same treatment were pooled and homogenized together.  On any given day a culture experiment was performed, the treatment groups included untreated control ovaries and one to three different growth factor treatments.

tag: organ culture batch

tag: rna prep batch

tag: scan date

value: Sprague-Dawley rat

value: Female

value: Rat ovary

tag: developmental stage

value: Rat ovary  at day P0 incubated for 1 more day

tag: treatment


title: Liver_G20_2

tag: tissue

tag: gender

value: Somatic cell clones of 20 generations G20-1


title: CPCs passage 6 rep3

source_name: human heart biopsies isolated cardiac precursor cells (CPCs) passage 6

value: cardiac precursor cells


title: E18.5 Get1 +/- Bladder 1-4

source_name: Bladder from Get1 +/- mouse, embryonic day 18.5

value: bladder


title: CPCs passage 9 rep2


title: CPCs passage 6 rep2


title: E18.5 Get1 +/- Bladder 2-6

value: Get1 +/-  mice


title: Liver_G20_1


title: CPCs passage 6 rep1


title: C01-665

description: Gene expression data from TNBC

value: Triple-negative breast cancer (TNBC)

value: no recurrence


title: C01-465

description: Gene expression data from TNBC

value: breast

value: recurrence

value: POST


title: C01-3906

description: Gene expression data from TNBC


title: E16.5 WT Bladder 1-1

description: Bladder, embryonic day 16.5

source_name: Mouse bladder, embryonic day 16.5

value: wildtype CB6 mice


title: E16.5 WT Bladder 1-3

description: Bladder, embryonic day 16.5


title: HL60 pre-mIR-150 virus 2

first: Vivian

middle: G.

last: Oehler

address: 1100 Fairview Ave. North, D4-100

department: Clinical Research Division

data_processing: Signal intensities were quantile normalized using the Bioconductor package “lumi”

source_name: HL60 cell line, AML cell line

growth_protocol: PL21 were cultured in RPMI 1640 (Gibco-Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS) (JR Scientific, Inc, Woodland, CA), 5% penicillin and streptomycin, and 5% L-glutamine (Gibco-Invitrogen). HL60 cells were cultured as above except with 10% cosmic calf serum (Hyclone, Logan, UT, USA).

extract_protocol: Total RNA was extracted using Trizol and the Qiagen miRNEasy isolation kit per the manufacturer's instructions.

tag: time

value: 27 days post transduction

tag: cell line


title: CPCs passage 9 rep3

tag: cell type

tag: passage


title: E16.5 WT Bladder 1-2

description: Bladder, embryonic day 16.5

tag: genotype


title: C01-382

description: Gene expression data from TNBC

tag: disease state

tag: prognosis

value: PRE


title: Liver_G20_3

value: liver

value: female

value: neonate


title: E14.5 WT Bladder 1-3

description: Bladder, embryonic day 14.5

source_name: Mouse bladder, embryonic day 14.5


title: Liver_CC_1

description: Gene expression of neonatal liver from cumulus cell derived clone mouse.

source_name: Somatic cell clone CC-1

value: Somatic cell clone CC-1


title: C01-2780

description: Gene expression data from TNBC

tag: age (years)

tag: menopausal status


title: HL60 empty control virus 1

description: control

value: control


title: HL60 empty control virus 2

description: control


title: E14.5 WT Bladder 1-6

description: Bladder, embryonic day 14.5


title: C01-3726

description: Gene expression data from TNBC


title: Liver_CC_3

source_name: Somatic cell clone CC-3

tag: age

value: Somatic cell clone CC-3

tag: genetic background


title: Liver_CC_4

source_name: Somatic cell clone CC-4

value: Somatic cell clone CC-4


title: Liver_CC_2

source_name: Somatic cell clone CC-2

value: Somatic cell clone CC-2


title: C01-2726

description: Gene expression data from TNBC


title: PL21 pre-mIR-150 virus 2

source_name: PL21 cell line, AML cell line

value: 17 days post transduction


title: Liver_NC_4

description: Gene expression of neonatal liver from normal control produce by ICSI.

source_name: Normal control produced by ICSI NC-4

value: Normal control produced by ICSI NC-4


title: Liver_NC_3

source_name: Normal control produced by ICSI NC-3

value: Normal control produced by ICSI NC-3


title: C01-2392

description: Gene expression data from TNBC

value: Triple-negative breast cancer (TNBC)

value: breast


title: PL21 pre-mIR-150 virus 1


title: ESC in maintenance culture, biological rep 1

city: Ann Arbor

first: K Sue

last: OShea

state: MI

address: 3051 BSRB, 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

description: Gene expression data from uninduced ESC

hyb_protocol: fragmented cRNA hybridized to Affymetrix mouse 430 2.0 arrays for 16h, 45oC

scan_protocol: Array was washed and stained using an Affymetrix Gene Chip Fluidics Station 450, then scanned with an Affymetrix gene chip scanner 3000 7G with autoloader

data_processing: Signal intensity was normalized by MAS 5.0.

source_name: RNA from mouse ESC in maintenance culture

label_protocol: Biotinylated cRNA prepared following Affy protocols from 20 ug total RNA

growth_protocol: DMEM with 10% FBS, 10-4M beta-mercaptoethanol, 0.22 ug/ml l-glutamine, 1.33 ug/ml HEPES, 10000 U/ml hrLIF, 1.5ug/ml puromycin, 350 ug/ml G418

extract_protocol: Trizol extraction of total RNA performed following manufacturer's instructions

treatment_protocol: Transgene induction in the presence (and absence, controls) of 1 ug/ml doxycycline, for 24, 48, 72h

value: ES Cells

value: 129P2/OlaHsd (E14, Ainv15)

tag: age in vitro


title: Liver_NC_2

source_name: Normal control produced by ICSI NC-2

value: Normal control produced by ICSI NC-2


title: Liver_NC_1

source_name: Normal control produced by ICSI NC-1

value: Normal control produced by ICSI NC-1


title: ESC in maintenance culture, biological rep 2

description: Gene expression data from uninduced ESC


title: C01-2378

description: Gene expression data from TNBC

source_name: TNBC patient with residual disease

value: no recurrence

value: PRE


title: C01-2273

description: Gene expression data from TNBC

value: recurrence

value: POST


title: C01-1259

description: Gene expression data from TNBC

value: PERI


title: ESC in maintenance culture, biological rep 3

description: Gene expression data from uninduced ESC


title: HL60 pre-mIR-150 virus 1

value: 27 days post transduction


title: ESC expressing Neurog1 at 72h, biological rep 2

description: Gene expression data from ESC after 72h of transgene induction vs uninduced ESC

source_name: RNA from mouse ESC after 72h transgene induction


title: C01-1219

description: Gene expression data from TNBC


title: ESC expressing Neurog1 at 72h, biological rep 3


title: Brain_G20_4

description: Gene expression of neonatal brain from cumulus cell derived 20th generation clone mouse.

source_name: Somatic cell clones of 20 generations G20-1

value: brain

value: female

value: neonate


title: C01-0653-T02726

description: Gene expression data from TNBC


title: C01-0646-T02371

description: Gene expression data from TNBC


title: PL21 empty control virus 1

description: control

value: 17 days post transduction

value: control


title: Brain_G20_1

value: Somatic cell clones of 20 generations G20-1


title: Brain_G20_2


title: ESC expressing Neurog1 at 48h, biological rep 3

description: Gene expression data from ESC after 48h of transgene induction vs uninduced ESC

source_name: RNA from mouse ESC after 48h transgene induction


title: Brain_G20_3


title: ESC expressing Neurog1 at 48h, biological rep 2


title: PL21 empty control virus 2

description: control


title: ESC expressing Neurog1 at 72h, biological rep 1


title: Brain_CC_3

description: Gene expression of neonatal brain from cumulus cell derived clone mouse.

value: Somatic cell clone CC-3


title: C01-0617-T02021

description: Gene expression data from TNBC

value: Triple-negative breast cancer (TNBC)

value: breast


title: C01-0629-T02148

description: Gene expression data from TNBC


title: SSB447_IPTG-_rep2

city: Paris

first: Harald

last: Putzer

address: 13, rue P. et M. Curie

department: UPR9073, IBPC

country: France

institute: CNRS

description:
Cells grown in supplemented SMS minimal medium without IPTG harvested near OD600=0.6
RNaseYdepleted_Rep2

hyb_protocol: Hybridization was performed by Roche NimbleGen (Madison, WI, USA) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

data_processing:
An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region as described in (Nicolas et al., 2012 PMID: 22383849).
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347)
Normalization relied on a least variant gene set as described in (Durand et al. 2012 PMID: 22412379).
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: B. subtilis 168 Rnase Y depletion strain SSB447

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).

growth_protocol: B. subtilis RNase Y depletion strain SSB447 was grown in SMS minimal medium (Spizizen, 1958) supplemented with 0.75 % fructose, 0.1% L-glutamine and 2 mM IPTG. Antibiotics were added, at the following concentrations : 0.25 microg/ml erythromycin, 12.5 microg/ml lincomycin (mls  resistance) and 5 microg/ml kanamycin.

extract_protocol: Total RNA was isolated by the method described by Eymann et al. (PMID: 11948165) with minor modifications. The quality of the RNA preparations was assessed by means of the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were washed in SMS medium without IPTG and inoculated in fresh SMS medium at an OD600 of 0.05, with or without IPTG. The cultures were grown at 37°C and cell density was monitored every 20 min. When a first slow-down in growth became measurable, typically at an OD600 of 0.5, cells were harvested.

tag: crowth condition

value: IPTG-


title: SSB447_IPTG-_rep1

description:
Cells grown in supplemented SMS minimal medium without IPTG harvested near OD600=0.5
RNaseYdepleted_Rep1


title: ESC expressing Neurog1 at 48h, biological rep 1

value: ES Cells

value: 129P2/OlaHsd (E14, Ainv15)


title: Brain_CC_2

value: Somatic cell clone CC-2


title: C01-0639-T02292

description: Gene expression data from TNBC

value: no recurrence

value: PRE


title: ESC expressing Neurog1 at 24h, biological rep3

description: Gene expression data from ESC after 24h of transgene induction vs uninduced ESC

source_name: RNA from mouse ESC after 24h transgene induction


title: Brain_CC_1

value: Somatic cell clone CC-1


title: ESC expressing Neurog1 at 24h, biological rep2


title: C01-0590-T01554

description: Gene expression data from TNBC

value: recurrence

value: POST


title: Brain_CC_4

value: brain

value: female

value: Somatic cell clone CC-4


title: 159A-Ikaros transduced cells 48h, biological rep2

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
Gene expression data from 48h 159A transduced B3 cells
159A-Ikaros-48h_2

hyb_protocol: cRNA from two biological replicates per condition was hybridised to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) and Fragmented and labelled cDNA from three biological replicates per condition was hybridised to GeneChip Mouse Gene 1.0 ST (Affymetrix).

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

data_processing: Mouse Genome 4302 arrays were normalised using GCRMA within the GCRMA R/Bioconductor package (v.2.20.0) and hybridisation batch effects removed using the Limma R/Bioconductor package. Mouse Gene 1.0 ST arrays were normalised using RMA implemented in the Affy R/Bioconductor package (v.1.26.1).

source_name: 159A-Ikaros transduced cells 48h

label_protocol: GeneChip IVT labelling kit (Affymetrix) for hybridization on 430 2.0 arrays and GeneChip WT Terminal Labeling Kit (Affymetrix) for hybridization on MoGene 1.0 ST v1 arrays were used according to Affymetrix protocol.

growth_protocol: Mouse pre-B cell line B3 was grown in IMDM, 10% FCS and  1% penicillin-streptomycin.

extract_protocol: RNA was isolated with RNAbee (Ambion). Total RNA was amplified using either GeneChip Two-Cycle cDNA synthesis kit (Affymetrix) or GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix).

treatment_protocol: B3 cells were transduced as described  (Thompson et al., 2007, Immunity 26:335-344) with mouse stem cell virus (MSCV) vectors encoding wild-type Ikaros tagged with a haemagglutinin (HA) epitope followed by an internal ribosomal entry site (IRES) and GFP (HA-Ikaros-IRES-GFP), or the DNA binding-deficient Ikaros mutant 159A (HA-159A Ikaros-IRES-GFP). Ikaros inducible cells were generated by transducing B3 cells with a construct encoding a fusion protein of HA-tagged Ikaros and the estrogen receptor hormone-binding domain (HA-Ikaros-ERt2-IRES-GFP) or an ERt2-IRES-GFP control vector.

value: pre-B cells

tag: transduced with


title: ESC expressing Neurog1 at 24h, biological rep1


title: 159A-Ikaros transduced cells 48h, biological rep1

description:
Gene expression data from 48h 159A transduced B3 cells
159A-Ikaros-48h_1

value: Ikaros mutant 159A (HA-159A Ikaros-IRES-GFP)


title: Brain_NC_2

description: Gene expression of neonatal brain from normal control produce by ICSI.

value: neonate

value: Normal control produced by ICSI NC-2


title: C01-0530-T01146

description: Gene expression data from TNBC

value: Triple-negative breast cancer (TNBC)

value: breast


title: C01-0527-T01087

description: Gene expression data from TNBC


title: Brain_NC_4

value: Normal control produced by ICSI NC-4


title: Brain_NC_1

value: Normal control produced by ICSI NC-1


title: Ikaros transduced cells 48h, biological rep2

description:
Gene expression data from 48h Ikaros transduced B3 cells
Ikaros-48h_2

source_name: Ikaros transduced cells 48h

value: wild type Ikaros (HA-Ikaros-IRES-GFP)


title: SSB447_IPTG+_rep2

description:
Cells grown in supplemented SMS minimal medium with IPTG harvested near OD600=0.8
Reference_Rep2

value: IPTG+


title: Brain_NC_3

value: Normal control produced by ICSI NC-3


title: Ikaros transduced cells 48h, biological rep1

description:
Gene expression data from 48h Ikaros transduced B3 cells
Ikaros-48h_1


title: SSB447_IPTG+_rep1

description:
Cells grown in supplemented SMS minimal medium with IPTG harvested near OD600=0.7
Reference_Rep1


title: C01-0534-T01233

description: Gene expression data from TNBC

value: no recurrence


title: C01-0512-T0787

description: Gene expression data from TNBC


title: CRC_22

status: Public on Jan 14 2013

city: Macclesfield

first: Garry

last: Beran

address: Mereside, Alderley Park

department: Oncology

institute: AstraZeneca

description: Sample name: EA09076_94782_H133+_CRC-CL-022

hyb_protocol: Fragmentation, hybridization and scanning were conducted according to the Affymetrix Expression Analysis Technical Manual, following the procedures for format 49 arrays.

scan_protocol: Standard Affymetrix procedures using the GeneChip Scanner GS3000 and GeneChip Operating Software (GCOS) were utilized.

data_processing: Data were analyzed with R/Bioconductor; RMA expression values were calculated using justRMA as implemented in the affy package version 1.24.2; probe sets were annotated using the hgu133plus2.db version 2.3.5

source_name: Large Intestine, Adenocarcinoma

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3’ IVT Express kit with 100 ng input total RNA, essentially according to the instructions included with the kit.

extract_protocol: Total RNA was extracted (RNeasy Mini kit, Qiagen) from homogenized tissue samples. Integrity was verified by capillary gel electrophoresis (Bio Analyzer, Agilent Technologies).

tag: subtype

value: Y

value: N

value: MSS

value: Male

tag: ethnicity

value: Caucasian


title: CRC_40

description: Sample name: EA09076_93371_H133+_CRC-CL-040

tag: gender

value: Female

value: Asian/Pacific Islander


title: CRC_68

description: Sample name: EA09076_93366_H133+_CRC-CL-068-B

source_name: Mucinous Adenocarcinoma


title: CRC_57

description: Sample name: EA09076_93367_H133+_CRC-CL-057

source_name: Large Intestine, Mucinous Adenocarcinoma


title: CRC_38

description: Sample name: EA09076_93370_H133+_CRC-CL-038


title: CRC_06

description: Sample name: EA09076_93364_H133+_CRC-CL-006


title: CRC_62

description: Sample name: EA09076_93368_H133+_CRC-CL-062


title: CRC_03

description: Sample name: EA09076_93360_H133+_CRC-CL-003


title: CRC_30

description: Sample name: EA09076_93362_H133+_CRC-CL-030-A


title: CRC_49

description: Sample name: EA09076_93372_H133+_CRC-CL-049


title: Hardy Fraction F cell, rep 4

city: Memphis

first: Shann-Ching

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 8 microgram of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: Hardy Fraction F cell

label_protocol: RNA amplification and labeling was performed using the Nugen Ovation Pico Sustem

growth_protocol: RNA was extracted from flow sorted B cell subpopulations from Pax5 wild type C57BL/6 mice.

extract_protocol: Arcturus PicoPure

tag: strain

tag: genotype/variation

value: Pax5 wildtype

value: flow sorted B cell precursor populations

tag: fraction

value: Hardy Fraction F


title: CRC_50

description: Sample name: EA09076_93358_H133+_CRC-CL-050


title: CRC_11

description: Sample name: EA09076_93353_H133+_CRC-CL-011


title: CRC_36

description: Sample name: EA09076_93363_H133+_CRC-CL-036


title: CRC_55

description: Sample name: EA09076_93361_H133+_CRC-CL-055-A

source_name: Large Intestine, Villous Adenoma


title: CRC_58

description: Sample name: EA09076_93359_H133+_CRC-CL-058


title: CRC_17

description: Sample name: EA09076_93356_H133+_CRC-CL-017


title: Hardy Fraction F cell, rep 3

tag: cell type


title: Hardy Fraction F cell, rep 2


title: CRC_37

description: Sample name: EA09076_93351_H133+_CRC-CL-037


title: CRC_10

description: Sample name: EA09076_93357_H133+_CRC-CL-010


title: CRC_52

description: Sample name: EA09076_93349_H133+_CRC-CL-052-A


title: Hardy Fraction F cell, rep 5


title: CRC_21

description: Sample name: EA09076_93354_H133+_CRC-CL-021


title: Hardy Fraction F cell, rep 1


title: CRC_13

description: Sample name: EA09076_93347_H133+_CRC-CL-013

source_name: Large Intestine, Adenocarcinoma in Villous Adenoma


title: Hardy Fraction E cell, rep 4

source_name: Hardy Fraction E cell

value: Hardy Fraction E


title: CRC_15

description: Sample name: EA09076_93352_H133+_CRC-CL-015


title: CRC_41

description: Sample name: EA09076_93350_H133+_CRC-CL-041


title: CRC_60

description: Sample name: EA09076_93348_H133+_CRC-CL-060-A


title: Hardy Fraction E cell, rep 5


title: CRC_69

description: Sample name: EA09076_93345_H133+_CRC-CL-069-A

value: MSI


title: 1469-Pre

city: Rochester

first: Animesh

last: Pardanani

state: MN

address: 200 1st St SW

department: Hematology

institute: Mayo Clinic

data_processing: Data were quantile normalized using Illumina Genome Studio 2011 software

label_protocol: 300 ng of total RNA from each sample was labeled using the Illumina Total Prep RNA Amplification Kit following manufacturer's directions

extract_protocol: PBMCs were purified from whole blood by Ficoll separation. Total RNA was isolated using Qiagen

value: PBMC

value: F

tag: anemia response to treatment (responder / non-responder)

value: Non-responder

tag: pre or post-treatment

value: pre


title: CRC_64

description: Sample name: EA09076_93341_H133+_CRC-CL-064


title: CRC_14

description: Sample name: EA09076_93343_H133+_CRC-CL-014


title: 1200-Post

value: M

value: responder

value: post


title: 1200-Pre


title: CRC_12

description: Sample name: EA09076_93342_H133+_CRC-CL-012

value: N

value: Y

value: MSS


title: Hardy Fraction E cell, rep 1


title: CRC_04

description: Sample name: EA09076_93346_H133+_CRC-CL-004

value: Female

value: Caucasian


title: 1270-Post


title: CRC_31

description: Sample name: EA09076_93344_H133+_CRC-CL-031

value: Male


title: 1891-Post


title: Hardy Fraction E cell, rep 3

value: Pax5 wildtype

value: flow sorted B cell precursor populations


title: Hardy Fraction D cell, rep 5

source_name: Hardy Fraction D cell

value: Hardy Fraction D


title: 1469-Post


title: 1270-Pre


title: 1891-Pre


title: Hardy Fraction E cell, rep 2

value: Hardy Fraction E


title: CRC_08

description: Sample name: EA09076_93340_H133+_CRC-CL-008


title: 1973-Pre

value: PBMC


title: Hardy Fraction D cell, rep 3


title: Hardy Fraction D cell, rep 4


title: 1973-Post

value: F


title: CRC_23

description: Sample name: EA09076_93339_H133+_CRC-CL-023

value: MSI


title: 2032-Pre

value: pre


title: Hardy Fraction D cell, rep 2


title: CRC_43

description: Sample name: EA09076_93338_H133+_CRC-CL-043


title: 1892-Pre

value: M


title: Hardy Fraction C cell, rep 5

source_name: Hardy Fraction C cell

value: Hardy Fraction C


title: 1737-Pre

value: Non-responder


title: Hardy Fraction D cell, rep 1


title: CRC_70

description: Sample name: EA09076_93336_H133+_CRC-CL-070

value: N


title: 1943-Pre

value: responder


title: 1895-Post

value: post


title: CRC_33

description: Sample name: EA09076_93335_H133+_CRC-CL-033-A

value: Y

value: MSS


title: 1943-Post


title: 1892-Post


title: CRC_29

description: Sample name: EA09076_93337_H133+_CRC-CL-029-A

value: Female

value: Caucasian


title: 1848-Pre


title: Hardy Fraction C cell, rep 1

value: Pax5 wildtype

value: flow sorted B cell precursor populations


title: CRC_39

description: Sample name: EA09076_93333_H133+_CRC-CL-039


title: 1895-Pre


title: 601-Pre


title: 1737-Post


title: 601-Post


title: Hardy Fraction C cell, rep 4


title: 1848-Post


title: 1860-Post


title: Hardy Fraction C cell, rep 3


title: 2032-Post


title: Hardy Fraction B cell, rep 7

source_name: Hardy Fraction B cell

value: Hardy Fraction B


title: CRC_35

description: Sample name: EA09076_93334_H133+_CRC-CL-035-A

value: Male


title: CRC_34

description: Sample name: EA09076_93331_H133+_CRC-CL-034


title: 1860-Pre

value: PBMC


title: 1899-Post

value: F


title: Hardy Fraction C cell, rep 2


title: CRC_09

description: Sample name: EA09076_93332_H133+_CRC-CL-009


title: 1899-Pre

value: pre


title: 1836-Post

value: M


title: CRC_27

description: Sample name: EA09076_93330_H133+_CRC-CL-027


title: Hardy Fraction B cell, rep 6


title: CRC_16

description: Sample name: EA09076_93329_H133+_CRC-CL-016


title: Hardy Fraction B cell, rep 5


title: 1836-Pre


title: Hardy Fraction B cell, rep 4


title: CRC_66

description: Sample name: EA09076_93327_H133+_CRC-CL-066

source_name: Adenocarcinoma


title: CRC_47

description: Sample name: EA09076_93328_H133+_CRC-CL-047-A


title: 1883-Pre


title: 1883-Post


title: Hardy Fraction B cell, rep 2


title: 1941-Pre


title: 1941-Post


title: Hardy Fraction B cell, rep 3


title: Hardy Fraction A cell, rep 7

source_name: Hardy Fraction A cell

value: Hardy Fraction A


title: CRC_18

description: Sample name: EA09076_93326_H133+_CRC-CL-018-A


title: Nr30_LFK3

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

description: enriched guard cell fraction of Arabidopsis thaliana

hyb_protocol: one-color microarray-based gene expression analysis protocol provided by Agilent including the one-color RNA spike-in kit (v5.0.1, 2006)

scan_protocol: Agilent Microarray Scanner,extended dynamic range (XDR) at high resolution (5 µm)

data_processing: The data were normalized using quantile-quantile as normalization method

organism: Arabidopsis thaliana

source_name: Col-0 ; replicate 2

growth_protocol: Arapidopsis thaliana  plants were grown in soil and cultivated in a greenhouse under short-day conditions (8 h light/16 h darkness, 22°C/16°C) with illumination by 100 µmol m-2 sec-1 white light. Samples were collected after 4-5h of illumination.

extract_protocol: RNeasy Plant Mini Kit, according to the manufacturers protocol

treatment_protocol:
low humidity treatment: The soil surface of single potted 6-7 week old Arabidopsis thaliana plants was covered with foil to prevent excessive water evaporiation. The plants were subjected to an air stream of 20 ± 5 % rh in a climate chamber at 22 ± 2 °C and 100 µmol m-2 sec-1 white light. Controls were kept at >80% rh.
ABA-Spray treatment: Leaves were sprayed with 50 µM +/- abscisic acid solution, containing 25 µM biologically active ABA and 0.01% (v/v) Triton X-100.After 4 hours epidermal peels were harvested.

tag: protocol

value: 4h >85% relative humidity


title: CRC_61

description: Sample name: EA09076_93325_H133+_CRC-CL-061-D

value: N


title: CRC_45

description: Sample name: EA09076_93324_H133+_CRC-CL-045-A


title: CRC_19

description: Sample name: EA09076_93323_H133+_CRC-CL-019

value: MSI


title: Nr28_LF4

source_name: Col-0 ; replicate 4

label_protocol: one-color microarray-based gene expression analysis protocol provided by Agilent including the one-color RNA spike-in kit (v5.0.1, 2006)

value: 4h 20% relative humidity


title: Hardy Fraction B cell, rep 1


title: Nr31_LFK4

source_name: Col-0 ; replicate 3


title: CRC_02

description: Sample name: EA09076_93321_H133+_CRC-CL-002

value: Y


title: Nr32_LFK5


title: Nr26_LF2


title: Hardy Fraction A cell, rep 2


title: CRC_59

description: Sample name: EA09076_93322_H133+_CRC-CL-059

value: MSS


title: Nr29_LFK2

source_name: Col-0 ; replicate 1


title: Nr27_LF3


title: Hardy Fraction A cell, rep 3


title: Hardy Fraction A cell, rep 4


title: Hardy Fraction A cell, rep 5


title: Nr25_LF1


title: Nr24_gl11Kontr

source_name: gl1-1 ; replicate 4

value: 4h control-Spray


title: CRC_46

description: Sample name: EA09076_93320_H133+_CRC-CL-046-A

source_name: Large Intestine, Adenocarcinoma

value: Caucasian


title: CRC_32

description: Sample name: EA09076_93318_H133+_CRC-CL-032-A


title: Hardy Fraction A cell, rep 1

value: Pax5 wildtype


title: CRC_51

description: Sample name: EA09076_93316_H133+_CRC-CL-051


title: Hardy Fraction CLP cell, rep 7

source_name: Hardy Fraction CLP cell

value: flow sorted B cell precursor populations

value: Hardy Fraction CLP


title: Hardy Fraction CLP cell, rep 6


title: Nr22_gl11Kontr

source_name: gl1-1 ; replicate 2


title: Hardy Fraction CLP cell, rep 4


title: Nr23_gl11Kontr

source_name: gl1-1 ; replicate 3


title: Hardy Fraction CLP cell, rep 5


title: Bcell02

type: genomic

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: The intensities of the images are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Naive B-cells

label_protocol: Standard Illumina labelling protocol

extract_protocol: genomic DNA extraction

value: Male

tag: health state

value: Healthy donor

value: Naive B-cells

value: Non-mutant donor


title: Nr21_gl11Kontr

source_name: gl1-1 ; replicate 1


title: CRC_05

description: Sample name: EA09076_93319_H133+_CRC-CL-005


title: Bcell01

value: Female


title: CRC_20

description: Sample name: EA09076_93315_H133+_CRC-CL-020


title: CRC_24

description: Sample name: EA09076_93317_H133+_CRC-CL-024


title: Bcell03


title: PBMC014

source_name: Peripheral blood mononuclear cells

value: Peripheral blood mononuclear cells


title: LCL7

source_name: Immortalized B-cells

value: EBV immortalized B-cells


title: Nr20_gl11ABA

value: 4h ABA Spray


title: LCL6


title: LCL5


title: Hardy Fraction A cell, rep 6

value: Hardy Fraction A


title: PBMC012


title: Nr19_gl11ABA


title: CRC_44

description: Sample name: EA09076_93314_H133+_CRC-CL-044

value: N


title: CRC_63

description: Sample name: EA09076_93312_H133+_CRC-CL-063

value: Y


title: AG07896

source_name: Werner Syndrome

value: Werner Syndrome

value: WRN mutation


title: AG03364

value: Non-mutant patient


title: AG11385


title: Hardy Fraction CLP cell, rep 3

value: Pax5 wildtype


title: Hardy Fraction CLP cell, rep 2

value: flow sorted B cell precursor populations


title: Nr18_gl11ABA_v5


title: CRC_42

description: Sample name: EA09076_93313_H133+_CRC-CL-042

value: MSS

value: Caucasian


title: Nr15_BL22

description: leaf of Arabidopsis thaliana

value: 5h light


title: Nr14_BL21

description: leaf of Arabidopsis thaliana


title: Hardy Fraction CLP cell, rep 1

value: Hardy Fraction CLP


title: Nr16_BL23

description: leaf of Arabidopsis thaliana


title: Nr17_gl11ABA


title: NORMALparotid 2

city: Grand Rapids

first: Karl

last: Dykema

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data were obtained from normal tissue, untreated tumors, and tumors treated with rapamycin.

hyb_protocol: Agilent hybridization protocol 65C 10rpm 17 h.

scan_protocol: Agilent arrays were scanned using the Agilent Scanner G2565BA.

data_processing: The data was first processed by background correction and then quantile normalization.

label: Agilent  part #5190-0442 Quick-Amp Labeling kit 1-color.

source_name: Mus musculus

label_protocol: 300 ng of Qiagen-purified total RNA

value: parotid

tag: treatment


title: NORMALSubmandibular

value: Submandibular


title: CRC_01

description: Sample name: EA09076_93310_H133+_CRC-CL-001

value: MSI

value: Male


title: TUMOR_rap3

value: TUMOR

value: rapamycin

tag: days


title: TUMOR_rap14 2


title: CRC_65

description: Sample name: EA09076_93311_H133+_CRC-CL-065

source_name: Adenocarcinoma

value: N

value: Female


title: CRC_28

description: Sample name: EA09076_93309_H133+_CRC-CL-028-A

value: Y


title: Nr13_BL20

description: leaf of Arabidopsis thaliana


title: PBMC011

value: Healthy donor

value: Peripheral blood mononuclear cells

value: Non-mutant donor


title: Nr8_L24

description: enriched guard cell fraction of Arabidopsis thaliana


title: TUMOR 2


title: AG19911

value: Werner Syndrome

value: EBV immortalized B-cells

value: LMNA mutation


title: Nr7_L23

value: 5h light


title: AG15693

source_name: Hutchinson-Gilford Progeria Syndrome

value: Hutchinson-Gilford Progeria Syndrome

value: Non-mutant patient


title: Insulinoma metastasis 21

status: Public on Jan 13 2013

city: Utrecht

first: Floryne

last: Buishand

address: Yalelaan 108

department: Clinical Sciences of Companion Animals

country: Netherlands

institute: Faculty of Veterinary Medicine, Utrecht University

description: Insulinoma lymph node metastasis from dog 21, DFI 63 days, ST 442 days

hyb_protocol: Microarray slides were washed for 1 min in 2x SSC containing 0.05% Sodium dodecyl sulphate (SDS) at room temperature (RT), incubated in 0.25% sodium borohydride and 0.25% SDS in 2x SSC for 30 min at 420C  and then rinsed 5 times in double distilled water at RT.  Slides were incubated for 45 minutes at 420C in pre-warmed pre-hybridization buffer (2X) consisting of 10xSSC, 25% formamide, 0.1% SDS and 1% BSA. Slides were washed 5 times in water followed by 5 times in isopropanol at RT and air dried. To 40 µl containing 2.5 µg of each Cy3 and Cy5 labeled RNA 40 µl hybridization buffer was added consisting of 50% formamide, 0.2% SDS and 200 µg/ml sheared herring sperm DNA. The mixture was heated at 95°C for 5 min, centrifuged for 2 min at 12,000xg and hybridized to the slides at 420C for 16 hours using hybridization chambers (Corning Life Sciences) in a water bath. After hybridization, slides were washed three times: first a low-stringency wash for 4 min at RT in 1xSSC and 0.2% SDS, next a high-stringency wash in 0.1% SDS and 0.2% SDS for 4 min and finally 2 washes in 0.1xSSC at room temperature. Slides were blown dry using compressed nitrogen.

scan_protocol: Slides were scanned using an Agilent G2565AA DNA microarray scanner (100% laser power, 30% photomultiplier tube).

data_processing: Image analysis was carried out using Imagene 5.0 software (Biodiscovery Inc). Data were normalized based on Lowess print-tip normalization by using the gene spots to calculate the Lowess line for each sub grid and then applying the these lines to all spots.

organism: Canis lupus familiaris

source_name: Insulinoma metastasis 21

label_protocol: Total RNA isolated from snap frozen insulinoma tissue was used for cRNA synthesis. About 2 µg total RNA was reverse transcribed using Superscript II reverse transcriptase and T7 promoter coupled poly T primers (5' GGCCAGTGAATTGTAATACGACTCACCTATAGGGAGG CGGT). After second strand synthesis, cDNA products were purified using QIAquick PCR Purification Kit and transcribed using the T7 Megascript kit (Ambion) using a UTP to 5-(3-aminoallyl)-UTP ratio of 1/3.5. The RNeasy mini kit (Qiagen) was used to clean the resulting cRNA. Three µg cRNA was coupled to Cy3 or Cy5 fluorophores. Labeled cRNA was cleaned using ChromaSpin-30 columns and cRNA samples with specific activity of 2-5% dye-labeled nucleosides were used for microarray hybridization.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Leusden, The Netherlands) according to the manufacturer’s protocol. To prevent contamination of the samples with genomic DNA, an on-column DNAse treatment was performed.

tag: dog id

tag: tissue

value: Lymph node metastasis

tag: disease free interval (days)

tag: survival time (days)

tag: disease state

value: insulinoma

source_name: Reference pool

tag: sample type

value: All 20 INS samples

value: primary and metastatic tumors


title: Insulinoma metastasis 20

description: Insulinoma lymph node metastasis from dog 20, DFI 0 days, ST 1 day

source_name: Insulinoma metastasis 20


title: Nr6_L22

source_name: Col-0 ; replicate 2


title: AG15695

tag: gender


title: TUMOR_rap14

tag: subtype

value: TUMOR

value: rapamycin


title: Primary insulinoma 21

description: Primary insulinoma from dog 21, DFI 63 days, ST 442 days

source_name: Primary insulinoma 21

value: Primary tumor


title: Primary insulinoma 14

description: Primary insulinoma from dog 14, DFI and ST not applicable, since dog did not underwent surgery

source_name: Primary insulinoma 14


title: Primary insulinoma 9

description: Primary insulinoma from dog 9, DFI 546 days, ST 1045 days, alive with disease at end of follow-up

source_name: Primary insulinoma 9


title: NORMALparotid

value: parotid


title: Insulinoma metastasis 15

description: Insulinoma liver metastasis from dog 15, DFI 0 days, ST 0 days

source_name: Insulinoma metastasis 15

value: Liver metastasis


title: Insulinoma metastasis 16

description: Insulinoma lymph node metastasis from dog 16, DFI 7 days, ST 69 days

source_name: Insulinoma metastasis 16


title: Primary insulinoma 20

description: Primary insulinoma from dog 20, DFI 0 days, ST 1 day

source_name: Primary insulinoma 20


title: Primary insulinoma 15

description: Primary insulinoma from dog 15, DFI 0 days, ST 0 days

source_name: Primary insulinoma 15


title: Nr5_L21

source_name: Col-0 ; replicate 1


title: Insulinoma metastsis 14

description: Insulinoma liver metastasis from dog 14, DFI and ST not applicable, since dog did not underwent surgery

source_name: Insulinoma metastasis 14


title: Insulinoma metastsis 9

description: Insulinoma lymph node metastasis from dog 9, DFI 546 days, ST 1045 days, alive with disease at end of follow-up

source_name: Insulinoma metastsis 9


title: Insulinoma metastasis 17

description: Insulinoma lymph node metastasis from dog 17, DFI 509 days, ST 645 days

source_name: Insulinoma metastasis 17


title: Insulinoma metastasis 13

description: Insulinoma lymph node metastasis from dog 13, DFI 1565 days, ST 1565 days, alive and well without disease at end of follow-up

source_name: Insulinoma metastasis 13


title: Primary insulinoma 16

description: Primary insulinoma from dog 16, DFI 7 days, ST 69 days

source_name: Primary insulinoma 16


title: Primary insulinoma 13

description: Primary insulinoma from dog 13, DFI 1565 days, ST 1565 days, alive and well without disease at end of follow-up

source_name: Primary insulinoma 13


title: Primary insulinoma 19

description: Primary insulinoma from dog 19, DFI 122 days, ST 166 days

source_name: Primary insulinoma 19

source_name: Reference pool


title: B728a_Apoplastic_LabC_Rep2

status: Public on Jan 12 2013

city: Ames

first: Gwyn

middle: A

last: Beattie

state: IA

address: 207 Science I

department: Dept of Plant Pathology & Microbiology

institute: Iowa State University

hyb_protocol: Hybridization was performed by Roche NimbleGen Inc., Reykjavík, Iceland, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Apoplastic_LabC.txt  (linked as supplementary file on Series record).

organism: Pseudomonas syringae pv. syringae B728a

source_name: Pseudomonas syringae B728a wild type, Apoplastic cells

label_protocol: Labeling was performed by Roche NimbleGen Inc., Reykjavík, Iceland, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells were grown on solid King’s B medium containing rifampin (50 μg/ml).  Cells were transferred to liquid HMM and subcultured twice in HMM with aeration via shaking at 25°C.  HMM medium contained 0.2% D-fructose, 0.2% D-mannitol, 0.2% succinate, 10 mM L-glutamine, 10 µM FeCl3, 10 µM N-(β-ketocaproyl)-L-homoserine lactone (AHL), 50 mM potassium phosphate buffer, 7.6 mM (NH4)2SO4, 1.7 mM MgCl2, and 1.7 mM NaCl.   When the cells reached late-log phase (5x108 CFU/ml), they were collected by centrifugation at 5,000xg for 10 min.

extract_protocol: In the in vitro treatments, RNA was stabilized using RNAprotect Bacteria Reagent (Qiagen Inc., Valencia, CA).  In the in planta treatments, RNA was stabilized using an acidic phenol RNA stabilizing solution due to the large volumes required.  Total RNA was extracted from the cells using a Qiagen RNeasy mini kit and DNA was removed using the on-column DNase I digestion with subsequent DNase I removal.  RNA integrity was evaluated using an Agilent 2100 bioanalyzer.

treatment_protocol:
Cells were inoculated by vacuum infiltration into bean leaves.  Plants were incubated at 25°C for 48 h with supplemental lighting, and cells were recovered by submersion, maceration, and sonication.
For the in vitro treatments, the HMM-grown cells were resuspended in HMM medium lacking L-glutamine, FeCl3, AHL and (NH4)SO4, designated HMM-FeN medium.  The cells were washed in HMM-FeN and resuspended in HMM-FeN to a final density of 2.5x109 CFU/ml.  Aliquots were transferred to 5 test tubes and diluted to 2.5x108 CFU/ml with either 1) HMM medium, 2) HMM medium with NaCl to a final concentration of 0.23 M, 3) HMM medium with H2O2 to a final concentration of  0.5 mM, 4) HMM medium lacking FeCl3 but with N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) to a final concentration of 100 µM, or 5) HMM medium lacking L-glutamine, (NH4)SO4 and AHL; these were designated as the basal medium, osmotic stress, Apoplastic growth, iron limitation and nitrogen limitation treatments, respectively. At the end of the treatments, the cells were immediately diluted with an RNA stabilizing agent, harvested by centrifugation, and stored as cell pellets at -20°C.  All treatments were performed at 25°C with aeration via shaking.
For the in planta treatments, the HMM-grown cells were suspended in water containing 0.01% of the biosurfactant Silwet L-77 to a density of 1x106 CFU/ml.  To establish epiphytic populations, bacteria were spray inoculated onto leaves.  Plants were incubated for 24 h in a 95% RH mist chamber, at which time the chamber was partially opened until the water on the leaves had visibly evaporated and was then re-sealed to allow incubation without active humidification for another 48 h.  The incubations were at 25°C with ambient but not supplemental lighting.  A total of 400 to 600 primary leaves were collected, immediately submerged in an RNA stabilizing solution, sonicated for 10 min, and then physically removed from the solution.  To establish apoplastic populations, bacteria were introduced by vacuum infiltration into leaves that were submerged in the inoculum.  Plants were incubated for 48 h under plant growth lights with a 12-h photoperiod.  A total of 40 to 80 leaves were collected and immediately submerged in an RNA stabilizing solution.  The leaves were cut into squares (~ 3x3 mm2) while submerged, and the plant tissues and liquid were sonicated for 10 min.  The solution was filtered through Whatman filter paper #1, with repeated filter changes.
For both in planta treatments, the cells in the suspension (epiphytic cells) or filtrate (apoplastic cells) were collected by centrifugation, suspended in the residual supernatant, separated from plant debris by filtration through a 5-µm filter with repeated filter changes, again harvested by centrifugation, and stored as cell pellets at -20°C.

tag: genotype

value: Wild type

value: Apoplastic

tag: lab

value: C


title: Primary insulinoma 17

description: Primary insulinoma from dog 17, DFI 509 days, ST 645 days

source_name: Primary insulinoma 17


title: B728a_Apoplastic_LabC_Rep1


title: B728a_Apoplastic_LabB_Rep2

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Apoplastic_LabB.txt  (linked as supplementary file on Series record).

value: B


title: Primary insulinoma 11

description: Primary insulinoma from dog 11, DFI 462 days, ST 464 days

source_name: Primary insulinoma 11


title: AG15694

source_name: Hutchinson-Gilford Progeria Syndrome

value: Female

tag: cell type

value: EBV immortalized B-cells

tag: genotype/variation


title: Insulinoma metastasis 11

description: Insulinoma lymph node metastasis from dog 11, DFI 462 days, ST 464 days

source_name: Insulinoma metastasis 11


title: B728a_Apoplastic_LabB_Rep1


title: B728a_Apoplastic_LabA_Rep2

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Apoplastic_LabA.txt  (linked as supplementary file on Series record).

value: A


title: B728a_Apoplastic_LabA_Rep1


title: B728a_Epiphytic_LabC_Rep2

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Epiphytic_LabC.txt  (linked as supplementary file on Series record).

source_name: Pseudomonas syringae B728a wild type, Epiphytic cells

treatment_protocol:
Cells were inoculated by spray application onto bean leaves.  Plants were incubated at 25°C for 24 h in a mist chamber with humidification to 95% RH and then for 48 h in the absence of visible water on the leaf surfaces, and cells were recovered by submersion and sonication.
For the in vitro treatments, the HMM-grown cells were resuspended in HMM medium lacking L-glutamine, FeCl3, AHL and (NH4)SO4, designated HMM-FeN medium.  The cells were washed in HMM-FeN and resuspended in HMM-FeN to a final density of 2.5x109 CFU/ml.  Aliquots were transferred to 5 test tubes and diluted to 2.5x108 CFU/ml with either 1) HMM medium, 2) HMM medium with NaCl to a final concentration of 0.23 M, 3) HMM medium with H2O2 to a final concentration of  0.5 mM, 4) HMM medium lacking FeCl3 but with N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) to a final concentration of 100 µM, or 5) HMM medium lacking L-glutamine, (NH4)SO4 and AHL; these were designated as the basal medium, osmotic stress, Apoplastic growth, iron limitation and nitrogen limitation treatments, respectively. At the end of the treatments, the cells were immediately diluted with an RNA stabilizing agent, harvested by centrifugation, and stored as cell pellets at -20°C.  All treatments were performed at 25°C with aeration via shaking.
For the in planta treatments, the HMM-grown cells were suspended in water containing 0.01% of the biosurfactant Silwet L-77 to a density of 1x106 CFU/ml.  To establish epiphytic populations, bacteria were spray inoculated onto leaves.  Plants were incubated for 24 h in a 95% RH mist chamber, at which time the chamber was partially opened until the water on the leaves had visibly evaporated and was then re-sealed to allow incubation without active humidification for another 48 h.  The incubations were at 25°C with ambient but not supplemental lighting.  A total of 400 to 600 primary leaves were collected, immediately submerged in an RNA stabilizing solution, sonicated for 10 min, and then physically removed from the solution.  To establish apoplastic populations, bacteria were introduced by vacuum infiltration into leaves that were submerged in the inoculum.  Plants were incubated for 48 h under plant growth lights with a 12-h photoperiod.  A total of 40 to 80 leaves were collected and immediately submerged in an RNA stabilizing solution.  The leaves were cut into squares (~ 3x3 mm2) while submerged, and the plant tissues and liquid were sonicated for 10 min.  The solution was filtered through Whatman filter paper #1, with repeated filter changes.
For both in planta treatments, the cells in the suspension (epiphytic cells) or filtrate (apoplastic cells) were collected by centrifugation, suspended in the residual supernatant, separated from plant debris by filtration through a 5-µm filter with repeated filter changes, again harvested by centrifugation, and stored as cell pellets at -20°C.

value: Epiphytic


title: B728a_Epiphytic_LabA_Rep1

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Epiphytic_LabA.txt  (linked as supplementary file on Series record).


title: B728a_Epiphytic_LabA_Rep2


title: B728a_Epiphytic_LabC_Rep1


title: B728a_Epiphytic_LabB_Rep2

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Epiphytic_LabB.txt  (linked as supplementary file on Series record).


title: B728a_Epiphytic_LabB_Rep1


title: B728a_Low N_LabC_Rep1

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Low N_LabC.txt  (linked as supplementary file on Series record).

source_name: Pseudomonas syringae B728a wild type, Nitrogen limited

treatment_protocol:
Washed, late log-phase cells were incubated in HMM medium lacking L-glutamine, (NH4)SO4 and AHL and 2.5x109 CFU/ml for 2 h at 25°C.
For the in vitro treatments, the HMM-grown cells were resuspended in HMM medium lacking L-glutamine, FeCl3, AHL and (NH4)SO4, designated HMM-FeN medium.  The cells were washed in HMM-FeN and resuspended in HMM-FeN to a final density of 2.5x109 CFU/ml.  Aliquots were transferred to 5 test tubes and diluted to 2.5x108 CFU/ml with either 1) HMM medium, 2) HMM medium with NaCl to a final concentration of 0.23 M, 3) HMM medium with H2O2 to a final concentration of  0.5 mM, 4) HMM medium lacking FeCl3 but with N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) to a final concentration of 100 µM, or 5) HMM medium lacking L-glutamine, (NH4)SO4 and AHL; these were designated as the basal medium, osmotic stress, Apoplastic growth, iron limitation and nitrogen limitation treatments, respectively. At the end of the treatments, the cells were immediately diluted with an RNA stabilizing agent, harvested by centrifugation, and stored as cell pellets at -20°C.  All treatments were performed at 25°C with aeration via shaking.
For the in planta treatments, the HMM-grown cells were suspended in water containing 0.01% of the biosurfactant Silwet L-77 to a density of 1x106 CFU/ml.  To establish epiphytic populations, bacteria were spray inoculated onto leaves.  Plants were incubated for 24 h in a 95% RH mist chamber, at which time the chamber was partially opened until the water on the leaves had visibly evaporated and was then re-sealed to allow incubation without active humidification for another 48 h.  The incubations were at 25°C with ambient but not supplemental lighting.  A total of 400 to 600 primary leaves were collected, immediately submerged in an RNA stabilizing solution, sonicated for 10 min, and then physically removed from the solution.  To establish apoplastic populations, bacteria were introduced by vacuum infiltration into leaves that were submerged in the inoculum.  Plants were incubated for 48 h under plant growth lights with a 12-h photoperiod.  A total of 40 to 80 leaves were collected and immediately submerged in an RNA stabilizing solution.  The leaves were cut into squares (~ 3x3 mm2) while submerged, and the plant tissues and liquid were sonicated for 10 min.  The solution was filtered through Whatman filter paper #1, with repeated filter changes.
For both in planta treatments, the cells in the suspension (epiphytic cells) or filtrate (apoplastic cells) were collected by centrifugation, suspended in the residual supernatant, separated from plant debris by filtration through a 5-µm filter with repeated filter changes, again harvested by centrifugation, and stored as cell pellets at -20°C.

value: Nitrogen limited


title: B728a_Low N_LabB_Rep2

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Low N_LabB.txt  (linked as supplementary file on Series record).


title: B728a_Low N_LabC_Rep2


title: B728a_Low N_LabB_Rep1


title: B728a_Low Fe_LabB_Rep2

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Low Fe_LabB.txt  (linked as supplementary file on Series record).

source_name: Pseudomonas syringae B728a wild type, Iron limited

treatment_protocol:
Washed, late log-phase cells were incubated in HMM medium lacking FeCl3 but with the strong chelator N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) at a final concentration of 100 µM and 2.5x109 CFU/ml for 2 h at 25°C.
For the in vitro treatments, the HMM-grown cells were resuspended in HMM medium lacking L-glutamine, FeCl3, AHL and (NH4)SO4, designated HMM-FeN medium.  The cells were washed in HMM-FeN and resuspended in HMM-FeN to a final density of 2.5x109 CFU/ml.  Aliquots were transferred to 5 test tubes and diluted to 2.5x108 CFU/ml with either 1) HMM medium, 2) HMM medium with NaCl to a final concentration of 0.23 M, 3) HMM medium with H2O2 to a final concentration of  0.5 mM, 4) HMM medium lacking FeCl3 but with N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) to a final concentration of 100 µM, or 5) HMM medium lacking L-glutamine, (NH4)SO4 and AHL; these were designated as the basal medium, osmotic stress, Apoplastic growth, iron limitation and nitrogen limitation treatments, respectively. At the end of the treatments, the cells were immediately diluted with an RNA stabilizing agent, harvested by centrifugation, and stored as cell pellets at -20°C.  All treatments were performed at 25°C with aeration via shaking.
For the in planta treatments, the HMM-grown cells were suspended in water containing 0.01% of the biosurfactant Silwet L-77 to a density of 1x106 CFU/ml.  To establish epiphytic populations, bacteria were spray inoculated onto leaves.  Plants were incubated for 24 h in a 95% RH mist chamber, at which time the chamber was partially opened until the water on the leaves had visibly evaporated and was then re-sealed to allow incubation without active humidification for another 48 h.  The incubations were at 25°C with ambient but not supplemental lighting.  A total of 400 to 600 primary leaves were collected, immediately submerged in an RNA stabilizing solution, sonicated for 10 min, and then physically removed from the solution.  To establish apoplastic populations, bacteria were introduced by vacuum infiltration into leaves that were submerged in the inoculum.  Plants were incubated for 48 h under plant growth lights with a 12-h photoperiod.  A total of 40 to 80 leaves were collected and immediately submerged in an RNA stabilizing solution.  The leaves were cut into squares (~ 3x3 mm2) while submerged, and the plant tissues and liquid were sonicated for 10 min.  The solution was filtered through Whatman filter paper #1, with repeated filter changes.
For both in planta treatments, the cells in the suspension (epiphytic cells) or filtrate (apoplastic cells) were collected by centrifugation, suspended in the residual supernatant, separated from plant debris by filtration through a 5-µm filter with repeated filter changes, again harvested by centrifugation, and stored as cell pellets at -20°C.

value: Iron limited


title: B728a_Low Fe_LabB_Rep1


title: B728a_Low Fe_LabA_Rep1

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Low Fe_LabA.txt  (linked as supplementary file on Series record).


title: B728a_Low Fe_LabA_Rep2


title: B728a_Low Fe_LabC_Rep1

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Low Fe_LabC.txt  (linked as supplementary file on Series record).


title: B728a_Low Fe_LabC_Rep2


title: B728a_Low N_LabA_Rep1

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_Low N_LabA.txt  (linked as supplementary file on Series record).


title: B728a_Low N_LabA_Rep2


title: B728a_H2O2_LabC_Rep2

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_H2O2_LabC.txt  (linked as supplementary file on Series record).

source_name: Pseudomonas syringae B728a wild type, Oxidative stress

treatment_protocol:
Washed, late log-phase cells were incubated in HMM medium amended H2O2 to a final concentration of 0.5 mM and 2.5x109 CFU/ml for 15 min at 25°C.
For the in vitro treatments, the HMM-grown cells were resuspended in HMM medium lacking L-glutamine, FeCl3, AHL and (NH4)SO4, designated HMM-FeN medium.  The cells were washed in HMM-FeN and resuspended in HMM-FeN to a final density of 2.5x109 CFU/ml.  Aliquots were transferred to 5 test tubes and diluted to 2.5x108 CFU/ml with either 1) HMM medium, 2) HMM medium with NaCl to a final concentration of 0.23 M, 3) HMM medium with H2O2 to a final concentration of  0.5 mM, 4) HMM medium lacking FeCl3 but with N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) to a final concentration of 100 µM, or 5) HMM medium lacking L-glutamine, (NH4)SO4 and AHL; these were designated as the basal medium, osmotic stress, Apoplastic growth, iron limitation and nitrogen limitation treatments, respectively. At the end of the treatments, the cells were immediately diluted with an RNA stabilizing agent, harvested by centrifugation, and stored as cell pellets at -20°C.  All treatments were performed at 25°C with aeration via shaking.
For the in planta treatments, the HMM-grown cells were suspended in water containing 0.01% of the biosurfactant Silwet L-77 to a density of 1x106 CFU/ml.  To establish epiphytic populations, bacteria were spray inoculated onto leaves.  Plants were incubated for 24 h in a 95% RH mist chamber, at which time the chamber was partially opened until the water on the leaves had visibly evaporated and was then re-sealed to allow incubation without active humidification for another 48 h.  The incubations were at 25°C with ambient but not supplemental lighting.  A total of 400 to 600 primary leaves were collected, immediately submerged in an RNA stabilizing solution, sonicated for 10 min, and then physically removed from the solution.  To establish apoplastic populations, bacteria were introduced by vacuum infiltration into leaves that were submerged in the inoculum.  Plants were incubated for 48 h under plant growth lights with a 12-h photoperiod.  A total of 40 to 80 leaves were collected and immediately submerged in an RNA stabilizing solution.  The leaves were cut into squares (~ 3x3 mm2) while submerged, and the plant tissues and liquid were sonicated for 10 min.  The solution was filtered through Whatman filter paper #1, with repeated filter changes.
For both in planta treatments, the cells in the suspension (epiphytic cells) or filtrate (apoplastic cells) were collected by centrifugation, suspended in the residual supernatant, separated from plant debris by filtration through a 5-µm filter with repeated filter changes, again harvested by centrifugation, and stored as cell pellets at -20°C.

value: Oxidative stress


title: MHCC97H_PTvsLM

city: Pokfulam, Hong Kong

first: Wing Lung

middle: Simon

last: Yau

address: 21 Sassoon Road

department: Surgery

country: Hong Kong

institute: The University of Hong Kong

description: Analysis carried out by comparing the primary tumor cell line established from primary liver tumor in mice and its corresponding lung metastatic tumor cell line

hyb_protocol: The two differentially labeled reactions were combined into one tube and the volume was reduced by half in a SpeedVac® Concentrator.  BSA (50mg/ml) was then added to a total volume of 28.5ul.  The samples were incubated with 28.5ul of 2X Enhanced hybridization buffer at 65oC for 10 min and then loaded onto NCode™ Multi-Species miRNA Microarrays V2.  The arrays were mounted with the Maui Mixer SL and hybridized overnight (16-20 h) at 52oC with constant mixing.

scan_protocol: The washes were performed following the standard protocol recommended in the NCode™ Rapid miRNA Labeling System Manual, and the arrays were scanned using a GenePix® 4000B microarray scanner (Molecular Devices).

data_processing: The scanned array images were annotated and analyzed using the GenePix software and the .GAL files containg the array list name for the human samples.Analysis was performed by Microsoft Excel

label_protocol: Each total RNA sample, 1μl of NCode™ Multi-Species miRNA Microarray Controls (2fmol/ul) was spiked, and Poly (A) tailing reactions were set up following the protocol recommended in the NCode™ Rapid miRNA Labeling System Manual. The Poly (A) tailed reactions were ligated to labeled DNA polymers by using the 6X Alexa Fluor® 3 (A3) Rapid Ligation Mix or 6X Alexa Fluor® 5 (A5) Rapid Ligation Mix following the protocol recommended in the NCode™ Rapid miRNA Labeling System Manual.

growth_protocol: All cell lines are maintain at 37oC incubator with 5% CO2 with DMEM supplement with 10% FBS

extract_protocol: Total RNA were extracted by Trizol reagent accroding to manufacturer's protocol

value: Primary human HCC tumor cell line

tag: cell line (derived)

value: Metastatic human HCC tumor cell line


title: MHCC97H_LMvsPT


title: B728a_H2O2_LabC_Rep1


title: B728a_H2O2_LabB_Rep2

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_H2O2_LabB.txt  (linked as supplementary file on Series record).


title: PLC_LMvsPT

source_name: PLC-LM

source_name: PLC-PT


title: B728a_H2O2_LabB_Rep1


title: Patient Derived Xenograft LTL-331R

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

description: Sample 23

hyb_protocol: 5ug of Cy5-labeled sample was combined with 5ug of Cy3-labeled male reference, and samples were hybridized and washed by following Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol v6.2 on on Agilent SurePrint G3 Human Catalog CGH 8x60K (Design ID 021924) or SurePrint G3 Human Catalog CGH 4x180K (Design ID 022060)

scan_protocol: scanned at a 3um scan resolution and 20 bit tiff file setting on the Agilent DNA Microarray Scanner G2505C

data_processing: quantified signal intensities and pre-processed data with Agilent Feature Extraction 10.5.1.1. FE files loaded into Nexus Copy Number Software v.6  (Biodiscovery Inc.) for analysis.

label_protocol: 500ng gDNA labeled by following NimbleGen Arrays User’s Guide: CGH Analysis v5.0, which included a 98C heat fragmentation step and labeling with Cy-labeled random nanomers (TriLink Biotechnologies) and Klenow 3'-5'exo-(New England Biolabs).

extract_protocol: Genomic DNA extracted with Promega Wizard Genomic DNA Extraction Kit

value: prostate cancer tumor

tag: patient source

tag: tumor foci

value: Patient Derived Xenograft

tag: host genetic background

value: NOD/SCID

source_name: male reference DNA (Promega Corp)

value: male reference DNA (Promega Corp)


title: Patient Derived Xenograft LTL-331R-G7

description: Sample 24


title: B728a_H2O2_LabA_Rep2

data_processing:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance mates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356); this was performed on the datasets within a laboratory and across the three laboratories (.txt files).
B728a_H2O2_LabA.txt  (linked as supplementary file on Series record).

value: Wild type

tag: treatment


title: B728a_H2O2_LabA_Rep1


title: Patient Derived Xenograft LTL-418-G6

description: Sample 22


title: Patient Derived Xenograft LTL-412-G5

description: Sample 21


title: Patient Derived Xenograft LTL-352-G13

description: Sample 20