title: E. amylovora Ea1189_rcsC mutant_pear_rep2

city: Urbana

first: Frank

last: Zhao

state: IL

address: 1210 Gregory Dr.

department: Crop Sciences

institute: University of Illinois

description: An oligonucleotide microarray was designed at the James Hutton Institute (formerly SCRI), and synthesized by Agilent Technologies, Inc. (Palo Alto, CA). Each slide contains 8 arrays and each array has nearly 15,000 spots, containing our probes in triplicate. The main E. amylovora ATCC 49946 genome (accession NC_013971, Sebaihia et al. 2010) had 3483 target sequences (annotated genes and pseudo-genes), plus a further 483 target genes or simple gene predictions from five sequenced plasmids: plasmids 1 and 2 for the same strain (accessions NC_013972, NC_013973, Sebaihia et al. 2010), pEL60 and pUE30 (accessions NC_005246, NC_005247, Foster et al., 2004), and pEI70 (Spanish strain Erwinia amylovora IVIA1614-2a, unpublished, Lopez and Llop, personal communication). Due to the high similarity between E. amylovora ATCC 49946 plasmid 1 (NC_013972, 2.8kb) and the previously published pEA29 (NC_005706, 2.8kb, McGhee and Jones 2000), the later was not used. Up to five sense orientation candidate probes per target were designed with the Agilent eArray webtool, using temperature matching methodology, a preferred probe melting temperature of 80.0C, no 3' bias, and a target length of 60bp. Any short probes were later extended to 60bp using the Agilent linker. BLASTN (Altschul et al., 1997) and Biopython (Cock et al., 2009) were used to identify potential cross-hybridization in order to rank the candidate probes. Selecting one probe per genome target, and up to five probes per plasmid target, allowed all our probes to be present in triplicate. Using the spare array capacity for multiple plasmid probes aimed to increase the chance of hybridization with plasmid transcripts from other E. amylovora strains.

hyb_protocol: 1. Add 20 μl water to dissolve the dried labeled-cDNA (600ng).  2. Add 5 μl 10 × Blocking Agent  3. Add 25 μl 2 × GE × Hybridization Buffer H1-RPM. Mix well by pipetting to reduce bubble formation. Spin for 1 min and place on ice.    Prepare the hybridization assembly  1. Load a clean gasket slide into the Agilent Suretlyb chamber base with the label facing up.  2. Slowly dispense 40 μl hybridization samples onto the gasket well. To minimize bubble formation.  3. Slowly place an array “active side (Agilent facing down)” onto the gasket slide.  4. Place the SureHyb chamber clamp cover on the sandwiched slides and slide the clamp assembly onto both pieces.  5. Hand-tighten the clamp on to the chamber. Rotate the gasket slide when tightening.  6. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  7. Place assembled slide chamber in a hybridization oven set to 65°C, 15 rpm.  8. Hybridize at 65°C for 17 h.    Washing  This step is performed under dark conditions.  1. Add triton into the X-102 to Gene Expression washing buffer 1 and 2.  2. Pre-warm gene expression wash buffer 2 in a 37°C water bath O/N  3. Dessemble the hybridization chamber, put gaskets and slide into Washing Buffer 1. Use a tweezer to separate the slide from the cover slide.  4. Put the slide into the washing container and array side facing out. Wash for 1 min  5. Transfer the slide into another container containing Washing Buffet 2 and wash for another min.  6. Remove the slide slowly to minimize the attachment of water. Put the slide into a 50 ml tubes in dark places.

scan_protocol: Slides were scanned using an Agilent Scanner (Agilent technologies, Santa Clara, CA, USA) at 5-µm resolution. All slides were scanned using 100% laser power; PMT voltages were automatically adjusted using the Genepix Pro 6.0 software acquisition system to obtain maximal signal intensities with <0.02% probe saturation. The resulting 16 bit images were processed using the GenePix Pro 6.0 image analysis software (v6.0.1.26).

data_processing: Microarray data normalization  Microarray normalization is carried out using maanova function in R program version 2.2.1. Eight arrays in one slide were globally normalized using glowess method.  1. library(maanova)  go to the directory:  setwd(C:\\Documents and Settings\\Wang\\Desktop\\Erwinia in vivo\\rcsC MBMA)  2. Read data:  Data = read.madata(NormInput.txt, designfile=Designfile1.txt, header=TRUE, spotflag=TRUE, metarow=1, metacol=2, row=3, col=4, geneID=5, pmt=6)  3. Log transformation:  LogData = createData(Data, n.rep=1, log.trans=TRUE)  4. Normalization by Glowess method:  NormalData=transform.madata(LogData, method=c(glowess))  5. Save the plot files  postscript(file=PlotRawData.ps)  riplot(LogData, onScreen=FALSE)  postscript(file=PlotGLOWESS.ps)  riplot(NormalData, onScreen=FALSE)  6. close the graph:  graphics.off()  norm.temp<-cbind(NormalData$metarow, NormalData$metacol,NormalData$row, NormalData$col, NormalData$geneID, NormalData$data)  7. output:  write.table(norm.temp, file=Normal_Data.csv, sep=,, row.names=FALSE, col.names=TRUE, quote=FALSE)    Data selection  Statistical comparisons were performed using multiple testing procedures to evaluate statistical significance for differentially expressed genes. A modified t-test (p-value) was computed to measure the significance associated with each differential expression value. A gene expression value was decided to be significantly different in the mutant and over-expression strains when the p-value was less than 0.05 (except otherwise mentioned) and the expression ratio was ≥ 2.0or ≤ 0.5.

label: Alexa Fluor 555

organism: Erwinia amylovora

source_name: E. amylovora Ea1189 rcsC mutant cells, pear

label_protocol: cDNA labeling was carried out using the FairPlay III Microarray Labeling Kit from Agilent.    Reverse transcription  10 μ g total RNA was used to generate cDNA. Add 1 μl of 500 ng/ μl random primers into the 10 μg total RNA which is dissolved in 12 μl RNase free water. Incubate at 70°C for 10 min in a PCR machine. Cool samples immediately on ice until ready for use. Combine the following components in a sterile, RNase and DNase free tube: 2 μl 10 × AffinityScript RT Buffer; 1 μl 20 × dNTP mix; 1.5 μl 0.1 M DTT; 0.5 μl 40 U/ul RNase Block. Add the annealed primers and RNA into the mixture. Add 3 μl of AffinityScript RT and incubate at 42°C for 60 min. Add 10 μl of 1 M NaOH and incubate at 70°C for 10 min to hydrolyzed RNA. Cool to room temperature and add 10 μl 1 M HCL to neutralize the solution.    cDNA purification  Add 4 μl of 3 M sodium acetate pH 5.5 to the reaction. Add 1 μl of 20 mg/ml glycogen to the reaction. Add 100 μl ice cold 100% ethanol and incubate at -20°C overnight. Spin the reaction at 13.2 rpm for 15 min at 4°C and decant the supernatant (You should see some white pellet at the bottom of the tube). Wash with 200 μl ice cold 70% ethanol and spin 5 min. Decant supernatant carefully and allow for air dry for about 30 min to eliminate ethanol.    cDNA labeling with a reaction fluorescence dye  Prepare the amine-modified cDNA. Thoroughly dissolve the amine-modified DNA in 5 μl of nuclease-free water, warm in a 42°C water bath for 5 min. Prepare labeling buffer: 2.5 g sodium bicarbonate in 100 ml water. Add 3 μl labeling buffer to the amine-labeled cDNA. Dissolve one vial of dye in 2 μl of high quality DMSO, vortex for 10 s. Add the 8 ul amine-modified cDNA into the dissolved dye. Incubate the reaction in dark for 1 h.    Purification of dye-labeled cDNA using QIAquick PCR Purification column  Add 8 μl of nuclease-free water and 2 μl 3 M sodium acetate pH 5.5 to the reaction mixture. Add 100 μl buffer PB to the mixture. Apply the sample to the QIAquick column and centrifuge for 60 s. Discard flow-through and place the QIAquick column back into the same tube. To wash, add 0.75 ml buffer PE to the column and centrifuge for 60 s. Centrifuge in a 2 ml collection tube for 1 min. Place QIAquick column in a clean 1.5 ml tube. Add 50 μl buffer EB and centrifuge for 1 min.

growth_protocol: Bacterial strains were grown overnight in LB media supplemented with or without antibiotic and diluted in 5 ml MBMA media at an OD600 of 0.005. After 18 hours growth at MBMA medium at 28°C, 2 ml of RNA Protect Reagent (Qiagen) was added to 1 ml bacterial cultures (at OD600 of about 0.5-0.8) to stabilize RNA. For in vivo condition, bacterial strains were grown overnight in LB media and bacterial cells were collected by centrifugation. The cells were resuspended in PBS, adjusted to an OD600 to 0.2 to 0.3 and inoculated onto immature pear fruit surface by cutting the fruit in half. For rcs mutants, more pear slices were inoculated and pooled in order to recover sufficient bacterial cells for RNA extraction. After incubation at 28°C for up to 18 h with high humidity, bacterial cells were collected by washing with a solution containing 2 ml RNA Protect Reagent (Qiagen) and 1 ml RNase-free water.

extract_protocol: Transfer 700 μl lysate into RNeasy Mini column place in a 2 ml collection tube and centrifuge for 30 s at highest speed. Add 350 μl Buffer RW1 to the column and centrifuge for 30 s. Discard flow-through and reuse the collection tube. Add 10 μl DNase stock solution to 70 μ l RDD Buffer. Add the DNase I solution into the column and incubate at RT for 15 min. Add 350 μl Buffer RW1 to the column and wait for 5 min, centrifuge for 30 s. Discard the flow-through and collection tubes. Place the RNeasy Mini spin column in a new 2 ml collection tube. Add 500 μl Buffer RPE to the column. Centrifuge for 30 s. Place the column in a new 1.5 ml tube, and centrifuge for 1 min to eliminate any residue ethanol. Place the column in a new collection tube. Add 50 μl RNase free water, centrifuge for 1 min. Store RNA samples at -20°C.

treatment_protocol: Add 100 μl 1 mg/ml lysozyme buffer (TE buffer: 10 mM Tris-HCL, 1 mM EDTA pH=8.0 containing 1 mg/ml lysozyme). Vortex for 10 s and incubate at RT for at least 15 min. Add 350 μl Buffer RLT and vortex vigorously. Add 250 μl 100% ethanol, mix by pipetting.

value: rcsC mutant

tag: growing condition

value: pear fruits

tag: Stage

value: logarithm phase


title: Picea mariana_phelloderm_rep2

status: Public on Feb 18 2012

type: RNA

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

country: Canada

institute: Université Laval

description: Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Slide scanning was performed at 5 micron resolution on a ScanArray Express (Perkin Elmer, Waltham MA, USA) microarray scanner and image analysis was carried out using QuantArray v3.0 (Packard BioChip Technologies, Billerica, MA, USA).

data_processing: Data (spot intensity means) analyses were performed using customized scripts for R and Bioconductor (http://www.r-project.org and http://www.bioconductor.org). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background intensities were subtracted from the foreground intensities. Background-subtracted data were log2-transformed and normalized using quantile correction approach.   A filtering step was applied to select positive genes to be used for further analysis. The mean intensity of spots containing buffer only was calculated for each row of sub-grids, and was taken as the minimum intensity of probes for that subgrid. A probe was called positive (detected above background) when its signal intensity was above the buffer intensity on at least 50% of slides within a given sample type. When determining differential expression, positive probes were probes that were detected according to this criterion in at least one of the tissues (e.g. phelloderm and xylem). Mean probe intensity was determined for genes represented by more than one positive probe.   The average signal intensity was determined from all of the slides available for a sample type. The genes were then ranked based on their average signal intensities within a tissue type and equally divided into 10 separate classes according to their signal intensity. Genes from class 1 or class 10 were the 10% with lowest and highest signal intensities, respectively.

label: Alexa 555

molecule: total RNA

organism: Picea mariana

source_name: Picea mariana, phelloderm

label_protocol: Total RNA (1 µg) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 555 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: Nursery planting stock (from open-pollinated seed lots) were obtained as 3-year-old seedlings of Picea glauca, Picea sitchensis and Picea mariana, were transferred to 8-inch pots and grown in a greenhouse under natural light conditions. Sampling of tissues was timed with the ending of primary shoot elongation, i.e. after 6 to 8 weeks of growth, and was as described (Pavy et al. 2008). For each tissue type five biological samples were prepared by pooling 6 independent trees.

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the trees and stored at -80°C. Tissues were ground under liquid nitrogen and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008) for all of the sample types.

tag: tissue

value: phelloderm

tag: time of collection

value: am

tag: replicate

tag: slide batch


title: Med13 TG heart

city: Dallas

first: Chad

last: Grueter

state: Texas

address: 6000 Harry Hines Blvd

country: USA

institute: UT Southwestern Medical Center

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

organism: Mus musculus

source_name: Med13 TG heart

label_protocol: cRNA were prepared for Illumina arrays

growth_protocol: RNA from hearts of 3, 4 week old Med13 alpha MHC TG mice and wild-type littermates

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

tag: age

value: 4 week-old

tag: gender

value: male

tag: genotype

value: Med13 alphaMHC transgenic

value: heart


title: wild-type zebrafish, biological rep1

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

description: Gene expression data from upper digestive tract tissue of 3 wild-type zebrafish

hyb_protocol: After purification of cRNAs by GeneChip Sample Cleanup Module (Affymetrix), 15 µg of cRNA was fragmented at 94°C for 35 min. Approximately 12.5 µg of fragmented cRNA was used in a 250-µl hybridization mixture containing herring-sperm DNA (0.1 mg/ml; Promega), plus bacterial and phage cRNA controls (1.5 pM BioB, 5 pM BioC, 25 pM BioD, and 100 pM Cre) to serve as internal controls for hybridization efficiency. Aliquots (200 µl) of the mixture were hybridized to arrays for 16 h at 45°C in a GeneChip Hybridization Oven 640 (Affymetrix). Each array was washed and stained with streptavidin–phycoerythrin (Invitrogen) and amplified with biotinylated anti-streptavidin antibody (Vector Laboratories) on the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned with the GeneArray G7 scanner (Affymetrix) to obtain image and signal intensities

data_processing: Data analysis was performed using the Affymetrix MAS5 algorithm.

label: biotin

organism: Danio rerio

source_name: upper digestive tract tissue from 3 wild-type zebrafish

label_protocol: Biotinylated cRNAs were generated from cDNAs by in vitro transcription and amplified by using the BioArray T7 RNA polymerase labeling kit (Enzo Diagnostics).

growth_protocol: Zebrafish were obtained from the Zebrafish International Resource Center (Eugene, OR). To generate zCdx1b transgenic fish, AB* line was used. Fish were housed in an automatic fish housing system (Aquaneering, San Diego, CA) at 28.5°C and maintained according to the established procedures

extract_protocol: The upper digestive tract tissue from 3 adult zebrafish (3 months old) was dissected and pooled as one sample. Three zCdx1b transgenic samples were used for microarray, and 2 wild type samples were used for control. The total RNA was extracted using TRIzol according to the manufacturer's instructions.

treatment_protocol: Transgenic zebrafish were generated by microinjection of one cell stage fertilized AB* zebrafish eggs with a mixture of pmini Tol2-zK5p-zCdx1b-EGFP (80µg/ml) and Tol2 transposase RNA (4 µg/ml)

value: upper digestive tract

tag: genetic background

value: AB

value: 3 months

value: wild-type


title: Med13 TG WAT

source_name: Med13 TG WAT

growth_protocol: RNA from liver, WAT and BAT of 3, 4 week old Med13 alpha MHC TG mice and wild-type littermates

treatment_protocol: Mice were fasted over night

value: gonadal white adipose tissue


title: Picea mariana_phelloderm_rep1


title: E. amylovora Ea1189_rcsC mutant_pear_rep1

tag: strain


title: Picea mariana_xylem_rep1

source_name: Picea mariana, xylem

value: xylem


title: zCdx1b transgenic zebrafish, biological rep1

description: Gene expression data from upper digestive tract tissue of 3 zCdx1b transgenic zebrafish

source_name: upper digestive tract tissue from 3 zCdx1b transgenic zebrafish


title: HSC engrafted-2

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

data_processing:
Data was processed using the softwares SDS2.3 and RQ Manager 1.2 from Applied Biosystems.
dCt for delta Ct, defined by the formula (Ct of the specific miRNA-Ct of the endogenous control RNU48) for each sample. RQ for relative quantification, defined by the formula 2^-dCt . Small nuclear RNA (RNU48) was used as an endogenous control.

label: FAM

organism: Homo sapiens

source_name: engrafted hematopoietic stem cells (CD45+CD34+CD38-)

label_protocol: Standard Taqman assay.

growth_protocol: Lin- CB cells were transplanted in irradiated 6-week-old NSG mice. After 8 weeks, bones were harvested and engrafted human HSCs were sorted (CD45+CD34+CD38-).

extract_protocol: Total RNA was extracted with the Total RNA kit from Norgen.

tag: cell type


title: Picea mariana_xylem_rep2


title: E. amylovora Ea1189_rcsB mutant_pear_rep2

source_name: E. amylovora Ea1189 rcsB mutant cells, pear

value: rcsB mutant


title: Dime-2 vs WT no nitrogen rep2

city: Berkeley

first: Elizabeth

middle: Ann

last: Hutchison

state: CA

address: 111 Koshland Hall

department: Plant & Microbial Biology

institute: UC Berkeley

hyb_protocol: The Pronto! Hybridization kit (Corning) was used for microarray hybridization per the manufacturer's instructions

scan_protocol: Slides were scanned using a GenePix 4000B scanner (Axon Instruments)

data_processing: Hybridization signals were quantified and analyzed using GenePix Pro6 software. Hybridization spots were adjusted as needed and inspected manually for quality control. Normalized gene expression values were analyzed using BAGEL (Bayesian Analysis of Gene Expression Levels; PMID 12537560)

organism: Neurospora crassa

source_name: Dime-2 mycelia grown on minimal media for 16h and transferred to minimal media-nitrogen for 4h

label_protocol: 10 mg of total RNA were used in the ChipShot Indirect Labeling/Clean-up Kit (Promega) and CyDye Post-Labeling Reactive Dye Pack were used to synthesize and label the total RNA

growth_protocol: Strains were grown overnight (16h) with shaking at 25 dg C in 250 mL flasks

extract_protocol: Total RNA was extracted using Trizol per the manufacturer's instructions

treatment_protocol: Strains were washed once with Vogel's minimal media-nitrogen and centrifuged to collect mycelia. Mycelia were transferred to fresh flasks containing minimal media-nitrogen and grown at 25 dgC with shaking for an additional 4h. Mycelia were then harvested by filtration.

tag: condition

value: minimal media-nitrogen

source_name: WT mycelia grown on minimal media for 16h and transferred to minimal media-nitrogen for 4h

value: FGSC 2489

value: WT


title: Dime-2 vs WT no nitrogen rep1


title: Adult repeat 2

city: Cambridge

first: Doug

last: Melton

state: MA

address: 7 Divinity Ave

department: Stem Cell and regenerative Biology

institute: Harvard University

description: replicate 2

data_processing: rank invariant

source_name: Mouse beta-cells

label_protocol: Biotinylated cRNA was prepared from ≥ 100 ng of isolated RNA using Illumina TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: Islets were isolated from heterozygous Pdx1–GFP (crossed with ICR) animals and further dissociated into single cells with 0. 25% Trypsin-EDTA (Invitrogen). GFP+ cells were isolated using FACSaria (BD Bioscience). Total RNA was extracted with RNeasy RNA extraction kit (Qiagen).

value: Pdx1-GFP tg x ICR

value: 5 weeks

value: Islets of Langerhans


title: HSC engrafted-1

value: engrafted hematopoietic stem cells (CD45+CD34+CD38-)


title: WT vs Dime-2 no nitrogen


title: FB HSC-1

source_name: fetal blood-derived hematopoietic cells (CD34+CD45+ sorted)


title: MPB HSC-2

source_name: mobilized peripheral blood-derived hematopoietic cells (CD34+CD45+ sorted)


title: P10 repeat 2

description: replicate 2


title: E. amylovora Ea1189_WT_pear_rep2

source_name: E. amylovora Ea1189 cells, pear

value: wild type

value: pear fruits

value: logarithm phase


title: E. amylovora Ea1189_rcsB mutant_pear_rep1


title: E. amylovora Ea1189_WT_pear_rep1


title: E. amylovora Ea1189_rcsC mutant_MBMA_rep2

source_name: E. amylovora Ea1189 rcsC mutant cells, MBMA

value: rcsC mutant

value: MBMA minimal medium


title: MPB HSC-1

value: mobilized peripheral blood-derived hematopoietic cells (CD34+CD45+ sorted)


title: hESC-2

source_name: human embryonic stem cells

value: embryonic stem cells


title: E. amylovora Ea1189_rcsC mutant_MBMA_rep1


title: Adult repeat 3

description: replicate 3


title: Adult repeat 1

description: replicate 1


title: hESC-1


title: P1 repeat 3

description: replicate 3


title: hiPSC-2

source_name: human induced pluripotent stem cells

value: induced pluripotent stem cells


title: E. amylovora Ea1189_rcsB mutant_MBMA_rep2

source_name: E. amylovora Ea1189 rcsB mutant cells, MBMA


title: P10 repeat 1

description: replicate 1


title: P1 repeat 2

description: replicate 2


title: hESCphc-2

source_name: human embryonic stem cell-derived hematopoietic cells (CD34+CD45+ sorted)


title: hiPSC-1


title: hiPSCphc-1

source_name: human induced pluripotent stem cell-derived hematopoietic cells (CD34+CD45+ sorted)


title: hiPSCphc-2

value: induced pluripotent stem cell-derived hematopoietic cells (CD34+CD45+ sorted)


title: E. amylovora Ea1189_rcsB mutant_MBMA_rep1

value: rcsB mutant


title: P1 repeat 1

description: replicate 1


title: E. amylovora Ea1189_WT_MBMA_rep2

source_name: E. amylovora Ea1189 cells, MBMA


title: E. amylovora Ea1189_WT_MBMA_rep1


title: Tick-free control_ECM array

status: Public on Feb 17 2012

city: Galveston

first: Dar

last: Heinze

address: 301 University Blvd

department: Pathology

institute: University of Texas Medical Branch

description: Control  This sample contains 3 biological replicates

data_processing: Fold-changes in gene expression between test and control mice were calculated using the ΔΔCt method. For each included gene, individual measurements that were below the threshold selected (Ct >34) were excluded from further analysis.  Data normalization was based on correcting all Ct values for the average Ct values of the invariant endogenous control genes hypoxanthine guanine phosphoribosyl transferase (Hprt) and heat shock protein 90 alpha (Hsp90ab1).  These genes were selected based on analysis of tested housekeeping genes in geNorm (Vandesompele J et al. Genome Biol 2002, 3:RESEARCH0034).  Statistical significance was assessed using LIMMA (linear models in micro-array analysis) in HTqPCR, an R-based program designed for real-time PCR array data analysis (Dvinge H and Bertone P.  Bioinformatics 2009, 25:3325-3326).

label: SYBR Green

source_name: Tick-free control

label_protocol: For each array, 1υg total RNA purified from skin biopsies was converted into cDNA using the RT2 First strand kit (Qiagen).  Template cDNAs were mixed with RT2 SYBR Green/Fluorescein qPCR Master Mix (Qiagen) and loaded onto the array using an 8-channel pipette.  Arrays were run on an iCycler iQ5 real-time PCR System (Bio-Rad) under standard cycling conditions (10 min at 95°C, 15 s at 95°C, 1 min 60°C for 40 cycles, 55-95°C melt curve).

growth_protocol: 6-8 week old BALB/cJ mice were housed in microinsulator cages supplied with food and water ad libitum.

extract_protocol: Total RNA was isolated using a combination of Trizol reagent (Invitrogen) and RNeasy (Qiagen) protocols.

treatment_protocol: Mice were infested with Ixodes scapularis nymphs.

value: 4mm ear biopsy

value: BALB/cJ

value: Female


title: E18.5 repeat 4

description: replicate 4

value: Pdx1-GFP tg x ICR


title: 12hr_Primary Infestation_ECM array

description: Test  This sample contains 3 biological replicates

source_name: 12hr_Primary Infestation


title: 72hr_Primary Infestation_ECM array

source_name: 72hr_Primary Infestation


title: 48hr_Primary Infestation_ECM array

source_name: 48hr_Primary Infestation


title: 96hr_Primary Infestation_ECM array

source_name: 96hr_Primary Infestation


title: 12hr_Secondary Infestation_ECM array

source_name: 12hr_Secondary Infestation


title: 72hr_Secondary Infestation_ECM array

source_name: 72hr_Secondary Infestation


title: 48hr_Secondary Infestation_ECM array

source_name: 48hr_Secondary Infestation


title: 96hr_Secondary Infestation_ECM array

source_name: 96hr_Secondary Infestation


title: hESCphc-1

value: embryonic stem cell-derived hematopoietic cells (CD34+CD45+ sorted)


title: E18.5 repeat 3

description: replicate 3

source_name: Mouse beta-cells

value: Islets of Langerhans


title: E18.5 repeat 1

description: replicate 1


title: Picea mariana_phelloderm_rep11

source_name: Picea mariana, phelloderm

value: phelloderm

value: am


title: E18.5 repeat 2

description: replicate 2


title: pristine protocol biopsy pPB11

city: Edmonton

first: Konrad

middle: S

last: Famulski

state: Alberta

address: 250 HMRC

institute: University of Alberta

description: Samples with the same initial numbers in the sample names are replicates from the same patient. For the main analysis, only the earliest biopsy per patient was used, and only in those patients with a biopsy taken > 1 year post-transplant

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 Plus 2.0 Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Gene Array Scanner (Affymetrix) and processed with GeneChip Operating Software Version 1.4.0 (Affynetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: protocol biopsy

label_protocol: RNA (1-2µg) was labeled using GeneChip HT One-Cycle Target Labeling and Control kit. Quality of labeled cRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to HGU133Plus2.0. GeneChip (Affymetrix, Santa Clara, CA).

growth_protocol: All human renal allograft biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Following homogenization of the tissue in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA), total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 4µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: diagnosis

value: pristine protocol biopsy

value: kidney


title: pristine protocol biopsy pPB8


title: pristine protocol biopsy pPB7


title: GW-hMSC 1wk

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

hyb_protocol: Total of 12.5 ug of labeled aRNA was fragmented and hybridized (GeneChip Hybridization Oven 640, Affymetrix) onto a human array (HG-U133 Plus 2.0, Affymterix) followed by washing and staining (GeneChip Fluidics Station 450, Affymetrix) with GeneChip Wash and Stain Kit (Affymetrix) using the Command Console software (Affymetrix)

scan_protocol: Array was scanned with 7G GeneChip Scanner (Affymetrix) using the Command Console software (Affymetrix) and the image were checked for quality.

data_processing: The CHP file was created using the Expression Console software (Affymetrix) and MAS5 analysis.

label: Biotin

organism:
Homo sapiens
Mus musculus

source_name: Murine calvarial defect with GW-treated hMSCs, 1 week time point

label_protocol: Total of 200 ng of RNA sample was used to prepared labeled aRNA according to manufacturer’s instructions for GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: Human GFP-MSCs (passage 3-4) at 80% confluency were grown for 8 days in osteogenic medium containing 10uM GW9662 in DMSO

extract_protocol: Total RNA was extracted from the cranial bones using a total RNA isolation kit (High Pure, Roche). Bones were incubated in RNA extraction buffer at ambient temperature for 4 h and processed in accordance with the protocol.

treatment_protocol: After euthanasia, cranial bones were cut away using a rotary tool fitted with a 10-mm diameter diamond-cutting wheel. The top of the skull was gently removed, washed in PBS, and cleared of excess connective tissue. The tissue was flash-frozen in liquid nitrogen for RNA extractions.

value: female

value: 8 wk

value: Nu/J

tag: disease

value: calvarial defect

tag: treatment

value: 1 million GW-treated hMSCs

tag: treatment time

value: day 0


title: Pig14_Baseline

city: Uppsala

first: Per

last: Vikholm

address: Akademiska sjukhuset

department: Cardiothoracic Surgery

country: Sweden

institute: Uppsala University

description: Gene expression data from baseline sample

hyb_protocol: Affymetrix GeneChip® expression arrays (Porcine Genome Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev2, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450

scan_protocol: GeneChips were scanned using a GeneChip® Scanner 3000 7G

data_processing: The raw data was processed using Partek Genomic Suite software (Partek Inc, St Louis, MO). Two-way analysis of variance (ANOVA) method was used to calculate p values.

organism: Sus scrofa

source_name: Right ventricular free wall, baseline

label_protocol: 250 nanograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® 3’ IVT Express Kit Manual (PN 702646 Rev1, Affymetrix Inc., Santa Clara, CA)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy columns (Quiagen)

treatment_protocol: Heart failure induced by ligation of the coronary arteries on the free right ventricular wall. Heart failured was defined as right atrial pressure >20 mmHg.

tag: pig number

value: Right ventricular free wall

tag: breed

value: Mixed breed of Hampshire, Yorkshire and Swedish Landrace

tag: weight

tag: treatment group

value: Baseline


title: Pig5_Baseline

tag: tissue


title: Pig14_Failure

description: Gene expression data from acute ischemic heart failure sample

source_name: Right ventricular free wall, heart failure

value: Failure


title: Pig5_Failure


title: pristine protocol biopsy pPB6


title: Control hMSC 1wk

source_name: Murine calvarial defect with DMSO-treated hMSCs, 1 week time point

growth_protocol: Human GFP-MSCs (passage 3-4) at 80% confluency were grown for 8 days in osteogenic medium containing 0.1% DMSO

value: 1 million DMSO-treated hMSCs


title: GW-hMSC 2wk

source_name: Murine calvarial defect with GW-treated hMSCs, 2 week time point

value: day 0 and 7


title: Pig10_Failure


title: pristine protocol biopsy pPB5


title: Control hMSC 2wk

source_name: Murine calvarial defect with DMSO-treated hMSCs, 2 week time point


title: 96hr_Secondary Infestation_SigT array

value: 4mm ear biopsy

value: BALB/cJ

value: Female


title: pristine protocol biopsy pPB9

value: pristine protocol biopsy


title: Pig10_Baseline


title: Nephrectomy NEPH6

source_name: nephrectomy

value: Nephrectomy

value: kidney


title: AMB-1 ΔctrA + ctrA D51A ampR rep2

first: Arash

last: Komeili

address: 111 Koshland Hall #3102

department: Plant and Microbial Biology

description:
D51A tb 5
Nimb4PA02_dCtrA+Atb_5_415625_532.pair

hyb_protocol: Hybridization was performed by Fred Hutchinson Cancer Research Center, according to the standard operating protocol of NimbleGen Systems Inc., Madison, WI, USA.

scan_protocol: Scanning was performed by Fred Hutchinson Cancer Research Center, according to the standard operating protocol of NimbleGen Systems Inc., Madison, WI, USA.

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

organism: Paramagnetospirillum magneticum AMB-1

source_name: Magnetospirillum magneticum str. AMB-1 ΔctrA complemented with ctrA D51A (ampR)

label_protocol: 0.5µg cDNA was fluorescently-labeled with Cy3 using the Nimblegen One Color DNA Labeling kit as directed.

growth_protocol: All strains were grown to mid-exponential phase (OD400 0.04 to 0.08) in 50 mL conical tubes in magnetospirillum growth media (MG) amended with 1/100 volume Wolfe's vitamin solution and 1/100 volume 3mM ferric 9mM malate.  For ΔctrA deletion strains complemented with CtrA alleles, carbenicillin was added to 20ug/mL.

extract_protocol: Total RNA was extracted using the Trizol reagent as directed, DNase treated, and purified using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). RNA quality and concentration was determined by analysis with NanoDrop. cDNA was reverse transcribed using the Invitrogen Super Script RT III kit as directed and purified using a Qiagen PCR Clean Up kit.

treatment_protocol: All strains grown identically, excepting the addition carbenicillin for strains carrying plasmids.

tag: genotype/variation

value: ΔctrA complemented with ctrA D51A

tag: motility

value: non-motile

tag: growth conditions

value: MG + 20ug/ml carbenicillin


title: 72hr_Secondary Infestation_SigT array

tag: gender


title: AMB-1 ΔctrA ampR rep3

description:
tb 5
Nimb4PA02_dCtrA+tb_5_330368_532.pair

source_name: Magnetospirillum magneticum str. AMB-1 ΔctrA complemented with an empty vector (ampR)

value: ΔctrA complemented with an empty vector


title: Nephrectomy NEPH8


title: AMB-1 ΔctrA + ctrA D51A ampR rep3

description:
D51A tb 6
Nimb4PA01_dCtrA+Atb_6_330368_532.pair


title: AMB-1 ΔctrA ampRrep1

description:
tb 3
Nimb4PA03_dCtrA+tb_3_415625_532.pair


title: AMB-1 ΔctrA + ctrA D51E ampR rep3

description:
D51E tb 14
Nimb4PA04_dCtrA+Etb_14_415616_532.pair

source_name: Magnetospirillum magneticum str. AMB-1 ΔctrA complemented with ctrA D51E (ampR)

value: ΔctrA complemented with ctrA D51E


title: AMB-1 ΔctrA + ctrA D51A ampR rep1

description:
D51A tb 4
Nimb4PA01_dCtrA+Atb_4_415625_532.pair


title: Nephrectomy NEPH7


title: AMB-1 ΔctrA ampR rep2

description:
tb 4
Nimb4PA04_dCtrA+tb_4_415625_532.pair


title: 48hr_Secondary Infestation_SigT array


title: Nephrectomy NEPH4


title: Nephrectomy NEPH5


title: pristine protocol biopsy pPB2


title: 12hr_Secondary Infestation_SigT array

source_name: 12hr_Secondary Infestation


title: 96hr_Primary Infestation_SigT array

source_name: 96hr_Primary Infestation


title: 72hr_Primary Infestation_SigT array

source_name: 72hr_Primary Infestation


title: 12hr_Primary Infestation_SigT array

source_name: 12hr_Primary Infestation


title: Nephrectomy NEPH3


title: Tick-free control_SigT array

source_name: Tick-free control


title: 48hr_Primary Infestation_SigT array

source_name: 48hr_Primary Infestation


title: AMB-1 ΔctrA + ctrA D51E ampR rep2

description:
D51E tb 13
Nimb4PA03_dCtrA+Etb_13_415616_532.pair


title: 96hr_Secondary Infestation_Th17 array

source_name: 96hr_Secondary Infestation


title: AMB-1 ΔctrA + ctrA D51E ampR rep1

description:
D51E tb 12
Nimb4PA02_dCtrA+Etb_12_415616_532.pair


title: 72hr_Secondary Infestation_Th17 array

source_name: 72hr_Secondary Infestation


title: AMB-1 ΔdivK

description:
DivK 4
Nimb4PA04_divK_4_330368_532.pair

source_name: Magnetospirillum magneticum str. AMB-1 ΔdivK

value: ΔdivK

value: MG


title: AMB-1 WT rep4

description:
WT 3B2B
Nimb4PA04_3B2B_330326_532.pair

source_name: Magnetospirillum magneticum str. AMB-1 wild-type

value: wild-type


title: Nephrectomy NEPH2


title: AMB-1 ΔMAI

description:
MAI
Nimb4PA03_MAI_3_330368_532.pair

source_name: Magnetospirillum magneticum str. AMB-1 ΔMAI

value: ΔMAI


title: 48hr_Secondary Infestation_Th17 array

source_name: 48hr_Secondary Infestation


title: Acute kidney injury AKI 60A2AGX7

source_name: renal allograft biopsy

value: Acute kidney injury AKI


title: AMB-1 WT rep3

description:
WT 3B2A
Nimb4PA03_3B2A_330326_532.pair


title: AMB-1 WT rep1

description:
WT 3B1A
Nimb4PA01_3B1A_330326_532.pair


title: AMB-1 WT rep2

description:
WT 3B1B
Nimb4PA02_3B1B_330326_532.pair


title: 12hr_Secondary Infestation_Th17 array


title: AMB-1 ΔctrA

description:
CtrA 3
Nimb4PA01_dCtrA_3_415616_532.pair

source_name: Magnetospirillum magneticum str. AMB-1 ΔctrA

value: ΔctrA


title: Nephrectomy NEPH1

source_name: nephrectomy


title: Acute kidney injury AKI 49A1AGX7


title: Acute kidney injury AKI 56A2AGX7


title: 96hr_Primary Infestation_Th17 array

value: 4mm ear biopsy


title: Acute kidney injury AKI 47A1AGX7


title: Acute kidney injury AKI 24A1AGX7


title: Acute kidney injury AKI 49A2AGX7


title: 72hr_Primary Infestation_Th17 array

value: BALB/cJ


title: Acute kidney injury AKI 128A4AGX7


title: Acute kidney injury AKI 56A1AGX7


title: Acute kidney injury AKI 126A4AGX7


title: Acute kidney injury AKI 116A4AGX7


title: Acute kidney injury AKI 292A2AGX7


title: 12hr_Primary Infestation_Th17 array

value: Female


title: Acute kidney injury AKI 406A2AGX7


title: 48hr_Primary Infestation_Th17 array


title: Acute kidney injury AKI 72A3AGX9


title: Tick-free control_Th17 array


title: fetal_liver_proB

city: Bethesda

first: Stefan

middle: Adi

last: Muljo

state: MD

address: 10 Center Drive

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

hyb_protocol: Flow-cell hybridization was performed per manufacturer’s instructions at the DNA Sequencing and Digital Expression Core Facility (National Cancer Institute).

scan_protocol: Scanning was performed per manufacturer’s instructions at the DNA Sequencing and Digital Expression Core Facility (National Cancer Institute).

data_processing: Excel was used for data normalization. Per manufacturer's instructions, data were normalized to the sum of positive control count values provided in assay to account for lane to lane variation. Then the data were normalized again to the sum of the counts of the 75 highest expressing miRNAs in each sample. let-7 miRNAs that fell into the category of the 75 highest expressing miRNAs were excluded from the list. Thus, let-7a, let-7d, let-7f, let-7g and let-7i were excluded for fetal pro-B. Background levels were determined by calculating the mean plus two standard deviations of eight negative control detectors. By this method, a normalized count ≤40 is considered undetectable for this dataset.

label: NanoString oligonucleotide tag

source_name: fetal liver pro-B cells

label_protocol: Sample labelling was performed per manufacturer’s instructions at the DNA Sequencing and Digital Expression Core Facility (National Cancer Institute).

extract_protocol: RNAzol (Molecular Research Center, Inc) was used per manufacturer's instructions to extract total RNA.  100 ng total RNA was used as starting material. RNA concentration was determined using the Qubit RNA broad range assay and fluorometer (Invitrogen). To confirm the concentration and determine the integrity of the RNA, the Eukaryote Total RNA nano Series II chip on a 2100 Bioanalyzer (Agilent) was used.

treatment_protocol: FACS-sorted pro-B cells (B220+CD43+IgM-veCD19+CD24+) from the fetal livers of 10 embryonic mice (14.5 dpc) were pooled.

tag: developmental stage

value: fetus

tag: age

value: fetal liver

value: B220+CD43+IgM-veCD19+CD24+ pro-B cells


title: microRNA profile of double-positive thymocyte precursors (control cells not transduced by a retrovirus encoding Lin28a)

data_processing: Excel was used for data normalization. Per manufacturer's instructions, data were normalized to the sum of positive control count values provided in assay to account for lane to lane variation. Then the data were normalized again to the mean of five housekeeping mRNA controls (ACTB, B2M, GAPDH, RPL19 and RPLP0). Background levels were determined by calculating the mean plus two standard deviations of eight negative control detectors. By this method, a raw count ≤30 is considered undetectable for this dataset.

source_name: Lin28-RV GFP-ve DP thymocytes

growth_protocol: Retrogenic bone marrow chimeras were generated by transduction of wildtype bone marrow hematopoietic stem and progenitor cells with a retrovirus encoding Lin28a in vitro in the presence of SCF (50 ng/ml), IL-6 (10 ng/ml), IL-3 (5ng/ml), FLT-3L (5ng/ml) and IL- 7 (5ng/ml). A mixture of transduced and untransduced cells were injected into sublethally (450RADS) irradiated Rag1-/- hosts at 2-4 million cells per host.

extract_protocol: RNAzol (Molecular Research Center, Inc) was used per manufacturer's instructions to extract total RNA.  100 ng total RNA was used as starting material. RNA concentration was determined using the Qubit RNA broad range assay and fluorometer (Invitrogen). To confirm the concentration and determine the integrity of the RNA, we used the Eukaryote Total RNA nano Series II chip on a 2100 Bioanalyzer (Agilent).

treatment_protocol: Transduced (GFP+) and untransduced (GFP-) CD4+ CD8+ CD3- thymocytes were sorted and pooled from three recipients of lineage-depleted hematopoietic stem and progenitor cells transduced with Lin28-RV six weeks post-reconstitution. Total RNA was extracted and the NanoString protocol was followed.

tag: strain

value: thymus

tag: cell type

value: double-positive thymocyte precursors

tag: transduction


title: Acute kidney injury AKI 366A2AGX7

tag: diagnosis

value: kidney


title: yeast_Lcells_vs_Ucells_day20_repl3

city: Prague

first: Michal

last: Cap

address: Vinicna 5

department: genetics and microbiology

country: Czech Republic

institute: Faculty of Science, Charles University in Prague

hyb_protocol: hybridyzation overnight in 42°C in 50% formamide and 20xSSC buffer

scan_protocol: scanned on Axon scanner with GenePix software

data_processing: Features identified with Spotfinder (TIGR), low values replaced by arbitrary value, normalized with LOWESS method in MIDAS (TIGR), saturated spots replaced with values obtained from lower intensity scan. In the raw data files, column A represents channel 2 and column B represents channel 1.

organism: Saccharomyces cerevisiae

source_name: 20-day-old colony from lower layer

label_protocol: 2ug mRNA labelled with 1 nmol dUTP-Cy3 or dUTP-Cy5 using 2 ug random hexaprimers, 1 ug oligo d(T) and SuperScript III Rtase (Invitrogen)

growth_protocol: yeast colonies grown for 15 or 20 days on glycerol agar plates

extract_protocol: total RNA was extracted using hot phenol method and mRNA was isolated using Invitrogen mRNA  II Kit

treatment_protocol: cells from colonies were fractionated according to their size in sucrose gradient. Fractions 1 and 3 were used to isolate L-cells and U-cells, respectively.

value: L-cells day 20

source_name: 20-day-old colony from upper layer

value: U-cells day 20


title: adult_bone_marrow_proB

data_processing: Excel was used for data normalization. Per manufacturer's instructions, data were normalized to the sum of positive control count values provided in assay to account for lane to lane variation. Then the data were normalized again to the sum of the counts of the 75 highest expressing miRNAs in each sample. let-7 miRNAs that fell into the category of the 75 highest expressing miRNAs were excluded from the list. Thus, let-7a, let-7b, let-7c, let-7d, let-7f, let-7g and let-7i were excluded for adult pro-B. Background levels were determined by calculating the mean plus two standard deviations of eight negative control detectors. By this method, a normalized count ≤40 is considered undetectable for this dataset.

source_name: adult bone marrow pro-B cells

treatment_protocol: FACS-sorted pro-B cells (B220+CD43+IgM-veCD19+CD24+) from the bone marrow of 3 adult mice were pooled.

value: adult

value: bone marrow


title: yeast_Lcells_vs_Ucells_day20_repl1


title: microRNA profile of double-positive thymocyte precursors transduced with a retrovirus encoding Lin28a

source_name: Lin28-RV GFP+ DP thymocytes

value: retrovirus encoding Lin28a


title: Acute kidney injury AKI 337A2AGX7


title: yeast_Lcells_vs_Ucells_day15_repl4

source_name: 15-day-old colony from lower layer

value: L-cells day 15

source_name: 15-day-old colony from upper layer

value: U-cells day 15


title: yeast_Lcells_vs_Ucells_day20_repl2


title: yeast_Lcells_vs_Ucells_day15_repl3


title: yeast_Lcells_vs_Ucells_day15_repl1


title: Acute kidney injury AKI 338A2AGX7

value: Acute kidney injury AKI


title: Acute kidney injury AKI 82A4AGX7


title: yeast_Lcells_vs_Ucells_day15_repl2


title: Acute kidney injury AKI 397A3AGX7


title: Acute kidney injury AKI 332A2AGX7


title: Acute kidney injury AKI 289A1AGX8


title: Acute kidney injury AKI 281A2AGX7


title: pBAD-ctr.3 [13361666_A]

type: mixed

city: Würzburg

first: Kai

last: Papenfort

state: Würzburg

address: Josef-Schneider Str.2/BAU D15

department: RNA Biology

country: Germany

institute: IMIB Würzburg

hyb_protocol: Microarray slide were hybridized in a water bath over night at 63C. For detailed protocol see: http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: Axon GenePix4000A, 10nm resolution scan

data_processing: Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios.

molecule: genomic DNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella enterica SL1344

label_protocol: total RNA was labelled with Cy3 using random hexamers and reverse transcriptase (Stratagene AffinityScript) while genomicDNA was labelled with Cy5 using the Invitrogen BioPrime DNA Labeling System

growth_protocol: Salmonella carrying pBAD-ctr or pBAD-MicF were grown in LB-media to OD=1.5.

extract_protocol: SV40 RNA isolation Kit (promega). GenomicDNA was extracted using the Qiagen 'Genomic DNA' Kit

treatment_protocol: At OD=1.5, 0.2% (final conc.) L-arabinose was added. Total RNA was isolated 10 min post treatment.

value: pBAD-ctr


title: Acute kidney injury AKI 255A4AGX7


title: Acute kidney injury AKI 513A2AGX7


title: pBAD-ctr.2 [13361692_B]


title: pBAD-MicF 2

value: pBAD-MicF


title: pBAD-ctr.1 [13361692_A]


title: pBAD-MicF 3


title: pBAD-MicF 1


title: Acute kidney injury AKI 220A3AGX7


title: Acute kidney injury AKI 306A2AGX7


title: Acute kidney injury AKI 380A1AX13


title: Acute kidney injury AKI 95A2AGX7


title: Acute kidney injury AKI 374A2AGX7


title: P20_MUT1

status: Public on Feb 16 2012

type: genomic

city: New York

first: FANG

last: FANG

state: NY

address: 1275 York Avenue

department: The Human Oncology and Pathogenesis Program

institute: Memorial Sloan-Kettering Cancer Center

description: Gene methylation data data for glioma cell line

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: data was normalized and analyzed using partek software and R packages. Specifically centered logit transformation was used for data normalization.

source_name: human astrocytes

label_protocol: Standard Illumina protocol for Human Methylation27 DNA Analysis bead chip

extract_protocol: The genomic DNA was extracted from snap-frozen sections from the breast cancer patients by using a DNeasy Tissue kit (Qiagen)

tag: tissue type

value: cell line

value: astrocyte

tag: status


title: P10_MUT1


title: P10_WT1


title: P30_WT2


title: P30_MUT1


title: P50P


title: P50WT2


title: P10_MUT2


title: P20_MUT2


title: P30_P2


title: P20_WT1


title: P10_P2


title: P5_WT2


title: P5_MUT2


title: P20_WT2


title: P10_P1


title: P30_WT1


title: P5_P1


title: P10_WT2


title: P50MUT2


title: P20_P1


title: P50WT1


title: P30_MUT2


title: P5_P2


title: P20_P2


title: P5_WT1


title: P50MUT1


title: P5_MUT1


title: P40mut2


title: P30_P1


title: primary colon cancer GFPlow cells, biological rep2

city: Munich

first: David

last: Horst

address: Thalkirchner Str. 36

institute: Pathologisches Institut der LMU

description: Gene expression data from FACS sorted tumor cell fractions

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed using the dChip package with default analysis settings and global scaling as normalization method.

source_name: TOP-GFP transduced primary colon cancer xenograft, FACS sorted tumor cells for low GFP expression

label_protocol: Total RNA was converted to cDNA, linearly amplified using the NuGEN Ovation V2 Amplification System (NuGEN, San Carlos, CA), and converted to biotinylated cRNA for hybridization, according to the manufacturer's protocols

growth_protocol: TOP-GFP transduced colon cancers were grown subcutaneously in NOD/SCID mice

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

treatment_protocol: Tumors were manually and enzymatically disaggregated into single cell suspensions and FACS sorted for vital epithelial tumor cell fractions with high or low GFP fluorescence

value: Tumor tissue grown from patient dervived colon cancer specimen


title: primary colon cancer GFPlow cells, biological rep1


title: P40wt2


title: primary colon cancer GFPhigh cells, biological rep1

source_name: TOP-GFP transduced primary colon cancer xenograft, FACS sorted tumor cells for high GFP expression


title: Caco2 GFPlow cells, biological rep2

source_name: TOP-GFP transduced Caco2 colon cancer xenograft, FACS sorted tumor cells for low GFP expression

value: Tumor tissue grown from cultured colon cancer cell line

tag: cell line


title: primary colon cancer GFPhigh cells, biological rep2


title: Caco2 GFPlow cells, biological rep1


title: Caco2 GFPlow cells, biological rep3


title: P25MUT2


title: P40mut1


title: P40wt1


title: Caco2 GFPhigh cells, biological rep2

source_name: TOP-GFP transduced Caco2 colon cancer xenograft, FACS sorted tumor cells for high GFP expression


title: TGFB replicate 2

city: Adelaide

first: Sarah

middle: Anne

last: Robertson

state: SA

address: Frome Rd

department: paediatrics and Reproductive Health

country: Australia

institute: University of Adelaide

hyb_protocol: Genechips  were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.

scan_protocol: Genechips were scanned using the Affymetrix GSC3000 scanner.

data_processing: RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip.  Quality control was assessed using the affyQCreport package in R (v2.6.1).  The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity).  The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.

source_name: Ect1 cells

label_protocol: Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.

growth_protocol: Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).

extract_protocol: Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.

treatment_protocol: Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.

tag: treatment

value: rec human TGFβ3 (5 ng/ml)

tag: treatment time


title: TGFB replicate 4


title: TGFB replicate 1


title: TGFB replicate 3


title: Caco2 GFPhigh cells, biological rep1


title: seminal plasma replicate 3

value: 10% seminal plasma


title: seminal plasma replicate 2


title: seminal plasma replicate 4


title: P40Parental2


title: P40Parental1


title: seminal plasma replicate 1


title: P15WT2


title: control replicate 4

value: medium alone


title: P2MUT2


title: P25Parental2


title: P15MUT2


title: P25Parental1


title: P25WT2


title: P15Parental1


title: P2WT1


title: P2MUT1


title: P15WT1


title: P2WT2


title: control replicate 2


title: P2Parental2


title: control replicate 1


title: control replicate 3


title: P2Parental1


title: Caco2 GFPhigh cells, biological rep3


title: Mono-DEX-5-081707

city: Manhasset

first: Dennis

last: Davidson

state: New York

address: 350 Community Dr

department: Pediatrics

institute: The Feinstein Institute for Medical Research

description: Gene Expression data from the Umbilical Cord Blood Monocytes treated with 10^ -8 M Dexamethasone for 1 hr followed by 10ng/ml Lipopolysaccharide  stimulation for 4 hrs

hyb_protocol: Fragmented cRNA (n=5) were hybridized to Affymetrix Human U133 plus 2.0 microarray chips in hybridization oven for 18hr at 45˚C, processed by Gene Chip 450 fluidics station.

scan_protocol: Chips were scanned by Gene Chip 3000 scanner

data_processing: Raw data (n=5 patients) was uploaded onto GeneSifter (internet-based microarray data analysis software), log transformed and normalized using GC-RMA (v 1.1)

source_name: Umbilical Cord blood Monocytes; LPS+DEX

label_protocol: Total RNA was amplified and labled using Ambion MessageAmp II-Biotin enhanced kit. Total RNA and cRNA purity and integrity were monitored by 260/280 and 260/230 ratios respectively, using a Bioanalyzer .

growth_protocol: PMNs and MONOs were resuspended in RPMI 1640+10%FCS at 5x106 cells/mL.

extract_protocol: Total RNA was isolated using Qiagen RNeasy spin columns.

treatment_protocol: Cells were pre-incubated with PBS (vehicle control) or equimolar concentrations (10-8 M) of IL-10 or DEX for 1 h, then stimulated with LPS (10 ng/mL) for 4 h. Cells were harvested and suspended in RNAlater to preserve RNA.

value: Human umbilical cord blood

value: Monocytes


title: Mono-DEX-3-2106


title: Mono-DEX-2-2098


title: PMN-DEX-2-2094

description: Gene Expression data from the Umbilical Cord Blood Polymorphonuclear cells treated with 10^ -8 M Dexamethasone for 1 hr followed by 10ng/ml Lipopolysaccharide stimulation for 4 hrs

source_name: Umbilical Cord blood Polymorphonucler cells; LPS+DEX

value: Polymorphonuclear cells


title: PMN-DEX-4-061807


title: PMN-DEX-3-2102


title: Mono-DEX-4-061807


title: Mono-DEX-1-2090


title: P15Parental2


title: P15MUT1


title: P25WT1


title: PMN-DEX-5-081707


title: P25MUT1


title: 12 hrs post-infection

city: Stony Brook

first: Laurie

last: Krug

address: 130 Life Sciences Bldg

department: Molecular Genetics and Microbiology

institute: Stony Brook University

description: Custom tiled microarray

hyb_protocol: 300 ng linearly amplified cRNA  and hybridization buffer were added, and samples were applied to microarrays at 65 degrees C for 17 hrs.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and Agilent default normalization. Spike-in controls were used to calculate scale factor.

source_name: Infected NIH 3T3 fibroblasts

label_protocol: 1.0 µg of total RNA were labeled using Aglient “Quick Amp Labeling Kit Two-color” following manufacturer's instructions. Spike-in controls were labeled using Agilent “Two-color Spike-in Kit" following manufacturer's instructions.

growth_protocol: NIH 3T3 fibroblasts were cultured in DMEM supplemented in 10% serum.

extract_protocol: Total RNA was prepared using "Qiagen RNeasy midi Kit" following manufacturer's instructions.

treatment_protocol: Cells were infected in MHV68 WUMS strain at multiplicity of infection of 10 plaque forming units per ml.

tag: infection

value: murid herpesvirus 4 (MHV68 WUMS strain)

tag: timepoint

value: 12 hrs

value: 8 hrs reference


title: PMN-DEX-1-2086

tag: tissue


title: 18 hrs post-infection

description: Custom tiled microarray

value: 18 hrs


title: 10 hrs post-infection

description: Custom tiled microarray

value: 10 hrs


title: 2 hrs post-infection

description: Custom tiled microarray

value: 2 hrs


title: Control 0 hrs post-infection

description: Custom tiled microarray

value: 0 hrs


title: P40_idh1mut_rep1

description: Gene expression data for glioma primary tumor

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using  Affymetrix GeneArray scanner 7G.

data_processing: data was normalized and analyzed using partek software and R packages. Specifically log2 transformation was used for data normalization.

label_protocol: 200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: The RNA  was extracted using Agencourt RNAdvance Tissue Kit according to the manufacturer's instructions.

value: cell line


title: P40_idh1wt_rep2

description: Gene expression data for glioma cell line

value: astrocyte


title: P40_idh1mut_rep2


title: MARs 6h IFN-g rep1

city: London

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

country: United Kingdom

institute: Barts & The London School of Medicine & Dentistry

description: Biological replicate 1 of 2. 6 h of IFN g treatment

hyb_protocol: DNA were hybridized on custom made 244K genomic microarrays (Agilent) according to the manufacturer’s protocol.

scan_protocol: The arrays were scanned on an Agilent Microarray Scanner G2565BA at 5 μm resolution.

data_processing: The data from ChIP-chip experiments were normalized with GeneSpring software. Log2 ratios of test/control signal intensity were created and subsequently normalized by subtracting the weighted median for each array. The NGS analyser (Genomatix) was applied for significant peak mining. NGS analyser parameters were set as following: (1) the size of sliding window is 100 base-pairs, (2) the minimum number of reads per cluster (τ) was calculated from the dataset applying a Poisson distribution. In order to reduce the possibility of false-positive peaks, the top 25% positive peaks were selected.

source_name: 6 h of IFN g treatment, MARs

label_protocol: Purified DNA (500ng) samples were labelled with Cy3- and Cy5-labelled dCTPs using the Agilent labelling kit (Agilent) according to the manufacturer’s protocol.

growth_protocol: MRC5 lung fibroblasts were cultured in RPMI-1640 medium supplemented with 10% fetal calf serum and L-glutamine at 37°C in a 5% CO2 atmosphere, and grown to 70% confluence.

extract_protocol: Matrix and loop DNA samples were isolated from untreated and IFN−γ induced MRC5 cells using 2M NaCl.

treatment_protocol: Cells were treated with 200 IU/mL of IFN−γ (recombinant human IFN-γ, R&D Systems) for 30 min or 6 hr to induce transcriptional upregulation in the MHC.

value: MRC5 lung fibroblasts

tag: dna type

value: MARs associated

source_name: 6 h of IFN g treatment, loop associated

value: loop associated


title: 4 hrs post-infection

description: Custom tiled microarray

value: 4 hrs


title: P40_idh1par_rep1


title: P40_idh1par_rep2


title: P40_idh1wt_rep1


title: MARs 6h IFN-g rep2

description: Biological replicate 2 of 2. 6 h of IFN g treatment


title: 6 hrs post-infection

description: Custom tiled microarray

value: 6 hrs


title: MARs 30min IFN-g rep2

description: Biological replicate 2 of 2. 30 min of IFN g treatment

source_name: 30 min of IFN g treatment, MARs

source_name: 30 min of IFN g treatment, loop associated


title: Picea sitchensis_xylem_rep13

city: Québec

first: John

last: MacKay

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

institute: Université Laval

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Slide scanning was performed at 5 micron resolution. Microarray scanner and image analysis software used are described in the Samples section

data_processing: Data analyses were performed using customized scripts for R and Bioconductor (http://www.r-project.org and http://www.bioconductor.org). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background intensities were subtracted from the foreground intensities. Background-subtracted data were log2-transformed and normalized using quantile correction approach.   A filtering step was applied to select positive genes to be used for further analysis. The mean intensity of spots containing buffer only was calculated for each row of sub-grids, and was taken as the minimum intensity of probes for that subgrid. A probe was called positive (detected above background) when its signal intensity was above the buffer intensity on at least 50% of slides within a given sample type. When determining differential expression, positive probes were probes that were detected according to this criterion in at least one of the tissues (e.g. phelloderm and xylem). Mean probe intensity was determined for genes represented by more than one positive probe.   The average signal intensity was determined from all of the slides available for a sample type. The genes were then ranked based on their average signal intensities within a tissue type and equally divided into 10 separate classes according to their signal intensity. Genes from class 1 or class 10 were the 10% with lowest and highest signal intensities, respectively.

organism: Picea sitchensis

source_name: Picea sitchensis, xylem

label_protocol: Total RNA (1 µg) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 555 or 647 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: Nursery planting stock (from open-pollinated seed lots) were obtained as 3-year-old seedlings of Picea glauca, Picea mariana, Picea abies, Picea Sitchensis, Pinus strobus, Pinus resinosa and Larix laricina, were transferred to 8-inch pots and grown in a greenhouse under natural light conditions. Sampling of tissues was timed with the ending of primary shoot elongation, i.e. after 6 to 8 weeks of growth, and was as described (Pavy et al. 2008). For each tissue type five biological samples were prepared by pooling 6 independent trees.

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the trees and stored at -80°C. Tissues were ground under liquid nitrogen and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008) for all of the sample types.

value: xylem

tag: time of collection

value: am

tag: replicate

tag: slide batch

tag: gse35624 study sample accessions

tag: microarray scanner

value: ScanArray Express (Perkin Elmer, Waltham MA, USA)

tag: image analysis program

value: QuantArray v3.0 (Packard BioChip Technologies, Billerica, MA, USA)


title: 8 hrs post-infection

description: Custom tiled microarray

value: murid herpesvirus 4 (MHV68 WUMS strain)

value: 8 hrs


title: CTCF 30min IFN-g rep2

source_name: 30 min of IFN g treatment, CTCF IP

tag: cell type

tag: chip antibody

value: CTCF

source_name: 30 min of IFN g treatment, input

value: none (input)


title: BRG1 30min IFN-g rep1

description: Biological replicate 1 of 2. 30 min of IFN g treatment

source_name: 30 min of IFN g treatment, BRG1 IP


title: Picea sitchensis_xylem_rep15


title: CTCF 6h IFN-g rep1

source_name: 6 h of IFN g treatment, CTCF IP

source_name: 6 h of IFN g treatment, input


title: Picea sitchensis_xylem_rep14


title: RNAP_Rifampicin_LB_SL1344__BR1

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

description: biological replicate 1

hyb_protocol: Cy3 labeled ChIP DNA and Cy5 labeled control genomic DNAs were co-precipitated using standard sodium acetate/ethanol procedures and resuspended in hybridization buffer (Oxford Gene Technologies), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridiized for 24 hours at 55oC in an Agilent hybiridization oven at 5 rpm. After hybridization, slides were washed according to instructions provided by Oxford Gene Technologies

scan_protocol: The microarray slides were scanned using an Agilent G2505C scanner. Cy3 and Cy5 images were acquired at 3 micron resolution. Scanned images were analyzed using Feature extraction software (Agilent).

data_processing: median normalization of background subtracted Cy3/Cy5 (532/635) ratio values

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: RNAP-Rifampicin ChIP DNA from SL1344 cells

label_protocol: Fluorescent labeling of DNA samples were carried out using the BioPrime Random Labeling kit (Invitrogen) as follows: 60 ul of 2.5 x random primer solution, x* ul DNA, and (70.5-x) ul sterile water were heated at 100oC for 10 minutes, snap chilled on ice and following were then added – 15 ul dNTP mix (1mM dCTP, 2mM dGTP, dTTP, dATP), 1.5 ul 1 mM Cy3/Cy5 labeled dCTP (GE healthcare) and 3 ul Klenow fragment (40 U/ ul). *[20 ul of ChIP DNA and 300 ng of Input DNA were fluorescently labeled with Cy3 d-CTP and Cy5-dCTP respectively]. The Labeling reactions wereas carried out at 37 oC overnight and 15 ml of stop buffer added to terminate the reaction. Labeled DNAs were purified using G-50 columns (GE-healthcare), according to manufacturers instructions.

growth_protocol: SL1344 cells were inoculated 1:100 into 25 ml fresh Luria Broth (LB) and grown at 37degrees celsius in a shaking waterbath until OD600 2.0. The cells were then treated with Rifampicin (dissolved in methanol and added to a final concentration of 150 ug/ml) for a further 20 mins and then harvested for ChIP

extract_protocol: 25 ml of culture were harvested and re-suspended in 50 ml of PBS.  DNA-protein interactions were cross-linked by adding formaldehyde to a final concentration of 1% for 30 minutes. Glycine was then added to a final concentration of 0.125M to stop the cross-linking. The cells were pelleted, re-suspended in 0.6 ml of lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS, Roche protease inhibitor cocktail). 1.4 ml of IP dilution buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.01% SDS, Roche protease inhibitor cocktail) was added and the chromatin was sonicated on ice in a 5ml tube to reduce the DNA length to an average size of approximately 500 bp using the Sanyo/MES Soniprep sonicator (8 bursts at an amplitude 10 microns for 30 seconds, with 1 minute cooling between bursts). 1.0 ml of IP dilution buffer was added to the chromatin, which was then pre-cleared by adding 50 ul of normal rabbit IgG for 1 hour at 4°C on a rotating wheel. 100 ul of homogeneous Protein G-agarose suspension was added to the pre-cleared chromatin and the samples were incubated for 3 hours at 4°C on a rotating wheel. The samples were centrifuged at 7500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads and the supernatant was used to set up various immunoprecipitation conditions in 2 ml microfuge tubes. An aliquot of 200 ul of chromatin was stored at -20°C to be used as input DNA. Experimental ChIP conditions – 1350 ul chromatin + 10 μl of mouse monoclonal to the RNAP Polymerase β' subunit (Neoclone, catalogue number W0001) or 10 ug of mouse monoclonal to RpoD (Neoclone, catalogue number W0004). The samples were incubated at 4°C overnight on a rotating wheel. 50 μl of homogeneous protein G-agarose suspension was added to each sample and the samples were incubated at 4°C for at least 3 hours on a rotating wheel. The samples were centrifuged at 7,500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads. The supernatant was removed and the protein G-agarose beads were washed twice with 750 ul of cold IP wash buffer 1 (20 mM Tris-HCl pH 8.1, 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with 750 ul of cold IP wash buffer 2 (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholic acid) and twice with 750 ul of cold TE pH 8.0. DNA-protein-antibody complexes were eluted from the protein G-agarose beads by twice washing the beads with 225 ul of IP elution buffer (100 mM NaHCO3, 1% SDS) and both eluates were combined. 0.2 ul of RNase A (10 mg/ml) and NaCl (to a final concentration of 0.3 M) were added to each of the IP test and input samples and incubated at 65ºC for 6 hours to reverse the cross-links. 9 ul of Proteinase K (10 mg/ml) was then added to each sample and incubated at 45ºC for at least 3 hours. DNA was purified and recovered by performing a standard phenol-chloroform extraction, followed by ethanol precipitation with 5 ug of glycogen and 5 ug of yeast tRNA. The DNA pellets of the IP samples were re-suspended in 50 ul of sterile filtered water and 100 ul for the Input DNA samples

tag: strain

value: RNAP Polymerase β' subunit

tag: vendor

value: Neoclone

tag: catalogue#

source_name: Input DNA from SL1344

value: None, Input DNA


title: BRG1 0min IFN-g rep2

description: Biological replicate 2 of 2. Control

source_name: uninduced, BRG1 IP

source_name: uninduced, input


title: Picea glauca_phelloderm_rep28

department: Centre d'étude de la forêt

organism: Picea glauca

source_name: Picea glauca, phelloderm

value: phelloderm


title: Picea glauca_xylem_rep28

source_name: Picea glauca, xylem


title: MARs 30min IFN-g rep1

value: MRC5 lung fibroblasts


title: MARs 0min IFN-g rep1

description: Biological replicate 1 of 2. Control

source_name: uninduced, MARs

value: MARs associated

source_name: uninduced, loop associated


title: RpoD_LB_SL1344__BR2

description: biological replicate 2

source_name: RpoD ChIP DNA from SL1344 cells

growth_protocol: SL1344 cells were inoculated 1:100 into 25 ml fresh Luria Broth (LB) and grown at 37degrees celsius in a shaking waterbath until OD600 2.0

value: RpoD


title: CTCF 6h IFN-g rep2


title: Picea glauca_phelloderm_rep27


title: Picea glauca_xylem_rep27


title: Picea glauca_xylem_rep26


title: Picea glauca_phelloderm_rep26


title: RpoD_LB_SL1344__BR1

description: biological replicate 1


title: BRG1 30min IFN-g rep2


title: BRG1 0min IFN-g rep1

description: Biological replicate 1 of 2. Control


title: CTCF 0min IFN-g rep2

description: Biological replicate 2 of 2. Control

source_name: uninduced, CTCF IP


title: CTCF 0min IFN-g rep1

description: Biological replicate 1 of 2. Control


title: CTCF 30min IFN-g rep1


title: RNAP_LB_SL1344__BR2

description: biological replicate 2

source_name: RNAP ChIP DNA from SL1344 cells


title: Picea sitchensis_phelloderm_rep15

source_name: Picea sitchensis, phelloderm


title: RNAP_LB_SL1344__BR1

description: biological replicate 1


title: Picea sitchensis_phelloderm_rep14


title: Picea glauca_phelloderm_rep25


title: Picea glauca_xylem_rep24


title: Picea glauca_xylem_rep25


title: Picea sitchensis_xylem_rep11

source_name: Picea sitchensis, xylem


title: H-NS_LPM_SL1344__BR1

description: biological replicate 1

source_name: H-NS ChIP DNA from SL1344 cells

growth_protocol: SL1344 cells were inoculated 1:100 into 25 ml fresh Low phosphate media (LPM) and grown at 37degrees celsius in a shaking waterbath until OD600 1.4

extract_protocol: 25 ml of culture were harvested and re-suspended in 50 ml of PBS.  DNA-protein interactions were cross-linked by adding formaldehyde to a final concentration of 1% for 30 minutes. Glycine was then added to a final concentration of 0.125M to stop the cross-linking. The cells were pelleted, re-suspended in 0.6 ml of lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS, Roche protease inhibitor cocktail). 1.4 ml of IP dilution buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.01% SDS, Roche protease inhibitor cocktail) was added and the chromatin was sonicated on ice in a 5ml tube to reduce the DNA length to an average size of approximately 500 bp using the Sanyo/MES Soniprep sonicator (8 bursts at an amplitude 10 microns for 30 seconds, with 1 minute cooling between bursts). 1.0 ml of IP dilution buffer was added to the chromatin, which was then pre-cleared by adding 50 ul of normal rabbit IgG for 1 hour at 4°C on a rotating wheel. 100 ul of homogeneous Protein G-agarose suspension was added to the pre-cleared chromatin and the samples were incubated for 3 hours at 4°C on a rotating wheel. The samples were centrifuged at 7500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads and the supernatant was used to set up various immunoprecipitation conditions in 2 ml microfuge tubes. An aliquot of 200 ul of chromatin was stored at -20°C to be used as input DNA. Experimental ChIP conditions – 1350 ul chromatin + 10 μl of mouse monoclonal to the RNAP Polymerase β' subunit (Neoclone, catalogue number W0001) or 10 ug of FLAG monoclonal antibodies (Sigma-Aldrich, Cat. No. F3165). The samples were incubated at 4°C overnight on a rotating wheel. 50 μl of homogeneous protein G-agarose suspension was added to each sample and the samples were incubated at 4°C for at least 3 hours on a rotating wheel. The samples were centrifuged at 7,500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads. The supernatant was removed and the protein G-agarose beads were washed twice with 750 ul of cold IP wash buffer 1 (20 mM Tris-HCl pH 8.1, 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with 750 ul of cold IP wash buffer 2 (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholic acid) and twice with 750 ul of cold TE pH 8.0. DNA-protein-antibody complexes were eluted from the protein G-agarose beads by twice washing the beads with 225 ul of IP elution buffer (100 mM NaHCO3, 1% SDS) and both eluates were combined. 0.2 ul of RNase A (10 mg/ml) and NaCl (to a final concentration of 0.3 M) were added to each of the IP test and input samples and incubated at 65ºC for 6 hours to reverse the cross-links. 9 ul of Proteinase K (10 mg/ml) was then added to each sample and incubated at 45ºC for at least 3 hours. DNA was purified and recovered by performing a standard phenol-chloroform extraction, followed by ethanol precipitation with 5 ug of glycogen and 5 ug of yeast tRNA. The DNA pellets of the IP samples were re-suspended in 50 ul of sterile filtered water and 100 ul for the Input DNA samples

value: SL1344 hns::3xFLAG

value: FLAG monoclonal

value: Sigma-Aldrich


title: Picea sitchensis_phelloderm_rep12

value: am


title: Picea glauca_xylem_rep22

value: xylem

value: ScanArray Express (Perkin Elmer, Waltham MA, USA)


title: Picea glauca_xylem_rep23

value: QuantArray v3.0 (Packard BioChip Technologies, Billerica, MA, USA)


title: RNAP_LPM_SL1344__BR1

description: biological replicate 1


title: LeuO_LPM_SL1344__BR1

description: biological replicate 1

source_name: LeuO ChIP DNA from SL1344 cells

value: SL1344 leuO::3xFLAG


title: LeuO_LPM_SL1344__BR2

description: biological replicate 2


title: Picea sitchensis_phelloderm_rep13


title: Picea glauca_xylem_rep21


title: Picea sitchensis_xylem_rep9


title: Picea sitchensis_xylem_rep12


title: Picea sitchensis_phelloderm_rep11


title: Picea glauca_phelloderm_rep23


title: Muscle Invasive Tumor I14

city: ROTTERDAM

first: raju

last: kandimalla

address: DR molewaterplein 50

department: pathology

country: Netherlands

institute: erasmus mc

hyb_protocol: Hybridization was performed according to the manufacturer recommendations at Service XS limited, Leiden, Netherlands (The Agilent CGH protocols (Version 2.0 2006)are strictly followed for the hybridizations, washing, and scanning of the arrays except for the hybridization time. This was 16 hours in stead of 40 hours)

scan_protocol: For the scanning of the arrays, the XDR function is used to extend the dynamic range. For this, the arrays are scanned twice with 10% PMT and 100% PMT laser power

data_processing: The feature extraction software version 9.5, protocol ChIP-v1_95  from Agilent is used to generate the feature extraction data.  LOWESS normalization and LIMMA statistics were performed.

source_name: Bladder Cancer Tissue 43

label_protocol: Labeling was performed according to agilent technologies recommendation

extract_protocol: Genomic DNA is extracted and purified with Quiagen PCR purification kit according to the manufacturer recommendations

treatment_protocol: Differential Methylation Hybridization (DMH)

tag: nmi or mi

value: Muscle Invasive Tumor

tag: genotype

value: Muscle Invasive bladder tumor

source_name: Normal Blood Genomic DNA

tag: sample type

value: Commercial genomic DNA mixture of normal male and female (Promega)


title: MARs 0min IFN-g rep2

description: Biological replicate 2 of 2. Control

value: loop associated


title: Picea glauca_phelloderm_rep22


title: Picea sitchensis_phelloderm_rep10


title: Picea glauca_xylem_rep19


title: Picea sitchensis_xylem_rep10


title: Muscle Invasive Tumor I13

source_name: Bladder Cancer Tissue 42


title: Picea glauca_xylem_rep18


title: Picea sitchensis_xylem_rep8


title: Picea glauca_xylem_rep20


title: Picea glauca_phelloderm_rep24


title: Muscle Invasive Tumor I12

source_name: Bladder Cancer Tissue 41


title: Muscle Invasive Tumor I11

source_name: Bladder Cancer Tissue 40


title: Muscle Invasive Tumor I15

source_name: Bladder Cancer Tissue 44


title: Picea sitchensis_phelloderm_rep9


title: Picea sitchensis_phelloderm_rep8


title: Picea glauca_phelloderm_rep20

source_name: Picea glauca, phelloderm


title: Picea glauca_phelloderm_rep21


title: Picea sitchensis_phelloderm_rep7


title: Muscle Invasive Tumor I8

source_name: Bladder Cancer Tissue 37


title: Picea glauca_xylem_rep16

source_name: Picea glauca, xylem


title: Muscle Invasive Tumor I7

source_name: Bladder Cancer Tissue 36


title: Muscle Invasive Tumor I10

source_name: Bladder Cancer Tissue 39


title: Picea glauca_phelloderm_rep18


title: Picea sitchensis_xylem_rep5


title: Picea glauca_phelloderm_rep19


title: Picea glauca_phelloderm_rep17


title: Picea sitchensis_xylem_rep6


title: Picea glauca_xylem_rep15


title: Muscle Invasive Tumor I9

source_name: Bladder Cancer Tissue 38


title: Picea glauca_xylem_rep13


title: Muscle Invasive Tumor I5

source_name: Bladder Cancer Tissue 34


title: Muscle Invasive Tumor I6

source_name: Bladder Cancer Tissue 35


title: Muscle Invasive Tumor I3

source_name: Bladder Cancer Tissue 32


title: Picea sitchensis_xylem_rep4

source_name: Picea sitchensis, xylem


title: Picea glauca_xylem_rep14


title: Picea glauca_phelloderm_rep16


title: Muscle Invasive Tumor I2

source_name: Bladder Cancer Tissue 31


title: Picea sitchensis_phelloderm_rep6

source_name: Picea sitchensis, phelloderm


title: Muscle Invasive Tumor I1

source_name: Bladder Cancer Tissue 30

source_name: Normal Blood Genomic DNA


title: Picea glauca_phelloderm_rep14


title: Muscle Invasive Tumor I4

source_name: Bladder Cancer Tissue 33


title: RNAP_LPM_SL1344__BR2

description: biological replicate 2

source_name: RNAP ChIP DNA from SL1344 cells

value: RNAP Polymerase β' subunit

value: Neoclone

source_name: Input DNA from SL1344

value: None, Input DNA


title: Picea glauca_xylem_rep12


title: Picea glauca_phelloderm_rep15

source_name: Picea glauca, phelloderm

value: phelloderm


title: Picea sitchensis_xylem_rep7


title: Picea glauca_phelloderm_rep12


title: Picea sitchensis_phelloderm_rep4


title: Picea glauca_xylem_rep11


title: Picea sitchensis_phelloderm_rep5


title: Picea sitchensis_phelloderm_rep3


title: Non Muscle Invasive tumor FGFR3 Wild type SW10

source_name: Bladder Cancer Tissue 29

value: Non Muscle Invasive tumor

value: FGFR3 Wild type

value: Non Muscle Invasive bladder tumor


title: Non Muscle Invasive tumor FGFR3 Wild type SW9

source_name: Bladder Cancer Tissue 28


title: Picea glauca_phelloderm_rep13


title: Non Muscle Invasive tumor FGFR3 Wild type SW6

source_name: Bladder Cancer Tissue 25


title: Picea sitchensis_xylem_rep2


title: Picea glauca_xylem_rep10

source_name: Picea glauca, xylem


title: Picea sitchensis_xylem_rep3


title: Non Muscle Invasive tumor FGFR3 Wild type SW7

source_name: Bladder Cancer Tissue 26


title: Non Muscle Invasive tumor FGFR3 Wild type SW8

source_name: Bladder Cancer Tissue 27


title: Non Muscle Invasive tumor FGFR3 Wild type SW4

source_name: Bladder Cancer Tissue 23


title: Non Muscle Invasive tumor FGFR3 Wild type SW5

source_name: Bladder Cancer Tissue 24


title: Picea glauca_xylem_rep17


title: Picea glauca_phelloderm_rep11


title: Picea glauca_xylem_rep9


title: early tumors from fallopian tubes of Dicer/PTEN knockout mice, biological rep 3

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

source_name: mouse tumor

label_protocol: According to Illumina protocol.

growth_protocol: We used a mouse genetics strategy to conditionally delete both Dicer and the Pten tumor suppressor in the female reproductive tract using anti-Müllerian hormone receptor type 2 (Amhr2-Cre). These Dicer-Pten DKO (Dicer flox/flox Pten flox/flox Amhr2 cre/+) mice universally develop high-grade serous epithelial cancers.

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (ABI). RNA quality were inspected on a 2100 Bioanalyzer (Agilent).

tag: disease state

value: ovarian tumor

value: Dicer/PTEN KO


title: Picea sitchensis_phelloderm_rep2

tag: tissue

value: am


title: early tumors from fallopian tubes of Dicer/PTEN knockout mice, biological rep 2


title: Picea sitchensis_xylem_rep1

source_name: Picea sitchensis, xylem

value: xylem

value: ScanArray Express (Perkin Elmer, Waltham MA, USA)


title: early tumors from fallopian tubes of Dicer/PTEN knockout mice, biological rep 1


title: normal mouse fallopian tube oviduct, biological rep3

source_name: normal mouse oviduct

value: normal

value: oviduct


title: Non Muscle Invasive tumor FGFR3 Wild type SW3

source_name: Bladder Cancer Tissue 22


title: Picea glauca_phelloderm_rep9

value: QuantArray v3.0 (Packard BioChip Technologies, Billerica, MA, USA)


title: Non Muscle Invasive tumor FGFR3 Wild type SW2

source_name: Bladder Cancer Tissue 21

source_name: Normal Blood Genomic DNA

value: Commercial genomic DNA mixture of normal male and female (Promega)


title: Non Muscle Invasive tumor FGFR3 Wild type SW1

source_name: Bladder Cancer Tissue 20


title: Picea sitchensis_phelloderm_rep1

source_name: Picea sitchensis, phelloderm


title: Picea glauca_phelloderm_rep10

source_name: Picea glauca, phelloderm


title: Pinus resinosa_xylem_rep4

organism: Pinus resinosa

source_name: Pinus resinosa, xylem

value: PowerScanner (Tecan Group Ltd., Männedorf, Switzerland)

value: ArrayPro Analyzer v. 6.3 (Media Cybernetics, Bethesda, MD, USA)


title: Larix laricina_phelloderm_rep4

organism: Larix laricina

source_name: Larix laricina, phelloderm


title: Picea glauca_xylem_rep8


title: Larix laricina_phelloderm_rep3


title: 24h CRE+  Mutant Liver, biological rep1

city: Boston

first: Lee

last: Quinton

address: 72 E Concord St

institute: Boston University School of Medicine

description: Gene expression data from adult mouse livers

hyb_protocol: 5 ug of labeled sense strand DNA were hybridized for 17h at 45 degrees C on a Genechip Mouse Gene Array 1.0 ST Array.  GeneChips were washed and stainied in the Affymetrix Fluiidix Station 450.

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

data_processing: CEL files were summarized using the Affymetrix Expression Console (version 1.1). The RMA (Robust Multi-Array Analysis) algorithm was used to generate gene-level data.

source_name: Liver collected from CRE+ mutant mice 24h after intratracheal innoculation of S. pneumoniae

label_protocol: Fragmented, biotinlyated sense strand DNA were prepared from 200 ng total RNA using the WT Target labeling kit according to the manufacturer's protocol (Affymetrix)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Life Technologies).  RNA was further purified using the the Qiagen RNEasy kit with the optional DNAse treatment.

value: Liver

tag: infection

value: intratracheal S. pneumoniae for 24h

value: CRE+ liver mutant

tag: genetic background


title: Picea abies_xylem_rep8

organism: Picea abies

source_name: Picea abies, xylem

tag: time of collection

tag: replicate


title: Pinus strobus_xylem_rep4

organism: Pinus strobus

source_name: Pinus strobus, xylem

tag: slide batch


title: normal mouse fallopian tube oviduct, biological rep2


title: Picea glauca_phelloderm_rep8

value: phelloderm

value: pm

tag: microarray scanner


title: Non Muscle Invasive tumor FGFR3 Mutant SM19

source_name: Bladder Cancer Tissue 19

value: Non Muscle Invasive tumor

value: FGFR3 Mutant

value: Non Muscle Invasive bladder tumor


title: Non Muscle Invasive tumor FGFR3 Mutant SM18

source_name: Bladder Cancer Tissue 18


title: Pinus strobus_xylem_rep3

value: am

tag: image analysis program


title: Picea mariana_phelloderm_rep7

organism: Picea mariana

source_name: Picea mariana, phelloderm


title: 24h CRE+  Mutant Liver, biological rep2

organism: Mus musculus


title: normal mouse fallopian tube oviduct, biological rep1


title: Non Muscle Invasive tumor FGFR3 Mutant SM17

source_name: Bladder Cancer Tissue 17


title: 24h CRE+  Mutant Liver, biological rep3


title: Non Muscle Invasive tumor FGFR3 Mutant SM16

source_name: Bladder Cancer Tissue 16


title: Non Muscle Invasive tumor FGFR3 Mutant SM15

source_name: Bladder Cancer Tissue 15


title: Pinus resinosa_phelloderm_rep4

source_name: Pinus resinosa, phelloderm


title: Picea mariana_phelloderm_rep6


title: Picea mariana_phelloderm_rep8


title: 24h CRE- Control Liver, biological rep3

source_name: Liver collected from C57BL/6 control mice 24h after intratracheal innoculation of S. pneumoniae

value: CRE- C57BL/6 control


title: Picea abies_phelloderm_rep8

source_name: Picea abies, phelloderm


title: Picea mariana_xylem_rep8

source_name: Picea mariana, xylem

value: xylem


title: Non Muscle Invasive tumor FGFR3 Mutant SM13

source_name: Bladder Cancer Tissue 13

source_name: Normal Blood Genomic DNA


title: Picea glauca_phelloderm_rep7

source_name: Picea glauca, phelloderm


title: Pinus resinosa_xylem_rep3

source_name: Pinus resinosa, xylem


title: 24h STAT3 Mutant Liver, biological rep1

source_name: Liver collected from mutant mice lacking STAT3 in hepatocytes 24h after intratracheal innoculation with S. pneumoniae

value: CRE+ liver STAT3 mutant


title: Picea glauca_phelloderm_rep6


title: Picea abies_xylem_rep7

source_name: Picea abies, xylem


title: Picea abies_phelloderm_rep7


title: 24h CRE- Control Liver, biological rep2


title: 24h STAT3 Mutant Liver, biological rep2


title: Non Muscle Invasive tumor FGFR3 Mutant SM12

source_name: Bladder Cancer Tissue 12


title: Larix laricina_xylem_rep4

source_name: Larix laricina, xylem


title: Non Muscle Invasive tumor FGFR3 Mutant SM14

source_name: Bladder Cancer Tissue 14


title: 24h STAT3 Mutant Liver, biological rep3


title: Picea glauca_phelloderm_rep5


title: Non Muscle Invasive tumor FGFR3 Mutant SM10

source_name: Bladder Cancer Tissue 10


title: 24h STAT3 Control Liver, biological rep3

source_name: Liver collected from wild-type control mice 24h after intratracheal innoculation of S. pneumoniae

value: CRE- wild-type littermate control


title: 24h CRE- Control Liver, biological rep1


title: Picea abies_xylem_rep6


title: Picea abies_phelloderm_rep6


title: Picea mariana_xylem_rep7


title: Picea abies_xylem_rep5


title: Non Muscle Invasive tumor FGFR3 Mutant SM9

source_name: Bladder Cancer Tissue 9


title: Pinus strobus_xylem_rep2

source_name: Pinus strobus, xylem


title: Picea abies_phelloderm_rep5


title: 24h STAT3 Control Liver, biological rep2


title: Picea mariana_xylem_rep6


title: Non Muscle Invasive tumor FGFR3 Mutant SM7

source_name: Bladder Cancer Tissue 7


title: Non Muscle Invasive tumor FGFR3 Mutant SM8

source_name: Bladder Cancer Tissue 8


title: Picea glauca_xylem_rep7

source_name: Picea glauca, xylem


title: Picea glauca_xylem_rep6


title: Non Muscle Invasive tumor FGFR3 Mutant SM11

source_name: Bladder Cancer Tissue 11


title: Picea abies_xylem_rep4


title: Pinus strobus_phelloderm_rep4

source_name: Pinus strobus, phelloderm


title: Larix laricina_xylem_rep3


title: Non Muscle Invasive tumor FGFR3 Mutant SM6

source_name: Bladder Cancer Tissue 6

source_name: Normal Blood Genomic DNA


title: Picea mariana_phelloderm_rep5

source_name: Picea mariana, phelloderm


title: 24h p65 Control Liver, biological rep3


title: Picea mariana_xylem_rep5

source_name: Picea mariana, xylem


title: 24h p65 Mutant Liver, biological rep3

source_name: Liver collected from mutant mice lacking RelA in hepatocytes 24h after intratracheal innoculation with S. pneumoniae

value: CRE+ liver RelA mutant


title: Non Muscle Invasive tumor FGFR3 Mutant SM5

source_name: Bladder Cancer Tissue 5

value: Commercial genomic DNA mixture of normal male and female (Promega)


title: Non Muscle Invasive tumor FGFR3 Mutant SM4

source_name: Bladder Cancer Tissue 4


title: 24h p65 Mutant Liver, biological rep1


title: 24h STAT3 Control Liver, biological rep1


title: 24h p65 Control Liver, biological rep2


title: Non Muscle Invasive tumor FGFR3 Mutant SM3

source_name: Bladder Cancer Tissue 3


title: Picea abies_phelloderm_rep4

source_name: Picea abies, phelloderm

value: PowerScanner (Tecan Group Ltd., Männedorf, Switzerland)


title: Non Muscle Invasive tumor FGFR3 Mutant SM2

source_name: Bladder Cancer Tissue 2


title: human fimbria, biological rep2

description: normal human fimbria, biological rep2

source_name: fimbria

value: human fimbria


title: Pinus resinosa_phelloderm_rep3

source_name: Pinus resinosa, phelloderm

value: ArrayPro Analyzer v. 6.3 (Media Cybernetics, Bethesda, MD, USA)


title: Non Muscle Invasive tumor FGFR3 Mutant SM1

source_name: Bladder Cancer Tissue 1


title: Picea abies_phelloderm_rep2


title: Picea abies_phelloderm_rep3


title: Picea mariana_phelloderm_rep3


title: Picea glauca_xylem_rep5


title: Picea mariana_phelloderm_rep4