title: B-cell 1 Axin

city: Oxford

first: Richard

middle: J

last: Gibbons

state: Oxon

address: John Radcliffe Hospital,

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

hyb_protocol: Hybridisation of labelled  DNA onto Microarrays 1. Prepare in 2μl eppendorf tube the hybridisation DNA mixtures for precipitation as follows: a. 160 μl Cy3 labelled DNA b. 160 μl Cy labelled DNA c. 135 μl Human Cot-1 DNA (Invitrogen 15279-011) d. 55 μl 3M NaAc ph 5.2 e. 6 μl yeast tRNA (Invitrogen 15401-011) f. 1000 μl 100% EtOH 2. Mix the tube gently, keep in dark and precipitate for 30 min – 1 h at –70^C 3. Pre heat hybridisation buffer in a 65^C heat block Hybridisation buffer (50 ml): 20X SSC 5 ml Deionised formamide 25 ml 100mM Tris-Hcl ph7.4 5 ml Dextran sulphate 2.5 g Tween 20 50 mcl HPLC water 15 ml 4. Spin the precipitated DNA for 20 min at 14000 rpm at 4^C 5. Wash the pellet in EtOH 70% 500 mcl and spin 5 min at 14000 rpm at 4^C 6. Leave the pellet drying 7. Resuspend pellet in 120-150 μl of hybridisation buffer (dependant on chamber size) and leave dissolving on 65^C heat block for 1+ hour 8. When the pellet is fully dissolved denature for 10 min at 100^C in darkness 9. Snap freeze on ice, spin down and leave on ice until loading in the liquid station.

scan_protocol: Slides were scanned with a Perkin Elmer Scanarray scanner using scanarray express software.

data_processing:
The Easy Quant (Perkin Elmer, Scan Array) analysis program with 'Adaptive circle' quantitation method with lowess normalization was used
The normalised value (Ch2 N Ratio of Means, column 57) for each probe (ID, column 7) is extracted from the raw text file and combined with the HG17 genomic coordinates of the probe in the file ProbeCoordinates_HG17.txt.  The final values are then moved over from the HG17 genome build to the HG18 genome build using the UCSC liftOver tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver) to produce the final reported processed values and coordinates.
The extraction process for these arrays needed three file.  The gal file to relates the spots on the array with the probe IDs and produce the raw data file.  The probe coordinate file then is used to relate the probe ID and normalised value in the raw data file.

source_name: B-cell

label_protocol: Random Labelling ChIP DNA for array CGH Equipment and reagents • BioPrime Labelling Kit (Invitrogen 18094-011) • 10X dNTP mix (Amersham 27-2035-01) • 1mM Cy3-dCTP (Amersham PA53021) • 1mM Cy5-dCTP (Amersham PA55021) • HPLC water BDH 152736D • Micro-spin G50 columns (Amersham, 275330-01) Method 1. Random label 450 ng of DNA in a final reaction volume of 150 μl by mixing the DNA with 60 μl 2.5X Random Primers Solution (from BioPrime Labelling Kit) and make up to 130 μl with HPLC water. Make 1 reaction for ChIP DNA and 1 reaction for input DNA. 2. Denature DNA in a heat block for 10 min at 100°C, and immediately cool on ice. 3. The following reagents are added on ice: 15 μl 10X dNTP mix (so prepared: dNTPs Amersham 27-2035-01 4x25umol C 1μl , A 2 μl, G 2 μl , T 2 μl , HPLC water 93 μl) 1.5 μl Cy3 (for ChIP DNA) or Cy5 (for input DNA) labelled dCTP (1 mM) from Amersham PA53021 and PA55021 3 μl Klenow Fragment from Biopreime Labelling Kit Mix gently but thoroughly. 4. Incubate the reaction @ 37°C overnight in darkness and then stop it by adding 15 μl of stop buffer (from BioPrime Labelling kit). Removal of Labelled Nucleotides from DNA Labelling Reactions (The recommended volume for application to a single column is 50 μl, you therefore have to use 3 columns per 150 µl labelling reaction) Column Preparation 1. Resuspend the resin in the columns by gentle vortexing. 2. Loosen the cap one-fourth turn and snap off the bottom closure. 3. Place the columns in a 1.5 ml screw-cap microcentrifuge tube for support. Alternatively, cut the cap from a flip-top tube and use this tube for support. 4. Pre-spin the columns for 1 minute at 2700 rpm. DO NOT pulse as this will override the variable speed setting. Wash columns applying 50 mcl of HPLC water to the resin and spin 1 min at 2700 rpm. Use columns immediately after preparation to avoid the resin drying out. Sample Application 1. Place the columns in a new 1.5 ml tube and slowly apply 50 μl to the centre of the angled surface of the compacted resin bed of each of the columns, being careful not to disturb the resin bed. Careful application of the sample to the centre of the bed is essential for good separation. Do not allow any of the samples to flow around the sides of the bed. 2. Spin the columns for 2 minutes at 2700 rpm. The purified samples are collected in the bottom of the support tube. 3. Discard the columns and retain the flow-through samples. 4. Combine the three samples and run 5 μl on a 1% agarose gel

growth_protocol: EBV-transformed lymphoblastoid (EBV B-lymphocyte) cell lines were cultured in RPMI 1640 supplemented with 10% (v/v) fetal calf serum, 2 mM L-glutamine, 50 U/ml penicillin and 50 µg/ml streptomycin. Basic Protocol 1: Preparation of Peripheral Blood Mononuclear Cells for Erythroid Cultures Cultures can be initiated with cells derived from a whole unit of blood obtained from normal donors (or polycythemic patients undergoing phlebotomy). The starting material, i.e., the “buffy-coat” fraction, is readily available, since it is routinely separated and discarded by the blood bank during preparation of packed red blood cells (RBC) and platelet-rich plasma. Anemic patients commonly show high frequencies of erythroid progenitors; cultures from anemic patients (e.g., thalassemia, sickle cell anemia) are usually initiated with cells derived from ~20 ml peripheral blood. Materials * Peripheral blood or buffy coat fraction * Phosphate-buffered saline (PBS), pH 7.4 (appendix 2A) * Ficoll-Hypaque (density = 1.077 g/ml) * 15- or 50-ml centrifuge tubes * Centrifuge 1. Dilute peripheral blood or the buffy coat fraction 1:1 (v/v) with PBS. Gently layer on top of a layer of Ficoll-Hypaque such that the Ficoll-Hypaque layer constitutes one-third of the total volume. Depending on the blood volume, use either 15- or 50-ml tubes. For convenience, tubes (available from Sigma) containing a special grid that separates the blood from the Ficoll can be used. 2. Centrifuge 20 min at 400 × g, at room temperature. Do not apply the brake. 3. Aspirate off the top layer (consisting of plasma and platelets), collect the interphase layer of mononuclear cells with a pipet, and transfer to a 50-ml tube. 4. Add 40 ml PBS, mix, then centrifuge 5 min at 160 × g, room temperature. Aspirate the supernatant, then resuspend the pellet in the residual buffer by tapping. 5. Add 40 ml PBS, mix, then centrifuge 5 min at 100 × g, room temperature, and aspirate the supernatant. Repeat this procedure for an additional wash. Use low-speed centrifugation in order to remove residual platelets. All procedures should be performed at room temperature. If the blood cannot be processed on the same day, leave overnight at room temperature. In experiments where Hb content is measured, special care has to be taken to avoid contamination by mature RBC that originated from the processed blood. This does not usually present a problem when normal blood is processed, but may occur with blood derived from patients, e.g., with thalassemia. The contaminating RBCs can be of patient origin and/or derived from transfused blood. In both cases, they may interfere with measurement of the Hb produced in vitro. When the interphase layer is heavily contaminated with RBC, the latter cells should be removed by osmotic hemolysis (see Support Protocol 6) prior to culturing. When only slightly contaminated, the mononuclear cells may be cultured without hemolysis; RBC tend to lyse and disappear during culture. Alternatively, they may be removed by Percoll separation at the second phase of the culture (see Support Protocol 7). [Top of Page] Basic Protocol 2: Erythroid Cell Culture Procedure The culture procedure is divided into two phases. The first is an EPO-independent phase in which peripheral blood mononuclear cells are isolated (described in Basic Protocol 1) and cultured in the presence of a combination of growth factors, but in the absence of EPO. During this phase, early erythroid-committed progenitors, called burst-forming units erythroid (BFUe), proliferate and differentiate into colony-forming unit erythroid (CFUe)–like progenitors. In the second phase, these cells, cultured in an EPO-supplemented medium, continue to proliferate and mature into orthochromatic normoblasts and enucleated erythrocytes. Materials * Complete MEM medium (see recipe) * Preselected FBS (see recipe); do not heat-inactivate * 50 mg/ml cyclosporin A (Sandoz) * Conditioned medium from 5637 human bladder carcinoma cell line (see recipe) * Mononuclear cells, washed (see Basic Protocol 1) * 10% (w/v) deionized BSA (see recipe) * 2-mercaptoethanol (Sigma) * 4 mg/ml dexamethasone sodium phosphate (Elkin-Sinn Pharmaceuticals, Cherry Hill N.J.) * Human holo-transferrin (Sigma) * Human recombinant stem cell factor (CytoLab Ltd.; http://www.cytolab.com/) * Human recombinant erythropoietin (EPO; Ortho Pharmaceutical) * 25- or 75-cm2 tissue culture flasks 1. Prepare Phase I medium by adding the following ingredients to complete MEM medium: * 10% (v/v) preselected FBS (not heat-inactivated) * 1 µg/ml cyclosporin A (add from 50 mg/ml stock) * 10% (v/v) conditioned medium from 5637 human bladder carcinoma cell line. 2a. For cells obtained from peripheral blood (10 to 20 ml): Plate the washed mononuclear cells in Phase I medium in 25-cm2 flasks at a culture volume equivalent to the original volume of blood. 2b. In the case of cells obtained from a whole blood unit (400 to 500 ml): Plate the washed mononuclear cells in Phase I medium in two 75-cm2 flasks at a culture volume of 80 to 100 ml. 3. Incubate the cultures at 37°C in a humidified, 5% CO2 incubator for 5 to 7 days. Full humidification is achieved by leaving a tray with water standing at the bottom of the incubator. 4. After the 5- to 7-day incubation in phase I, shake the cultures and harvest the nonadherent cells (do not trypsinize). 5. Centrifuge the cells 5 min at 160 × g, room temperature, and aspirate the supernatant. Fill the tube with complete MEM, centrifuge 5 min at 160 × g, room temperature, and aspirate the supernatant. Repeat for a second wash. 6. Prepare Phase II medium by adding the following ingredients to complete MEM medium: * 30% (v/v) preselected FBS (not heat-inactivated) * 1% (w/v) deionized BSA (add from 10% w/v stock) * 10–5 M 2-mercaptoethanol * 10–6 dexamethasone (add from 4 mg/ml stock) * 0.3 mg/ml human holo-transferrin * 10 ng/ml human recombinant stem cell factor * 1 U/ml human erythropoietin (EPO). 7. Plate cells in the original volume of phase II medium (as in step 2a or 2b according to the original blood volume) and incubate up to 14 days at 37°C in a humidified, 5% CO2, incubator.

extract_protocol: After collecting the washed cells by centrifugation the pellet was resuspended in lysis buffer (10mM Tris pH8.0, 10mM NaCl, 0.2% NP-40, 1x Complete proteinase inhibitor (Roche)) and lysed for 15 minutes on ice.  After collection of the cells by centrifugation, the pellet was washed with 1ml of 1 x Dpn II digestion buffer (NEB) and the pellet was re-suspended for digestion by the addition of 60 μl of x10 Dpn II buffer and 440 μl of sterile H2O.  To this was added 7.5 μl 20% SDS to a final concentration of 0.3% and the resulting mixture was incubated at 37OC for 1 hour with shaking.  The SDS was then sequestered by the addition of Triton X-100 to a final concentration of ~2% (50 μl 20% Triton X-100) and incubated at 37OC for 1 hour with shaking. 500U Dpn II (NEB 5x concentration R0543M) was added and incubated overnight at 37OC with shaking. The enzyme was inactivated at 65OC for 25 min with SDS added to a final concentration of 1.5% (40 μl of 20 % SDS), this was re-suspended in a final volume of 7ml 1x ligation buffer (40mM Tris pH8.0, 10mM MgCl2 and 0.5 mM rATP) with 1% Triton X-100.  Following incubation at 37OC for 1 hour to sequester the SDS, the samples were cooled on ice for 2 minutes and 240U high concentration T4 DNA ligase (Fermentas) was added.  Following incubation overnight at 16OC with shaking, 300 mg of proteinase K was added and crosslinks reversed by incubation at 65OC overnight with rotation.  The samples were treated with 15mg RNase (Roche) at 37OC for 30 minutes.  Following phenol/chloroform extraction and ethanol precipitation, DNA was re-suspended in 500 μl 1x ligation buffer and 60U high concentration T4 DNA ligase (Fermentas) and incubated for 2 hours at 16OC at 1200rpm (Eppendorf Thermomixer comfort). Following phenol/chloroform extraction and ethanol precipitation, DNA was re-suspended in 100 μl water, of which 10 μl was used as template in Advantage-GC PCR (Clontech) as per manufacturer’s instructions using 34 cycles of amplification (cycling conditions were 94OC for 2 minutes; 34 cycles of 94OC for 30 seconds, annealing temperature for 30 seconds, 68OC for 5 minutes followed by a single extension cycle at 68OC for 8 minutes).

treatment_protocol: 1x107 cells were fixed with 2% formaldehyde in 10 ml of their growth medium for 10 minutes at room temperature with agitation.  Following quenching with 1.5 ml of 1M glycine cells were collected at 1200 rpm (Heraeus Multifuge 3 SR) at 4 OC for 5 minutes, resuspended and washed in 10 ml of 1x sterile Phosphate buffered Saline (PBS Gibco pH7.4).

tag: cell type

value: B-cell

tag: sample type

value: DNA Input

value: DNA 4C amplified

tag: target

value: CTCF bound region


title: ΔMCR 0457 biological repl 2 repl spot 4

status: Public on Jun 06 2013

type: RNA

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

country: Netherlands

institute: Radboud University Medical Centre

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 2, replicate spot 4

hyb_protocol: 2 µg of labeled cDNA was applied to 4x72K custom design NimbleGen arrays. Overnight hybridization at 42°C and subsequent washing of arrays was performed according to the manufacturer’s instructions (available from www.nimblegen.com).

scan_protocol: Array images were acquired with a NimbleGen MS200 scanner following their standard operation protocol, using the autogain function per subarray.

data_processing: ANAIS (Simon and Biot, 2010, Bioinformatics 26;2468-2469) was used for intra-array (background adjustment) and inter-array (quantile) normalization to obtain normalized probe signal intensities (SI), three replicate spots per array (designated block1-3). Normalized probe SI were corrected for a threshold of seven times the median SI of the negative-control probes. Statistical analysis was performed on the SI (median of eight probes per gene) of the directed mutant strain and the parental wild-type strain using the CyberT implementation of Student’s t-test (cybert.microarray.ics.uci.edu). The false discovery rate (FDR) was calculated from the Bayesian p-value as described in (van Hijum et al., 2005, BMC Genomics 6; 77).

label: 5'Cy3-labeled random nonamers

molecule: total RNA

organism: Moraxella catarrhalis BBH18

label_protocol: Total RNA (5 µg) was labeled according to standard Nimblegen gene expression array protocols.

growth_protocol: M. catarrhalis BBH18 directed mutants (n = 3) and wild-type BBH18 strain (n = 4) were expanded to mid-log phase (OD620nm, 1.2 to 1.4) in brain heart infusion (BHI) medium (iron-rich) at 37°C 250 rpm.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by DNase digestion with the DNA-free kit (Ambion).

treatment_protocol: Bacteria were treated with 2 volumes of RNAprotect bacteria reagent (Qiagen).

tag: genotype

value: MCR_0457 deletion mutant

tag: growth phase

value: Exponential phase

tag: genbank


title: ΔMCR 0457 biological repl 2 repl spot 1

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 2, replicate spot 1


title: ΔMCR 0457 biological repl 1 repl spot 4

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 1, replicate spot 4


title: control exponential vs. iron limiting exponential Ratio 2-DF0_EXP_block1 and 2-DF30_EXP_block1

type: genomic

hyb_protocol: 2 µg of labeled cDNA was applied in duplicate to 4x72K custom design NimbleGen GAF arrays. Overnight hybridization at 42°C and subsequent washing of arrays was performed according to the manufacturer’s instructions (available from www.nimblegen.com).

data_processing: ANAIS (Simon and Biot, 2010, Bioinformatics 26;2468-2469) was used for intra-array (background adjustment) and inter-array (quantile) normalization to obtain normalized probe signal intensities (SI), three replicate spots per array (designated block1-3). Normalized probe SI were corrected for a threshold of five times the median SI of the negative-control probes. Statistical analysis was performed on the ratio between the SI of the control and challenge (iron-limiting) conditions using the CyberT implementation of Student’s t-test (cybert.microarray.ics.uci.edu). The false discovery rate (FDR) was calculated from the Bayesian p-value as described in (van Hijum et al., 2005, BMC Genomics 6; 77).

molecule: genomic DNA

source_name: Control DF0, exponential phase, biological replicate 2, replicate spot 1

label_protocol: Chromosomal DNA was digested with AluI restriction enzyme and purified using the MinElute reaction clean-up kit (Qiagen). 2 µg digested DNA served as a template for a T7 RNA polymerase reaction (MegaScript, Ambion) using the outward-facing T7 sites of the transposon element. The template DNA was degraded with DNase I and the T7 RNA was purified using the RNeasy Minelute kit (Qiagen). 2 µg T7 RNA was reverse transcribed into cDNA in the presence of 16.7 ng µl-1 actinomycin D (Sigma Aldrich) using 1 µg Cy3-labeled random nonamers (Nimblegen) for priming.

growth_protocol: Mutant library was pre-culture to mid-log, washed, and resuspended in PBS-gelatin

extract_protocol: Mutants were recovered at the mid-log and early-stationary phase. The recovered mutants were expanded for chromosomal DNA isolation using Genomic-tip 20/G columns.

treatment_protocol: Growth of the mutant library under control condition (DF0), sample taken at exponential phase

tag: transposon element

value: marinerT7 mutant library

tag: antibiotic resistance

value: spectinomycin resistance

tag: treatment

value: control

value: exponential

source_name: iron limiting DF30, exponential phase, biological replicate 2, replicate spot 1

treatment_protocol: Growth of the mutant library under iron limiting (DF30), sample taken at exponential phase

value: iron limiting


title: ΔMCR 0457 biological repl 3 repl spot 1

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 3, replicate spot 1


title: ΔMCR 0457 biological repl 2 repl spot 3

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 2, replicate spot 3


title: T Lymphocyte HBA

organism: Homo sapiens

source_name: T Lymphocyte

value: T Lymphocyte

source_name: Tlymphocyte

tag: tag

value: HBA promoter


title: control exponential vs. iron limiting exponential Ratio 1-DF0_EXP_block2 and 1-DF30_EXP_block2

source_name: Control DF0, exponential phase, biological replicate 1, replicate spot 2

source_name: iron limiting DF30, exponential phase, biological replicate 1, replicate spot 2


title: ΔMCR 0457 biological repl 1 repl spot 2

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 1, replicate spot 2


title: ΔMCR 0457 biological repl 1 repl spot 1

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 1, replicate spot 1


title: B-cell 2 HBB

value: HBB promoter


title: HCT116 shERRalpha, biological rep3

city: Sherbrooke

first: Julie

last: Carrier

state: Québec

address: 3001, 12ième avenue nord

department: Médecine(Gastroentérologie)

country: Canada

institute: Université de Sherbrooke

description: Gene expression data from HCT116 shERRalpha

hyb_protocol: Following fragmentation, 100 ng of total cRNA were hybridized at 60 rpm for ± 16 hr at 45°C in hybridization oven on GeneChip Human gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the gene chips Scanner 3000 7G series.

data_processing: Compiled data (RMA analysis) were screened using Flex Array 1.4.1 (Genome Quebec)

label: biotin

source_name: HCT116 infected with lentivirus shERRalpha

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1mg total RNA (gene chip whole transcript(WT) sense target labeling assay, 2005-2009, Affymetrix).

growth_protocol: The HCT116 cells were cultured  in 10% FBS DMEM without phenol red.

extract_protocol: Extraction of total RNA was performed according to the AMBION company instructions (Totally RNA kit) and purified on Qiagen column.

treatment_protocol: The HCT116 cells were infected with lentivirus for 48h and treated with puromycin 2mg/ml for 48h.

tag: cell line

value: lentivirus shERRalpha


title: HCT116 shERRalpha, biological rep2


title: Biopsy 4709

status: Public on Jun 07 2013

city: Bethesda

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

country: USA

institute: Uniformed Services University

description:
Simple annotation: Infection, Stomach cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76464.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4000B

data_processing: log RED/GREEN

organism: Macaca mulatta

source_name: 1.0 ug amplified normal monkey stomach cDNA

label_protocol: not provided

extract_protocol: not provided

tag: tissue

value: stomach

source_name: 1.0 ug amplified Biopsy 4709 cDNA

tag: infection


title: B-cell 2 Axin


title: HCT116 shscrambled, biological rep3

description: Gene expression data from HCT116 shscrambled

source_name: HCT116 infected with lentivirus shscrambled

value: lentivirus shscrambled


title: HCT116 shscrambled, biological rep1


title: Erythroblast JH2 HBB

source_name: Erythroblast

value: Erythroblast


title: HCT116 shscrambled, biological rep2


title: HCT116 shERRalpha, biological rep1


title: Biopsy 4689

description:
Simple annotation: Infection, Stomach cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76462.gif

source_name: 1.0 ug amplified Biopsy 4689 cDNA

value: treated


title: Δrnd biological repl 3 repl spot 4

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 3, replicate spot 4

value: rnd deletion mutant


title: B-cell 1 HBB

value: B-cell

value: DNA Input

value: DNA 4C amplified


title: Δrnd biological repl 3 repl spot 3

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 3, replicate spot 3

value: Exponential phase


title: Δrnd biological repl 3 repl spot 2

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 3, replicate spot 2


title: Δrnd biological repl 3 repl spot 1

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 3, replicate spot 1


title: Δrnd biological repl 2 repl spot 4

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 2, replicate spot 4


title: B-cell 1 HBA


title: B-cell 2 HBA


title: Δrnd biological repl 2 repl spot 2

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 2, replicate spot 2


title: Erythroblast JH2 HBA


title: Erythroblast JH1 HBA


title: Δrnd biological repl 2 repl spot 1

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 2, replicate spot 1


title: Erythroblast JH1 HBB


title: Δrnd biological repl 1 repl spot 2

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 1, replicate spot 2


title: Δrnd biological repl 1 repl spot 3

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 1, replicate spot 3


title: Sample-121-control

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

institute: RPCI

hyb_protocol: The labeled probes were then mixed with hybridization reagents and hybridized overnight to the HumanHT-12 v3 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files are analyzed with Illumina’s GenomeStudio gene expression module (V1.6.0)

source_name: blood

label_protocol: Initially, 250ng total RNA was converted to cDNA, followed by an in vitro transcription step to generate labeled cRNA using the Ambion Illumina Total Prep RNA Amplification Kit (Ambion, Austin, TX) as per manufacturer’s instructions.

extract_protocol: Total RNA from 10-20 mg fresh frozen tissues were prepared using the RNeasy midi kits (Qiagen, Valencia, CA) following manufacturer’s instructions. After elution, RNA samples were concentrated by EtOH precipitation at –20oC overnight, and resuspended in nuclease-free water.  Before labeling, RNA samples were quantitated using a ND-1000 spectrophotometer (NanoDrop Wilmington, DE) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples were required to have a RIN >6.5, an OD 260:280 of 1.9-2.1, an OD 260/230 >1.5 and >1.5 28S:18S ratio of the ribosomal bands for gene expression array analysis.

value: blood

tag: disease state

value: healthy


title: Sample-120-control


title: Sample-119-control


title: Biopsy 4691

description:
Simple annotation: Infection, Stomach cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76463.gif

source_name: 1.0 ug amplified Biopsy 4691 cDNA


title: Δrnd biological repl 1 repl spot 4

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 1, replicate spot 4


title: ΔMCR 0996 biological repl 3 repl spot 2

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 3, replicate spot 2

value: MCR_0996 deletion mutant


title: ΔMCR 0996 biological repl 3 repl spot 1

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 3, replicate spot 1


title: ΔMCR 0996 biological repl 2 repl spot 4

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 2, replicate spot 4


title: ΔMCR 0996 biological repl 2 repl spot 3

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 2, replicate spot 3


title: Δrnd biological repl 1 repl spot 1

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 1, replicate spot 1


title: ΔMCR 0996 biological repl 3 repl spot 3

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 3, replicate spot 3


title: ΔMCR 0996 biological repl 2 repl spot 2

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 2, replicate spot 2


title: ΔMCR 0996 biological repl 2 repl spot 1

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 2, replicate spot 1


title: Δrnd biological repl 2 repl spot 3

description: Moraxella catarrhalis BBH18 Δrnd, exponential growth phase, biological replicate 2, replicate spot 3


title: Sample-113-control


title: ΔMCR 0996 biological repl 1 repl spot 3

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 1, replicate spot 3


title: Sample-118-ovarian

value: ovarian cancer


title: Sample-111-ovarian


title: Sample-116-control


title: Sample-114-control


title: Sample-110-control


title: Sample-117-control


title: Sample-112-control


title: ΔMCR 0996 biological repl 1 repl spot 4

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 1, replicate spot 4


title: Sample-109-control


title: ΔMCR 0996 biological repl 1 repl spot 2

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 1, replicate spot 2


title: ΔMCR 0996 biological repl 1 repl spot 1

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 1, replicate spot 1


title: ΔrhlB biological repl 3 repl spot 4

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 3, replicate spot 4

value: rhlB deletion mutant


title: Sample-115-control


title: ΔrhlB biological repl 3 repl spot 2

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 3, replicate spot 2


title: ΔrhlB biological repl 3 repl spot 3

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 3, replicate spot 3


title: ΔrhlB biological repl 3 repl spot 1

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 3, replicate spot 1


title: Sample-107-control


title: Sample-105-control


title: ΔrhlB biological repl 2 repl spot 4

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 2, replicate spot 4


title: Sample-102-control


title: Sample-100-control


title: Sample-106-ovarian


title: Sample-108-control


title: Sample-101-control


title: Sample-98-control


title: Sample-103-control


title: ΔrhlB biological repl 2 repl spot 1

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 2, replicate spot 1


title: ΔrhlB biological repl 2 repl spot 3

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 2, replicate spot 3


title: ΔrhlB biological repl 2 repl spot 2

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 2, replicate spot 2


title: ΔrhlB biological repl 1 repl spot 4

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 1, replicate spot 4


title: Sample-104-control


title: ΔrhlB biological repl 1 repl spot 3

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 1, replicate spot 3


title: ΔrhlB biological repl 1 repl spot 2

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 1, replicate spot 2


title: Sample-99-ovarian


title: ΔrhlB biological repl 1 repl spot 1

description: Moraxella catarrhalis BBH18 ΔrhlB, exponential growth phase, biological replicate 1, replicate spot 1


title: ΔyggW biological repl 3 repl spot 4

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 3, replicate spot 4

value: yggW deletion mutant


title: ΔyggW biological repl 3 repl spot 3

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 3, replicate spot 3


title: ΔyggW biological repl 3 repl spot 2

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 3, replicate spot 2


title: Sample-95-control


title: Sample-96-control


title: Sample-97-control


title: Sample-91-control


title: Sample-93-control


title: Sample-94-control


title: ΔyggW biological repl 3 repl spot 1

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 3, replicate spot 1


title: ΔyggW biological repl 2 repl spot 4

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 2, replicate spot 4


title: ΔyggW biological repl 2 repl spot 3

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 2, replicate spot 3


title: Sample-89-control


title: ΔMCR 0996 biological repl 3 repl spot 4

description: Moraxella catarrhalis BBH18 ΔMCR_0996, exponential growth phase, biological replicate 3, replicate spot 4


title: ΔyggW biological repl 2 repl spot 2

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 2, replicate spot 2


title: ΔyggW biological repl 1 repl spot 1

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 1, replicate spot 1


title: ΔyggW biological repl 2 repl spot 1

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 2, replicate spot 1


title: Sample-92-control


title: ΔyggW biological repl 1 repl spot 4

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 1, replicate spot 4


title: ΔyggW biological repl 1 repl spot 2

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 1, replicate spot 2


title: ΔyggW biological repl 1 repl spot 3

description: Moraxella catarrhalis BBH18 ΔyggW, exponential growth phase, biological replicate 1, replicate spot 3


title: Sample-88-ovarian


title: Sample-86-control


title: Sample-87-control


title: Sample-90-control


title: Wild-type biological repl 4 repl spot 4

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 4, replicate spot 4

value: wild-type


title: Wild-type biological repl 4 repl spot 3

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 4, replicate spot 3


title: Sample-82-control


title: Sample-85-control


title: Sample-81-ovarian


title: Sample-84-control


title: Wild-type biological repl 4 repl spot 2

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 4, replicate spot 2


title: Sample-80-control


title: Sample-79-control


title: Sample-77-control


title: Wild-type biological repl 3 repl spot 4

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 3, replicate spot 4


title: Wild-type biological repl 3 repl spot 3

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 3, replicate spot 3


title: Sample-78-control


title: Wild-type biological repl 4 repl spot 1

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 4, replicate spot 1


title: Sample-83-control


title: Sample-74-ovarian


title: Wild-type biological repl 3 repl spot 2

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 3, replicate spot 2


title: Sample-75-control


title: Wild-type biological repl 3 repl spot 1

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 3, replicate spot 1


title: Wild-type biological repl 2 repl spot 4

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 2, replicate spot 4


title: Wild-type biological repl 2 repl spot 3

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 2, replicate spot 3


title: Wild-type biological repl 2 repl spot 2

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 2, replicate spot 2


title: Wild-type biological repl 2 repl spot 1

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 2, replicate spot 1


title: Wild-type biological repl 1 repl spot 4

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 1, replicate spot 4


title: Wild-type biological repl 1 repl spot 3

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 1, replicate spot 3


title: Wild-type biological repl 1 repl spot 2

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 1, replicate spot 2


title: Sample-72-control


title: Sample-69-control


title: Sample-70-control


title: Sample-73-ovarian


title: Sample-67-control


title: Sample-68-ovarian


title: Sample-76-control


title: Sample-65-ovarian


title: Sample-64-control


title: Sample-63-ovarian


title: Sample-61-ovarian


title: Sample-62-ovarian


title: Wild-type biological repl 1 repl spot 1

description: Moraxella catarrhalis BBH18 wild-type, exponential growth phase, biological replicate 1, replicate spot 1


title: Sample-71-control


title: Sample-60-ovarian


title: Sample-66-ovarian


title: Sample-56-ovarian


title: Sample-57-ovarian


title: Sample-58-ovarian


title: Sample-55-ovarian


title: Sample-53-ovarian


title: Sample-50-ovarian


title: Sample-59-ovarian


title: Sample-54-ovarian


title: Sample-49-ovarian


title: Sample-52-ovarian


title: Sample-46-ovarian


title: Sample-45-ovarian


title: Sample-47-ovarian


title: Sample-51-ovarian


title: Sample-48-ovarian


title: Sample-44-ovarian


title: Sample-41-ovarian


title: Sample-43-ovarian


title: High-grade osteosarcoma cell line ZK-58

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

description:
ZK-58*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

hyb_protocol: As per manufacturer's instructions.

scan_protocol: As per manufacturer's instructions.

data_processing:
On the Illumina BeadChips, each sample is hybridized on 2 chips, which together compromise all probes per sample. There are four columns in each raw data file. The first column represents the bead (there are approximately 30 replicate beads per probe on random positions on the Illumina BeadChip arrays), the second the signal, and the other 2 the X and Y locations on the chip. These 2 raw files can be imported into BeadStudio, the program developed by Illumina for analyzing these data, or into R  package beadarray.
Data were analyzed using the statistical language R. As Illumina identifiers are not stable and consistent between different chip versions, raw oligonucleotide sequences were converted to nuIDs. Data were transformed using the variance stabilizing transformation (vst) algorithm and subsequently normalized using robust spline normalization. Conversion to nuIDs, variance stabilizing transformation, and normalization of the data were all carried out using the Bioconductor package lumi. Quality control was performed using the Bioconductor package arrayQualityMetrics. Poor quality arrays were removed from further analyses.

source_name: High-grade osteosarcoma cell line

label_protocol: As per manufacturer's instructions.

extract_protocol: RNA isolation, cDNA synthesis, cRNA amplification, Illumina Human-6 v2.0 Expression BeadChip hybridization, qPCR validation, and microarray data analysis were performed as previously described (PMID: 21372215).


title: High-grade osteosarcoma cell line SAOS2

description:
SAOS2
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).


title: Sample-40-ovarian


title: Sample-39-ovarian


title: High-grade osteosarcoma cell line U2OS

description:
U2OS
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).


title: High-grade osteosarcoma cell line OSA

description:
OSA*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

value: OSA


title: Sample-38-ovarian


title: High-grade osteosarcoma cell line OS25-HAL

description:
OS25-HAL
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).


title: Sample-37-ovarian


title: High-grade osteosarcoma cell line MNNG-HOS

description:
MNNG-HOS
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

value: MNNG-HOS


title: Sample-42-ovarian


title: High-grade osteosarcoma cell line OHS

description:
OHS*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

value: OHS


title: Sample-35-ovarian


title: High-grade osteosarcoma cell line IOR-SARG

description:
IOR-SARG*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

value: IOR-SARG


title: High-grade osteosarcoma cell line MHM

description:
MHM*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

value: MHM


title: High-grade osteosarcoma cell line KPD

description:
KPD*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

value: KPD


title: Sample-32-ovarian


title: High-grade osteosarcoma cell line IOR_OS15

description:
IOR-OS15*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).


title: Sample-33-ovarian


title: High-grade osteosarcoma cell line IOR-OS10

description:
IOR-OS10*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).


title: High-grade osteosarcoma cell line IOR-OS9

description:
IOR-OS9*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).


title: High-grade osteosarcoma cell line IOR-MG63

description:
IOR-MG63*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).


title: High-grade osteosarcoma cell line IOR-MOS

description:
IOR-MOS*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

value: IOR-MOS


title: Sample-36-ovarian


title: High-grade osteosarcoma cell line IOR-OS14

description:
IOR-OS14*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).


title: High-grade osteosarcoma cell line IOR-OS18

description:
IOR-OS18*
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).


title: Sample-34-ovarian


title: Sample-31-ovarian


title: Sample-30-ovarian


title: High-grade osteosarcoma cell line HOS

description:
HOS
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

value: HOS


title: High-grade osteosarcoma cell line 143B

description:
143B
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).


title: Sample-26-ovarian


title: Sample-28-ovarian


title: CRPS patient P5

city: Daejeon

first: EunHeui

last: Jin

address: Munhwaro

country: South Korea

institute: Chungnam national university

description:
P5
We compared differentially expressed genes between CRPS patients and healthy controls to identify CRPS-related genes.

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12 V4.0 Expression BeadChip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner.

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0). Data were quantile normalized.

label: Biotin

source_name: Blood, CRPS patient

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: Trizol extraction of total RNA from blood.

tag: disease status

value: complex regional pain syndrome (CRPS)

tag: gender

value: male


title: Healthy control C14

description:
C14
We compared differentially expressed genes between CRPS patients and healthy controls to identify CRPS-related genes.

source_name: Blood, healthy control

value: blood


title: Healthy control C15

description:
C15
We compared differentially expressed genes between CRPS patients and healthy controls to identify CRPS-related genes.

value: healthy

value: female


title: Sample-23-ovarian

value: ovarian cancer


title: CRPS patient P6

description:
P6
We compared differentially expressed genes between CRPS patients and healthy controls to identify CRPS-related genes.


title: Sample-25-ovarian


title: Healthy control C5

description:
C5
We compared differentially expressed genes between CRPS patients and healthy controls to identify CRPS-related genes.


title: Sample-22-ovarian


title: Sample-21-ovarian


title: Healthy control C8

description:
C8
We compared differentially expressed genes between CRPS patients and healthy controls to identify CRPS-related genes.


title: Sample-19-ovarian


title: Sample-24-ovarian


title: Healthy control C2

description:
C2
We compared differentially expressed genes between CRPS patients and healthy controls to identify CRPS-related genes.


title: CRPS patient P3

description:
P3
We compared differentially expressed genes between CRPS patients and healthy controls to identify CRPS-related genes.


title: Sample-20-ovarian


title: Sample-17-ovarian


title: Sample-29-ovarian


title: Sample-18-ovarian


title: MCL-No Injury CX-Rep 2

city: Madison

first: Ray

last: Vanderby

state: WI

address: 1111 Highland Ave

department: Orthopedics and Rehabilitation

institute: University of Wisconsin

description: SAMPLE 8

hyb_protocol: GeneChips® (Affymetrix, Santa Clara, CA) were hybridized with biotin labeled cRNA in 300 µl, in 1 X Hybridization buffer (100 mM MES, 1M NaCl (Ambion, Austin, TX), 20 mM EDTA (Ambion, Austin, TX), and 0.01% Tween-20 (Pierce Chemical)), 50 pM control oligonucleotide B2 (Affymetrix, Santa Clara, CA), 0.1 mg/ml Herring Sperm DNA (Promega, Madison, WI Corporation), 0.5 mg/ml acetylated BSA (Invitrogen, Carlsbad, CA) and 1 X Eukaryotic Hybridization Controls (bioB, bioC, bioD, and cre at 1.5, 5, 25 and 100 pM respectively) (Affymetrix, Santa Clara, CA) for 16 hours at 45°C on a rotisserie at 60 rpm.  Prior to application to the GeneChip®, samples were heated (95°C for 5 minutes), incubated (45°C for five minutes), and spun (14,000-x g for five minutes).  Following hybridization, the labeled samples were removed from the GeneChip®, stored in the appropriate vial at –20C, and  filled with non-stringent buffer A containing 6X SSPE (Ambion, Austin, TX), 0.01% Tween 20.  All GeneChips® were post processed using the automated Affymetrix GeneChip® Fluidics Station 450. The post processing protocol of the Rat 2.0 Genome GeneChip® included: one wash (10 cycles with 2 mixes/cycle) of non-stringent buffer A at 25°C; one wash of 4 cycles comprised of 15 mixes/cycle with stringent buffer B (100mM MES, 0.1 M NaCl, 0.01% Tween 20) at 50C; staining of the probe array for 10 minutes at 25C in Streptavidin-Phycoerythrin (SAPE) solution (1X MES stain buffer (100 mM MES, 1 M NaCl, 0.05% Tween 20), 2 mg/ml acetylated BSA, 10 µg/ml SAPE (Molecular Probes); post staining consisting of 10 wash cycles of 4 mixes/cycle with non-stringent buffer A at 25°C; a second staining of the probe array for 10 minutes in antibody solution (1X MES stain buffer, 2 mg/ml acetylated BSA, 0.1 mg/ml Normal Goat IgG (Sigma-Aldrich, St. Louis, MO), 3 µg/ml biotinylated antibody (Vector Laboratories); a third stain of the probe array for 10 minutes in SAPE solution at 25C; and a final wash- 15 cycles of 4 mixes/cycle with non-stringent buffer A at 30°C.

scan_protocol: To quantify flourescence from each feature on the GeneChip, all GeneChips were scanned at a wavelength of 570 nm, using the GC3000 G7 scanner. Flourescent signals corresponding to hybridization intensities were analyzed via Affymetrix GCOS software

data_processing:
Quantification of GeneChips was performed by Affymetrix GeneChip Operating Software (AGCC version 2.0).
The data were compiled with EzArray using Affymetrix default analysis settings and global scaling as normalization method.   Data were analyzed using the two-sample Welch t-test to determine significance per gene. To minimize the false discovery rate, the Storey q-value method was performed and significance was based on q < .01. Any Q-value less than or equal to 0.01 per gene was considered significant. Paired t-tests were used to evaluate differences between intact and day 3, intact and day 7, or day 3 and day 7. A critical value of .05 was considered as the criterion to select a significant fold change in gene expression between days. Additionally, microarray data were log transformed [log (base 2)] and the log ratio between the intact ligament with day 3 or day 7 was calculated and expressed as fold change (e.g. (mean day 3-mean intact control)= day 3 difference; fold change=2^(day 3 difference).  A gene was considered up or down regulated if the day 3 or day 7 samples were at least 2 fold different than the intact controls.Data are presented as fold change of the means of day 3 and day 7 from the intact ligament values (fold change ± S.D.). Microarray data were functionally grouped using the Database for Annotation, Visualization, and Integrated Discovery (D.A.V.I.D.; http://david.abcc.ncifcrf.gov), integrating functional genomic annotations with intuitive graphical summaries. Using the Affymetrix probes as identifiers, the samples were subjected to functional annotation clustering based on function and gene ontology (GO). The categories of interest were further based on the enrichment score (ES) of the gene group. The ES, determined by the minus log transformation of the geometric mean p-values from all enriched annotation terms, ranks the biological significance of a gene cluster based on the scores of all the annotation terms.

organism: Rattus norvegicus

source_name: MCL-no injury-intact control

label_protocol: Second strand synthesis was performed by incubation with 1x second strand buffer, 200 μM dNTPs, 10 U DNA Ligase (Invitrogen, Carlsbad, CA), 40 U DNA Polymerase I (Invitrogen, Carlsbad, CA), and 2 U RNaseH (Invitrogen, Carlsbad, CA) for two hours at 16°C  followed by a five minute incubation with 10 U T4 Polymerase (Invitrogen, Carlsbad, CA).  Double stranded cDNA was purified via GeneChip Sample Cleanup Module kit (Affymetrix, Santa Clara, CA Inc.).  The biotin-labeled in vitro transcription reaction was performed using the cDNA template and the Affymetrix 3’-Amplification IVT Labeling kit.  Briefly, double stranded cDNA was incubated with 1x IVT Labeling buffer, 1x Labeling NTP mix, and 1x T7 Labeling Enzyme mix for 16 hours (37°C) to yield cRNA. The cRNA was purified using the GeneChip Sample Cleanup Module.  cRNA yield was determined by absorbance of 260 nM.  The cRNA was fragmented to a 0.5 µg/µl final concentration in 1x fragmentation buffer (40 mM Tris-acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate) for 32 minutes at 94°C.  The sizeof the cRNA before (0.1 kb and longer) and after (35-200 base fragments) was checked by agarose gel electrophoresis.

growth_protocol: Ligaments were snap frozen in liquid nitrogen immediately upon removal from the body. Tissue was stored at -70C until use

extract_protocol: Total RNA was isolated from the MCLs combining the TRIzol (Invitrogen, Carlsbad, CA) method with column fractionalization steps of the RNeasy Total RNA kit (Qiagen, Valencia, CA). Tissue was homogenized using a PowerGen 500 homogenizer (Fisher Scientific, Pittsburgh, PA). Subsequent to RNA isolation, yield and purity of RNA was quantified by nanodrop spectrophotometric measurement at 260 nm absorbance (Nanodrop Technologies, Wilmington, DE). Total RNA was converted to double-stranded cDNA using the oligo dT primer containing the T7 RNA polymerase promoter (5’ – GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-T24-3’).

treatment_protocol: Animals were subjected to bilateral MCL transections. At day 3 (n=9) or 7 post-injury (n=9), tissue was collected and used for microarray. Another 9 rats were used for intact MCL collection which served as the intact control.

tag: strain

value: Wistar

tag: weight

value: medial collateral ligament (MCL)

tag: sample group

value: no injury-intact control


title: MCL-Injured-Day 7-Rep 1

description: SAMPLE 4

source_name: MCL-injured_collected at day 7 post-injury

value: day 7 post-injury


title: MCL-No Injury CX-Rep 3

description: SAMPLE 9


title: MCL-No Injury CX-Rep 1

description: SAMPLE 7


title: Sample-16-ovarian


title: Sample-13-ovarian


title: MCL-Injured-Day 7-Rep 2

description: SAMPLE 5


title: Sample-15-ovarian


title: mir30b and let-7d, biological rep 3

city: Pittsburgh

first: Luai

last: Huleihel

state: PA

address: 450 technology drive

department: Regenerative medicine

institute: University of Pittsburgh

description: Fetal lung tissues were collected through the University of Pittsburgh Tissue Bank

hyb_protocol: Labeled RNA was hybridized for 17 hr at 65C on Agilent 8X44K microRNA array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x44K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters.

source_name: Human fetal lung fibroblast, biological replicate 3

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

growth_protocol: cells growth media : 15%FBS 5% L-glutamin, 5% penicillin-streptomycin, 5% non essential amino acids, 70% DMEM cells were incubated in 5% CO2 in 37 degrees

extract_protocol: Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: human fetal lung fibrobalst cells (150,000 cells per well of a 6-well plate) were plated at 70% confluence. After cells adhered, the medium was replaced by Opti-MEM I reduced serum medium (Invitrogen). Transfection of hsa-Let-7d precursor and hsa-mir30b precursor or negative control (all from Ambion, Austin, TX) were carried out at 100nM using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. RNA was isolated 24h post-transfection.

tag: cell type

value: Human fetal lung fibroblast

tag: genotype/variation

value: mir30b and let-7d


title: Sample-14-ovarian


title: let-7d over expressed, biological rep 5

source_name: Human fetal lung fibroblast, biological replicate 5

value: let-7d over expressed


title: mir30b and let-7d, biological rep 1

source_name: Human fetal lung fibroblast, biological replicate 1


title: MCL-Injured-Day 3-Rep 1

description: SAMPLE 1

source_name: MCL-injured_collected at day 3 post-injury

value: day 3 post-injury


title: MCL-Injured-Day 3-Rep 2

description: SAMPLE 2


title: MCL-Injured-Day 7-Rep 3

description: SAMPLE 6


title: mir30b over expressed, biological rep 5

value: mir30b over expressed


title: mir30b over expressed, biological rep 1


title: mir30b over expressed, biological rep 2

source_name: Human fetal lung fibroblast, biological replicate 2


title: mir30b and let-7d, biological rep 5


title: mir30b and let-7d, biological rep 2


title: CRPS patient P4

description:
P4
We compared differentially expressed genes between CRPS patients and healthy controls to identify CRPS-related genes.


title: mir30b over expressed, biological rep 4

source_name: Human fetal lung fibroblast, biological replicate 4


title: Sample-11-ovarian


title: mir30b and let-7d, biological rep 4


title: mir30b over expressed, biological rep 3


title: Sample-12-ovarian


title: let-7d over expressed, biological rep 4


title: MCL-Injured-Day 3-Rep 3

description: SAMPLE 3


title: let-7d over expressed, biological rep 3


title: CD4+CD25-GFP- conventional T cells

city: San Francisco

first: Jeffrey

middle: A.

last: Bluestone

state: CA

address: 513 Parnassus Ave

department: Diabetes Center

institute: UCSF

hyb_protocol: Hybridization was performed using Exiqon miRCURY LNA microRNA Array Hybridization and wash buffer according to the manufacturer's instructions.

scan_protocol: Slides were scanned using GenePix Pro 6.0.0.29 on a GenePix 4000B scanner at 10µm

data_processing: Removed flagged probes and calculated log2 transformed ratio Treg/Tconv of background subtracted raw fluorescence.

organism: Mus musculus

source_name: conventional CD4 T cells

label_protocol: Total RNA was labelled using the Exiqon miRCURY LNA microRNA Power labeling kit according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using Qiagen’s miRNeasy kit according to the manufacturer’s protocol; RNA integrity was tested using an Agilent Bioanalyzer Chip.

treatment_protocol: CD4+CD25-GFP- conventional T cells (Tconv) and CD4+CD25hiGFP+ Treg from pooled axillary, cervical and inguinal lymph nodes from three pooled female FoxP3-GFP-hCre(1ahigh) reporter mice were sorted on a Moflo flow cytometer

tag: Sex

source_name: regulatory CD4 T cells


title: let-7d over expressed, biological rep 1


title: let-7d over expressed, biological rep 2


title: control, biological rep 5

value: control


title: Sample-8-ovarian


title: zebrfish_spleen_MVAV6203_bath_28d_rep3

city: shanghai

first: zhang

last: hua

address: meilong road No.130

country: China

institute: ECUST Ehua institution

description:
Gene expression at 28 dpv of spleen in zebrafsih bath-vaccinted by MVAV6203
SAMPLE 6

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 10.5.1.1) was used to analyze the acquired array images. Median normalization and subsequent data processing were performed with using the GeneSpring GX v11.0 software package (Agilent Technologies). After median normalization of the raw data, genes that at least 3 out of 6 samples have flags in Present (“All Targets Value”) were chosen for further data analysis.

organism: Danio rerio

source_name: spleen_MVAV6203 bath_28d

label_protocol: 1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Six-month-old zebrafish weighing about 0.3g were obtained from a the animal center in our laboratory (Shanghai, China). They were reared in running areated water at 24℃ on a 12:12h light/dark rhythm and fed with commercial feed for aquatic animal twice per day.

extract_protocol: Tolal RNA was isolated from spleen samples by Trizol (invitrogen, USA) according to the manufacturer’s instructions. The RNA were digested with DNase (promega, USA) to eliminate genomic DNA contaminant. The quality of RNA samples was assessed using NanoDrop ND-1000 spectrophotometer (labtech, USA). The integrity of RNA was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: 10 zebrafish from control groups and vaccinated groups were euthanized and sacrificed to isolate the spleen tissue.

tag: immersed in

value: V.anguillarum MVAV6203-resuspended saline for 10min

tag: time point

value: 28 days post-vaccination

value: whole spleen

value: vaccinated


title: Sample-10-ovarian

value: blood


title: zebrfish_spleen_saline_bath_28d_rep3

description:
Gene expression at 28 dpv of spleen in zebrafsih bath-vaccinted by saline
SAMPLE 3

source_name: spleen_saline bath_28d

value: 2% saline for 10min

value: 28 days after treatment


title: Sample-3-ovarian

source_name: blood

value: ovarian cancer


title: Sample-5-ovarian


title: Sample-7-ovarian


title: zebrfish_spleen_MVAV6203_bath_28d_rep1

description:
Gene expression at 28 dpv of spleen in zebrafsih bath-vaccinted by MVAV6203
SAMPLE 4


title: Sample-6-ovarian


title: Sample-2-ovarian


title: zebrfish_spleen_saline_bath_28d_rep1

description:
Gene expression at 28 dpv of spleen in zebrafsih bath-vaccinted by saline
SAMPLE 1


title: Sample-4-ovarian


title: Control_1

city: Ann Arbor

first: Michael

middle: Dale

last: Brooks

state: Michigan

address: 2800 Plymouth Rd Building 26 Rm 329S

department: Internal Medicine

institute: University of Michigan

description: Control Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Adrenal Gland -normal

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

extract_protocol: RNA was extracted with the Qiagen RNeasy mini Kit according to manufacturers directions.

value: Virgin Females

value: Adrenal Gland

tag: developmental stage

value: Adult

value: normal mice


title: control, biological rep 4

value: Human fetal lung fibroblast


title: Sample-9-ovarian


title: zebrfish_spleen_saline_bath_28d_rep2

description:
Gene expression at 28 dpv of spleen in zebrafsih bath-vaccinted by saline
SAMPLE 2


title: control, biological rep 3


title: zebrfish_spleen_MVAV6203_bath_28d_rep2

description:
Gene expression at 28 dpv of spleen in zebrafsih bath-vaccinted by MVAV6203
SAMPLE 5


title: cKO_2

description: Conditional Knockout Replicate 2

source_name: Adrenal Gland -from Gata6 knockout

value: Gata6 knockout mice


title: control, biological rep 1


title: cKO_1

description: Conditional Knockout Replicate 1


title: sage overexpression rep2

city: Baltimore

first: Deborah

last: Andrew

address: 725 N. Wolfe St., Hunterian G-1

department: Cell Biology

institute: Johns Hopkins University School of Medicine

hyb_protocol: Samples and controls were prepared using the Affymetrix GeneChip hybridization, wash and stain kit (P/N 900720). Arrays were prehybridized for 10 minutes prior to sample addition. Following sample addition, arrays were hybridized for 16 hours at 45 Celsius, and shaken at 60 rpm. Arrays were stained and washed using the Affymetrix GeneChip Fluidics Station 450 and FS450_002 fluidics script.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 3000 and raw analysis was performed with Affymetrix Command Console and Expression Console.

data_processing: Data was normalized by RMA and statistical analysis was performed using Partek software. Further analysis was performed using Spotfire software.

organism: Drosophila melanogaster

source_name: Drosophila embryos

label_protocol: Amplification and labeling were performed using the Affymetrix GeneChip3' IVT express kit (P/N 901229) following the manufacturer's protocol.

growth_protocol: Embryos were collected and aged at 25 C.

extract_protocol: RNA was isolated by TriZol extraction and cleaned up using the Qiagen Rneasy kit.

treatment_protocol: Embryos were sorted on a COPAS biosorter prior to RNA extraction.

tag: genetic background

value: Oregon R

tag: genotype

value: UAS-Sage controlled by the tub-Gal4 driver

value: whole embryo

value: embryonic stages 11-16


title: control, biological rep 2

value: control


title: Control_2

description: Control Replicate 2


title: Sample-1-ovarian


title: sage overexpression rep3


title: sage overexpression rep1


title: Vehicle treated, biological rep2

city: Memphis

first: Meiyun

last: Fan

address: 19 S. Manassas Street

institute: University of Tennessee

hyb_protocol: Biotinylated cRNA were hybridized to the Affymetrix GeneChip® Mouse Gene 1.0 ST array per manufacturer's instructions

scan_protocol: GeneChips were scanned using the GeneArray Scanner

data_processing: The data were analyzed with Affymetrix GeneChip® Operating Software using default analysis settings and global scaling as normalization method.

source_name: breast tumor of MMTV-PyMT+ female mouse treated with vehicle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA

growth_protocol: MMTV-PyMT+ female mice were randomly divided into a DPM treatment group (n=10 mice, total of 100 glands) and a vehicle (control) group (n=7 mice, total of 70 glands). When mice were four weeks old, when hyperplasia lesions begin to develop in the FVB strain (21), DPM (10 mg/kg) or vehicle was injected IP into the peritoneum of each mouse on a 5 days on/2 days off dosing schedule for a total of 11 weeks (week one=injection one), until mice were 15 weeks of age.

extract_protocol: Total RNA was prepared using RNeasy mini kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Solid (non-necrotic) portions of breast tumors were used for RNA preparation

value: mammary gland tumor

value: MMTV-PyMT+

tag: age

value: 15 weeks

value: FVB

tag: treatment

value: vehicle


title: Vehicle treated, biological rep3

tag: tissue


title: Wild type rep3

value: wild type


title: Control_3

description: Control Replicate 3

value: Virgin Females


title: Wild type rep1


title: cKO_3

description: Conditional Knockout Replicate 3

value: Adrenal Gland


title: DPM treated, biological rep2

source_name: breast tumor of MMTV-PyMT+ female mouse treated with DPM

value: DPM


title: Sample-27-ovarian

value: blood

tag: disease state

value: ovarian cancer


title: Vehicle treated, biological rep1


title: Overexpression of Oxi-beta

status: Public on Jun 05 2013

city: SEOUL

first: Jin

last: Son

address: Daehyun-dong, Seodaemun-gu

department: Brain & Cognitive Sciences

institute: Ewha W. University

description: pool of 3 indepemndent samples

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each mouse-8 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).   Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data(Matrix non-normalized) were extracted using the software provided by the manufacturer(Illumina BeadStudio (Gene Expression Module). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected probe signal value was transformed by logarithm and normalized by quantile method.

source_name: SN4741 dopaminergic cell

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

growth_protocol: SN4741 cells were grown in RF medium at 33 C

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol.

treatment_protocol: Overexpression of Oxi-beta for 12 hours in SN4741 cells

value: immortalized dopaminergic neuronal cell

tag: cell line

value: Oxi-beta overexpression


title: Control

description: pool of 3 indepemndent samples


title: DPM treated, biological rep1


title: Infected-type-RR-time-72-rep-16

city: Hamilton

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: 3514_WAP_1_mouse_56_Inf-RR-72-R-24-m-G08-4101_01_9174

hyb_protocol: All cDNAs were hybridized to the commercial Affymetrix mouse 1.0 ST GeneChip

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

data_processing: The data were analyzed with EC 1.2 using Affymetrix default analysis for this chip design. Affymetrix-algorithm-name = rma-gene-default  (v.1.0), program-name = Expression Console (v. 1.1.2800.28061).

label_protocol: Fragmented ds cDNAs were then end-labeled with biotin using terminal transferase (Nugen Inc.)

growth_protocol: Prior to injection trophozoites were grown to log-phase

extract_protocol: Both RNA and genomic DNA were extracted using AllPrep DNA/RNA® 96 kit (Qiagen) following the manufacturer’s recommendations, except that RNA samples received an additional on-column DNase I treatment during extraction

treatment_protocol: 2x10^6 parasites were suspended in 150μl and injected intracecally

tag: strain background

value: containing the humanized LEPR R allele at codon 223

value: infected with Entamoeba histolytica and cleared

value: 72 h post-challenge

value: cecal tissues


title: Infected-type-RR-time-72-rep-11

description: 3509_WAP_1_mouse_51_Inf-RR-72-R-19-m-D04-4081_01_9260


title: Infected-type-RR-time-72-rep-12

description: 3510_WAP_1_mouse_52_Inf-RR-72-R-1-m-F02-4092_01_9221


title: Wild type rep2

value: Oregon R

value: whole embryo

value: embryonic stages 11-16


title: Infected-type-RR-time-72-rep-14

description: 3512_WAP_1_mouse_54_Inf-RR-72-R-37-m-F10-4096_01_9329


title: DPM treated, biological rep3

value: mammary gland tumor

value: MMTV-PyMT+

value: 15 weeks

tag: strain

value: FVB


title: Infected-type-RR-time-72-rep-9

description: 3507_WAP_1_mouse_49_Inf-RR-72-R-2-m-C10-4078_01_9314

value: infected with Entamoeba histolytica


title: Infected-type-RR-time-72-rep-4

description: 3501_WAP_1_mouse_43_Inf-RR-72-R-12-f-E06-4088_01_8367


title: Infected-type-RR-time-72-rep-6

description: 3503_WAP_1_mouse_45_Inf-RR-72-R-5-f-E12-4091_01_1450


title: Infected-type-RR-time-72-rep-7

description: 3505_WAP_1_mouse_47_Inf-RR-72-R-31-f-G09-4102_01_9187


title: Infected-type-RR-time-72-rep-2

description: 3499_WAP_1_mouse_41_Inf-RR-72-R-14-f-D02-4080_01_8478


title: Infected-type-RR-time-72-rep-10

description: 3508_WAP_1_mouse_50_Inf-RR-72-R-25-m-C12-4079_01_9172


title: Infected-type-RR-time-72-rep-1

description: 3498_WAP_1_mouse_40_Inf-RR-72-R-32-f-C02-4074_01_8474


title: Infected-type-RR-time-12-rep-12

description: 3496_WAP_1_mouse_38_Inf-RR-12-R-35-m-C04-4047_01_8533

value: 12 h post-challenge


title: Infected-type-RR-time-72-rep-13

description: 3511_WAP_1_mouse_53_Inf-RR-72-R-17-m-F08-4095_01_9286


title: Infected-type-RR-time-72-rep-8

description: 3506_WAP_1_mouse_48_Inf-RR-72-R-11-f-G06-4100_01_9180


title: Infected-type-RR-time-72-rep-3

description: 3500_WAP_1_mouse_42_Inf-RR-72-R-21-f-D05-4082_01_8505


title: Infected-type-RR-time-72-rep-15

description: 3513_WAP_1_mouse_55_Inf-RR-72-R-4-m-F12-4097_01_9298


title: Infected-type-RR-time-12-rep-11

description: 3495_WAP_1_mouse_37_Inf-RR-12-R-34-m-G04-4071_01_8832


title: Infected-type-RR-time-12-rep-13

description: 3497_WAP_1_mouse_39_Inf-RR-12-R-10-m-C11-4051_01_8495


title: Infected-type-RR-time-72-rep-5

description: 3502_WAP_1_mouse_44_Inf-RR-72-R-15-f-E09-4090_01_1381


title: Infected-type-RR-time-12-rep-7

description: 3491_WAP_1_mouse_33_Inf-RR-12-R-23-m-D12-4057_01_8724


title: Infected-type-RR-time-12-rep-10

description: 3494_WAP_1_mouse_36_Inf-RR-12-R-18-m-G02-4070_01_8589


title: Infected-type-RR-time-12-rep-8

description: 3492_WAP_1_mouse_34_Inf-RR-12-R-30-m-E02-4058_01_8419


title: Infected-type-RR-time-12-rep-9

description: 3493_WAP_1_mouse_35_Inf-RR-12-R-9-m-D06-4054_01_8746


title: Infected-type-RR-time-12-rep-6

description: 3490_WAP_1_mouse_32_Inf-RR-12-R-33-m-D09-4056_01_8360


title: Infected-type-RR-time-12-rep-5

description: 3489_WAP_1_mouse_31_Inf-RR-12-R-20-f-D01-4052_01_8355


title: Infected-type-RR-time-12-rep-4

description: 3488_WAP_1_mouse_30_Inf-RR-12-R-27-f-F11-4093_01_8573


title: Infected-type-QQ-time-72-rep-2

description: 3475_WAP_1_mouse_17_Inf-QQ-72-Q-3-m-C07-4077_01_8642

value: containing the humanized LEPR Q allele at codon 223


title: Infected-type-QQ-time-72-rep-5

description: 3478_WAP_1_mouse_20_Inf-QQ-72-Q-14-m-G01-4098_01_8631


title: Infected-type-RR-time-72-rep-17

description: 3515_WAP_1_mouse_57_Inf-RR-72-R-36-m-G10-4103_01_9235


title: Infected-type-QQ-time-12-rep-5

description: 3470_WAP_1_mouse_12_Inf-QQ-12-Q-17-m-F09-4068_01_8643


title: Control-type-RR-time-12-rep-1

description: 3479_WAP_1_mouse_21_Ctl-RR-12-R-29-f-F06-4066_01_8621

value: not infected (control)


title: Infected-type-QQ-time-12-rep-7

description: 3472_WAP_1_mouse_14_Inf-QQ-12-Q-18-m-G07-4073_01_8565


title: Infected-type-RR-time-12-rep-1

description: 3485_WAP_1_mouse_27_Inf-RR-12-R-26-f-E03-4059_01_3941


title: Infected-type-QQ-time-12-rep-6

description: 3471_WAP_1_mouse_13_Inf-QQ-12-Q-13-m-G05-4072_01_8641


title: Infected-type-RR-time-12-rep-2

description: 3486_WAP_1_mouse_28_Inf-RR-12-R-7-f-E11-4063_01_8420


title: Infected-type-QQ-time-72-rep-4

description: 3477_WAP_1_mouse_19_Inf-QQ-72-Q-2-m-F05-4094_01_8519


title: Infected-type-QQ-time-72-rep-1

description: 3474_WAP_1_mouse_16_Inf-QQ-72-Q-20-f-E08-4089_01_8835


title: Control-type-RR-time-12-rep-2

description: 3480_WAP_1_mouse_22_Ctl-RR-12-R-16-f-C08-4049_01_8559


title: Infected-type-QQ-time-72-rep-3

description: 3476_WAP_1_mouse_18_Inf-QQ-72-Q-5-m-D08-4083_01_8547


title: Infected-type-QQ-time-12-rep-8

description: 3473_WAP_1_mouse_15_Inf-QQ-12-Q-15-m-C09-4050_01_8575


title: Infected-type-RR-time-12-rep-3

description: 3487_WAP_1_mouse_29_Inf-RR-12-R-8-f-F07-4067_01_8412


title: Control-type-RR-time-72-rep-3

description: 3484_WAP_1_mouse_26_Ctl-RR-72-R-13-m-D10-4084_01_3938


title: Control-type-RR-time-72-rep-1

description: 3482_WAP_1_mouse_24_Ctl-RR-72-R-22-f-C06-4076_01_8290


title: Control-type-RR-time-72-rep-2

description: 3483_WAP_1_mouse_25_Ctl-RR-72-R-6-f-E04-4087_01_8599


title: Infected-type-QQ-time-12-rep-3

description: 3467_WAP_1_mouse_09_Inf-QQ-12-Q-9-f-C01-4046_01_4195


title: Infected-type-QQ-time-12-rep-4

description: 3468_WAP_1_mouse_10_Inf-QQ-12-Q-12-f-C05-4048_01_4261


title: Control-type-RR-time-12-rep-3

description: 3481_WAP_1_mouse_23_Ctl-RR-12-R-3-m-E10-4062_01_8288


title: Infected-type-QQ-time-12-rep-2

description: 3466_WAP_1_mouse_08_Inf-QQ-12-Q-7-f-F01-4064_01_4274


title: DCM10 mRNA

city: Atlanta

first: William

last: Lewis

state: Georgia

address: 101 Woodruff Circle

department: Pathology

institute: Emory University

hyb_protocol: Hybridization was completed using NimbleGen Hybridization Kit (Cat # 05583683001)following their standard operating protocol.

scan_protocol: Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol.

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

source_name: Total RNA from DCM Sample

label_protocol: DNA labeling was completed using NimbleGen labeling Kit (Cat #06370411001) following their standard operating protocol.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc.) and cDNA was synthesized using Superscript Double-Stranded cDNA Synthesis kit (Invitrogen/Life Technologies).  cDNA quality was determined using a Spectramax 190 plate reader (Molecular Devices) for A260 and A280 absorbance determination along with gel electrophoresis.

treatment_protocol: All human heart samples were obtained either from fresh, surgicaly-removed patients undergoing heart transplantation or non-failing controls unsuitable for organ donation. Each sample was quickly flash frozen in liquid nitrogen and stored at -80°C until needed.

value: heart left ventricle


title: DCM9 mRNA


title: DCM8 mRNA


title: DCM7 mRNA


title: Infected-type-QQ-time-12-rep-1

description: 3465_WAP_1_mouse_07_Inf-QQ-12-Q-10-f-F03-4065_01_7996


title: DCM5 mRNA


title: DCM6 mRNA


title: DCM2 mRNA


title: DCM3 mRNA


title: DCM1 mRNA


title: NF10 mRNA

source_name: Total RNA from NF Sample


title: NF6 mRNA


title: NF11 mRNA


title: NF3 mRNA


title: NF2 mRNA


title: NF12 mRNA


title: NF5 mRNA


title: KYSE180 cells transfected with siRNAs targeting HOTAIR

city: Beijing

first: Weidong

last: Han

address: #28 Fuxing Road, HaiDian District

department: School of Life Sciences

institute: Chinese PLA General Hospital

description: gene expression data from HOTAIR cell line transfected with HOTAIR siRNAs usng Lipofectamine2000

hyb_protocol: FS450_0002 for the human GeneChip PrimeView arrays

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing: GeneChip Command Console AGCC software 3.2.4 was used to generate the CEL files. The computational pipeline was run on the bioinformatics platform GenomeSpac. Data were extracted from the CEL files and preprocessed by applying RMA and the quantile normalization procedures implemented in the ExpressionFileCreator module of the GenePattern software platform.

label_protocol: Biotin: GeneChip ® 3' IVT Express labeling Kit

growth_protocol: KYSE180 cells were maintained in RMPI1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin

extract_protocol: RNA was extracted using TRIZOL Reagent following the manufacturer's instructions.

treatment_protocol: KYSE180 cells were transfected with HOTAIR vector and HOTAIR siRNAs, respectively for 48 hours.

tag: sample type

value: esophageal squanmous cell carcinoma (ESCC) cells

value: siRNAs targeting HOTAIR


title: NF7 mRNA


title: NF4 mRNA


title: KYSE180 control cells

description: gene expression data from Control KYSE180 cell line

source_name: Control KYSE180 cell line

value: control


title: DCM4 mRNA


title: KYSE180 cells transfected with HOTAIR vector

description: gene expression data from KYSE180 cell line transfected with HOTAIR using Polyfec

source_name: KYSE180 cell line transfected with HOTAIR using Polyfect

value: HOTAIR vector


title: NF9 mRNA


title: Mock 2PTB

city: Santa Cruz

first: Manny

last: Ares

address: 1125 High St

department: Molecular and Cellular Biology

institute: UCSC

hyb_protocol: The labeled, amplified cDNA was hybridized overnight to the MJAY Chip (Affymetrix)

scan_protocol: Chips were washed and labeled using the Affymetrix Fluidics Station 450, and scanned on an Affymetrix GeneChip scanner.

data_processing:
Intensity was calculated by AffyPowerTools using dabg , gc background correction, iter-plier and quantile normalization
Data was analyzed according to the methods in Sugnet et al. PLoS Comput Biol. 2006 Jan;2(1):e4. PMID: 16424921
probe group file: mjay.clf
meta-probeset file: mjay.pgf

source_name: C2C12 myoblasts

label_protocol: Amplified, labeled cDNA was produced using the GeneChip® Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix) according to the manufacturer’s instructions

growth_protocol: Mouse C2C12 myoblast cells (ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Invitrogen).

extract_protocol: Ribosomal RNAs were removed from three replicate individual total RNA preparation for each sample using the RiboMinus Transcriptome Isolation Kit (Invitrogen) according to the manufacturers instructions.

treatment_protocol: siRNA targeting Qk , PTB , and mock siRNA were used

value: C2C12 myoblast cells

tag: sirna

value: mock siRNA


title: Mock 1PTB


title: Mock 3PTB


title: Mock rep2


title: PTB rep2

value: PTB siRNA


title: PTB rep3


title: Mock rep1


title: Mock rep3


title: Qk rep1

value: Qk siRNA


title: Qk rep2


title: 72h rep3

source_name: C2C12 72hours

growth_protocol: Mouse C2C12 myoblast cells (ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Invitrogen). To induce myogenesis, 1.5 x 105 cells were plated in growth medium (DMEM + 10% FBS) per well in 6-well tissue culture-treated plates (Fisher) 12-18 hours prior to the addition of differentiation medium. Cells were washed once with differentiation medium (DMEM supplemented with 2% horse serum [Invitrogen]) prior to maintenance in the same medium. Media was changed every 24 hours, and myotube formation was visible

treatment_protocol: Differentiation was verified visually by myotube formation and via Western blot to visualize myogenic markers. RNA and protein were isolated either immediately prior to (zero time) or up to 72 hours after addition of differentiation medium.

tag: time differentiated

value: 72 hr


title: Qk rep3


title: 24h rep3

source_name: C2C12 24hrs

value: 24 hr


title: 72h rep1


title: 72h rep2


title: PTB rep1


title: 24h rep2


title: 24h rep1


title: 0h rep3

source_name: C2C12 undifferentiated

value: 0 hr


title: IL-4/IL-13-/- CCL4 rep 1

first: Sharon

last: Goh

state: California

address: 555 Mission Bay Blvd South

description: replicate 1

data_processing: The data were normalised with Rank Invariant method

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit (Ambion) for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Balb/c

tag: genotype/variation

value: 2 months

value: liver


title: IL-4/IL-13-/- CCL4 rep 2

description: replicate 2


title: WT CCL4 rep 2

description: replicate 2

source_name: WT CCL4

value: wild-type


title: WT CCL4 rep 3

description: replicate 3


title: 0h rep2


title: IL-4/IL-13-/- CCL4 rep 3

description: replicate 3


title: hox011

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: Gene expression data from human primary tumors

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were normalized with Partek Genomics Suite 6.6 and RMA summarized

source_name: Hoxb8 expressing immortalized cells

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

growth_protocol: In vitro cell culture in RPMI 1640 supplemented with 10% (v/v) fetal calf serum, 50 mM 2-mercaptoethanol and antibiotics (penicillin G (100 IU/ml) and streptomycin sulfate (100 IU/ml)), 1µM -estradiol and 5% FLT3 ligand-containing supernatant.

extract_protocol: Standard Trizol extraction of total RNA and purification using RNeasy Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Transformed with fusion construct encoding the hormone binding domain of the estrogen receptor and Hoxb8.

value: bone marrow

tag: cell type

value: early hematopoietic progenitor cells

value: Hoxb8 expressing


title: hox012


title: DCM-9 DNA

scan_protocol: Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol

data_processing: Each sample was processed utilizing NimbleScan software default values, including analysis of the 635/532 ratio utilizing a 500bp sliding window KS test according to manufacturer instructions.

source_name: Methylated Genomic DNA from DCM sample

label_protocol: DNA labeling was completed using NimbleGen Dual-Color DNA labeling Kit (Cat # 06370250001) following their standard operating protocol.

extract_protocol: DNA was extracted  using a MagNAPure DNA Extraction System (Roche), quantiated, sonicated and enriched using the MethylCollector Ultra Kit (Active Motif) following the manufacturer's protocol. Both methylated and input DNA was amplified using whole genome amplification (Sigma-Aldrich).

value: heart left ventricle

tag: dna type

value: Methylaed Genomic DNA

source_name: Total Genomic DNA from DCM Sample

value: total Genomic DNA


title: 0h rep1

value: C2C12 myoblast cells


title: WT CCL4 rep 1

description: replicate 1


title: IL-4/IL-13-/- Vehicle

description: replicate 1

source_name: IL-4/IL-13-/- Vehicle


title: WT Vehicle

description: replicate 1

source_name: WT Vehicle


title: DCM-4 DNA


title: hox002


title: DCM-10 DNA


title: hox001


title: DCM-6 DNA


title: DCM-2 DNA


title: pre-iPSC- siRNA to Cbx3- biological replicate2

first: Rupa

last: Sridharan

address: 2118 Wisconsin Institute for Discovery

institute: UW-Madison

hyb_protocol: Hybridisation was performed using Affymetrix protocol

scan_protocol: Gene ChiPs were scanned with a Gene Array Scanner

data_processing: CEL files generated were normalized by RMA normalization from the R statistical package

label_protocol: Standard Affymetrix protocol

growth_protocol: pre-iPSCs we re grown in standard embryonic stem cell media

extract_protocol: Trizol extraction was carried out according to manufacturer's instructions

treatment_protocol: pre-iPSCs were treated with indicated siRNA for 3 days and then RNA was extracted

value: pre-iPSCs

tag: sirna mediated knockdown

value: Cbx3 (HP1gamma)


title: pre-iPSC- siRNA to Cbx3- biological replicate3


title: DCM-5 DNA


title: NF-10 DNA

source_name: Methylated Genomic DNA from NF sample

source_name: Total Genomic DNA from NF Sample


title: DCM-7 DNA


title: genomic DNA from KYSE180 cells transfected with control vector

description: ESCC cell line

hyb_protocol: bisulphite converted DNA was amplified, fragmental and hybridised to Illumina Infinium HumanMethylation 450K Beadchip using standard Illumina protocol

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

data_processing: BeadStudio solfware v3.2

label: Cy5 and Cy3

source_name: KYSE180 cells

label_protocol: Standard Illumina Protocol

growth_protocol: KYSE180 cells were grown in RMPI-1640 (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS)(Gibico, BRL, Life Technologies, Inc., Maryland, USA), 100 units/ml penicillin and 100 mg/ml streptomysin according to the instructions provided

extract_protocol: genomic DNA was extracted and purified from KYSE180 cells and KYSE180_HOTAIR cells using Qiagen Dneasy Kit according to standard instrctions

treatment_protocol: KYSE180 cells were transfected with HOTAIR vector and control vector, respectively.

value: (esophageal squamous cell carcinoma) ESCC

value: control


title: genomic DNA from KYSE180 cells transfected with HOTAIR vector

description: ESCC cell line

value: HOTAIR vector


title: NF-5 DNA


title: NF-12 DNA


title: DCM-1 DNA


title: copt2-1 seedlings versus Col 0 seedlings in Fe and Cu deficient medium  replicate 3

city: Valencia

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP (UPV-CSIC)

hyb_protocol: DNA onto slides was rehydrated by placing the slide upside-down over a water bath at 60°C for 10 s, and snap dry onto a heat block at 65°C. Rehydratation was repeated 3 times. DNA was immobilized by UV light by exposing the slides DNA-side-up to 65 mJ in a UV cross-linker (Stratagene). Slides were then washed twice in 0.1% SDS and 4 times in water, 2 min each wash at RT, and finally dipped in 96% ethanol for 1 min and dried by centrifugation at 2000 rpm 1 min at RT. Slides were prehybridized for 30 min at 42°C with 100 µL of prehybridization solution (6x SSC (Sigma), 1% BSA (Sigma) and 0.5% SDS (Sigma)), under a 60x22 mm coverslip LifterSlip (Erie Scientific) in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were rinsed 5 times in H2O in a slide rack at RT and dried by centrifugation at 2000 rpm 1 min at RT. Slides were hybridized immediately.  Both coupled aa-aRNA (Cy3 and Cy5) were mixed and fragmented in the presence of 20 µg of tRNA (Ambion) and 20 µg of poly(A) (Roche) using the RNA fragmentation Reagent (Ambion) as described by the manufacturer, in a final volume of 10 µL. Fragmented aa-aRNA was used directly in the hybridization mix, which contains of 50 µL deionized formamide (Sigma), 30 µL 20x SSC, 5 µL 100x Denhardt´s solution (Sigma), and 5 µL 10% SDS in a final volume of 100 µL. Hybridization mixture was denatured at 95 °C for 5 min, spun briefly, and applied by capillary between a pre-treated slide (see above) and a 60x42 mm coverslip LifterSlip. Slides were incubated o/n at 37°C in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were washed sequentially once in 1x SSC 0.1% SDS 5 min at 30°C; once in 0.2x SSC 0.1% SDS 5 min at 30°C; twice in 0.1x SSC 2 min each at 30°C; and finally 0.01x SSC 10 sec at RT. Slides were dried by centrifugation at 2000 rpm 1 min at RT.

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 5-nm resolution and 100% laser power.

data_processing:
Spot intensities were quantified using GenePix Pro 6.0 microarray-analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than the median signal background plus twice standard deviations were removed as low signal spots.  Data were normalized by median global intensity using the GenePix Pro 6.0 software.
Linear normalized log2 ratio (copt2-1/Col-0). Values for copt2-1 vs Col 0 +Fe +Cu Rep 3, copt2-1 vs Col 0 +Fe +Cu Rep 4, copt2-1 vs Col 0 -Fe +Cu Rep 3, copt2-1 vs Col 0 -Fe +Cu Rep 4, copt2-1 vs Col 0 -Fe -Cu Rep 3 and copt2-1 vs Col 0 -Fe -Cu Rep 4  have been dye-swap corrected at Matrix table.

organism: Arabidopsis thaliana

source_name: 7 days seedlings of Col-0 mutant in Fe and Cu sufficient medium

label_protocol: RNA was amplified using the MessageAmp II aRNA Amplification kit (Ambion), basically as described by the manufacturer. 5-(3-aminoallyl)-UTP (aa-UTP) (Ambion) was incorporated into the amplified RNA (aRNA) at ratio 1:1 with UTP. After purification 7.5 µg of aminoallyl-aRNA (aa-aRNA) were used in a coupling reaction with either fluorescent Cy3 or Cy5 as reactive N-hydroxyl succinimidal dyes (NHS-dyes) (Amersham Pharmacia Biotech, Piscataway, NJ). For this, each aliquot of Cy3 or Cy5 were dissolved in 20 µL of DMSO and used in four coupling reactions. aa-aRNA was dissolved in 15 µL of freshly-made 0.1 M NaCO3 pH 9.0, and mixed with 5 µl of either Cy-3 or Cy-5 dye. Coupling was allowed for 1 h at RT in the dark. Reaction was stopped with 35 µL of 100 mM sodium acetate pH 5.2 and incubated 5 min in the dark. Fluorescent aa-aRNA was purified using a MegaClear purification column (Ambion) as described by the manufacturer. Coupled aa-aRNA (250-300 pmol Cy dye in 5-7 µg aa-aRNA) was dried in a speedvac and dissolved in 2.5 µL of filtered water.

growth_protocol: Seeds were surface sterilized by treatment with 70% ethanol for 20 min, followed by commercial bleach (2.5 % sodium hypochlorite) containing 0.05 % Triton X-100 for 10 min, and finally, four washes with sterile distilled water. Stratification of the seeds was conducted in the dark at 4ºC for 2 days. Seeds were sowed in  ½ MS medium (see specifications in treatment protocol) and grown for 7 days under  12 hours of light + 12 hours of darkness photoperiod conditions.

extract_protocol: Seedlings were frozen in liquid nitrogen, and grounded in mortars dipped in liquid nitrogen. Total RNA was extracted using the Quiagen Plant RNeasy Mini Kit followong the manufacturer´s recommendations

treatment_protocol: Seedlings in the Fe and Cu sufficient medium were grown in a ½ MS medium that includes macronutrients (10mM NH4NO3, 9.4mM KNO3, 0.37mM MgSO4.7H20, 0.62mM KH2PO4 and 1.13mM CaCl2), micronutrients (50μM H3BO3, 36.6μM MnSO4.2H20, 15μM ZnSO4.7H20, 0.57μM NaMoO4.2H2O and 0.05μM CoCl2.6H20), 50μM Fe-EDTA, 0.25mM KI, 1μM CuSO4, 0.05% MES, 1% sucrose and 0.8% phytoagar; pH 5.7-5.8. For the Fe deficient and Cu sufficient medium,  300μM ferrozine was added to the medium and Fe-EDTA was removed from it. For the Fe and Cu deficient medium, 300μM ferrozine was added to the medium and Fe-EDTA and CuSO4 were removed from it.

value: 7 days seedlings

tag: ecotype

value: wildtype

tag: growth condition

value: Fe and Cu deficient medium

source_name: 7 days seedlings of copt2-1 mutant in Fe and Cu sufficient medium

value: copt2-1 mutant


title: copt2-1 seedlings versus Col 0 seedlings in Fe and Cu deficient medium  replicate 4

tag: genotype


title: pre-iPSC- siRNA to Cbx3- biological replicate1


title: NF-6 DNA


title: copt2-1 seedlings versus Col 0 seedlings in Fe and Cu deficient medium  replicate 2


title: DCM-8 DNA


title: pre-iPSC- siRNA to Ehmt1, Ehmt2 and Setdb1- biological replicate2

value: Ehmt1, Ehmt2, Setdb1 (3XHMT)


title: DCM-3 DNA


title: pre-iPSC- siRNA to Ehmt1, Ehmt2 and Setdb1- biological replicate1


title: copt2-1 seedlings versus Col 0 seedlings in Fe and Cu deficient medium  replicate 1


title: NF-9 DNA


title: pre-iPSC- siRNA to luciferase- biological replicate1

description: pre-iPSC-control 1


title: pre-iPSC- siRNA to luciferase- biological replicate3

description: pre-iPSC-control 3


title: NF-3 DNA


title: copt2-1 seedlings versus Col 0 seedlings Fe deficient and Cu sufficient medium replicate 2

source_name: 7 days seedlings of copt2-1 mutant in Fe deficient and Cu sufficient medium

value: Fe deficient and Cu sufficient medium

source_name: 7 days seedlings of Col-0 mutant in Fe deficient and Cu sufficient medium


title: copt2-1 seedlings versus Col 0 seedlings Fe deficient and Cu sufficient medium replicate 4