title: LMNA pro-siRNA repeat2

city: Boston

first: Linfeng

last: Huang

state: Massachusetts

address: 200 Longwood Avenue

department: PCMM

institute: Boston Children's Hospital

description: Gene expression in cells transfected with siRNAs

hyb_protocol: The fragmented cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cDNA that has not hybridized to its complementary oligonucleotide probe. The bound cDNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: Data were analyzed using dChip (http://www.hsph.harvard.edu/cli/complab/dchip/). Expression was normalized to JL2012041024.

source_name: HeLa-d1EGFP cell line

label_protocol: Control RNA's - the Core spikes in four in vitro synthesized, polyadenylated B. subtilis mRNA's into each submitted sample.  cDNA synthesis I - double-stranded cDNA is synthesized from the RNA sample starting with T7 promoter-tailed random hexamers.  cRNA synthesis - cRNA is synthesized in a T7 polymerase catalyzed reaction containing unmodified ribonucleoside triphosphates.  cDNA synthesis II - single-stranded cDNA is synthesized from the cRNA template using random primers and dUTP, dTTP, dATP, dCTP and dGTP.  cRNA hydrolysis - the cRNA is hydrolyzed by RNase H, and the single-stranded cDNA is purified.  Fragmentation of a single-stranded cDNA - Uracil DNA glycosylase and Apurine/Apyrimidinic Endonuclease I are used to fragment the cDNA at Uracil-containing positions.  Biotinylation - The fragmented cDNA is end-labeled with a biotinylated nucleotide analog.

growth_protocol: Cells were grown in DMEM medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum.

treatment_protocol: siRNA transfections were performed using Lipofectamine 2000 following the manufacturer’s protocol. Briefly, cells were plated in 24 well plates (1×105 per well) and the transfection complex (containing 1.0 ml Lipofectamine 2000 and siRNAs) was added directly to the medium. RNA samples were isolated from cells 24 hr post-transfection.

tag: cell line

tag: sirna transfection

value: LMNA pro-siRNA


title: SCC_P-44

status: Public on Feb 06 2013

type: RNA

city: Leiden

first: Harry

last: Vrieling

address: Einthovenweg 20

department: Toxicogenetics, S4-P

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: The standard Illumina hybridization protocol was used. In brief, the samples were hybridized to the arrays at 58ºC overnight.

scan_protocol: The beadChips were scanned using the Illumina BeadArray Reader, using the standard Illumina scanning protocol

data_processing:
Raw data was extracted from the BeadChip data files in Illumina’s BeadStudio Version 3.2 software using the gene expression module (v 3.2.7). Background subtracted data was further analyzed in R-based Bioconductor package, lumi (version 1.12.4). In lumi, the data was transformed (variance-stabilizing transformation (VST)) and normalized (robust spline normalization (RSN)), resulting in log-transformed normalized data. The R-package illuminaHumanv2.db (version 1.4.1) was used for annotation. The data were purged of genes that did not meet the detection limit (expression-detection P-value >0.01) and/or were not annotated. The limma R-package (version 3.2.3) was used to identify differentially expressed genes (DEGs) between SCC, AK and NS. Gene set enrichment analysis (GSEA) was performed with the significantly DEGs from the limma analysis using DAVID Bioinformatic Resources v6.7 (http://david.abcc.ncifcrf.gov). GSEA on the entire data set was performed using the parametric gene set enrichment analysis (PGSEA) R-package (version 1.14.0).      To identify activation of transcription factors in AKs and SCCs, the DEGs from the limma analysis were investigated using the online analysis tool oPOSSUM.
Matrix normalized matrix shows VST-transformed, RSN-normalized data (used scripts from lumi package)
Matrix non-normalized: AVG_Signal: average signal for the probe; BEAD_STDERR: standard error of the beads; Avg_NBEADS: average number of beads for that probe; Detection Pval: detection p-value. All extracted from Beadstudio

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: cutaneous squamous cell carcinoma

label_protocol: 100 ng of total RNA was converted to cDNA and subsequently labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification kit (Ambion) according to manufacturer’s instructions

extract_protocol: RNA was isolated from SCC and AK samples that contained at least 70% tumor cells, as determined by haematoxylin and eosin stained frozen sections. From the sample of unexposed NS the epidermis was removed for further processing by cryosectioning parallel to the outer surface of the skin biopsy. RNA was extracted from frozen material using the RNeasy Fibrous Tissue kit (Qiagen), which included proteinase K treatment (10 min at 55˚C) of the lysed sample in RLT-buffer and on-column DNase treatment. RNA was quantified using a Nanodrop (NanoDrop technologies) and evaluated for degradation with a RNA 6000 Nano Labchip on the 2100 Bioanalyzer (Agilent Technologies)

tag: patient

tag: gender

value: male

tag: age

tag: location

value: dorsal hand

tag: transplanted organ

value: kidney

tag: immunosuppressive drugs

value: azathioprine + prednison

tag: sample type

value: squamous cell carcinoma

tag: cell type

value: keratinocyte


title: SINV 8d rep2

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

country: France

institute: CNRS

description: Analytic steps were performed using the programs within Affymetrix Microarray Suite 5.0 (Affymetrix) or Excel (Microsoft, Redmond, WA) with a combination of built in functions and custom formulae. The raw data were sorted using the Absent/Marginal/Present flags generated by the Microarray Suite functions. Whilst an Absent might indicate that there was no mRNA of particular type present in a sample, Marginal and Absent flags may indicate problems with the hybridization, therefore only data points marked as present were retained.

hyb_protocol: cRNA was fractionated to produce fragments of between 35-200 bp, and 15 µg of each resultant sample was mixed with microarray hybridization buffer as described by the Affymetrix manufacturer’s instructions. The samples were incubated at 99°C for 5 min, then at 45°C for a further 5 min. Affymetrix Drosophila GeneChip cassettes were prehybridized in 200 µl of hybridization buffer for 30 min at 45°C, rotating at 60 rpm in a hybridization oven (Affymetrix). Once the hybridization buffer had been removed, samples were added to the cassettes and hybridization was carried out over 16 h at 45°C, rotating at 60 rpm.

scan_protocol: After hybridization, the cassettes were washed and stained in an Affymetrix wash station according to the manufacturer’s instructions. The cassettes were put through an initial cycle of washes and staining with streptavidin phycoerythrin (SAPE), and then were scanned with a laser at 570 nm (Affymetrix). Cassettes were reinserted into the wash station, and signal amplification was carried out by using a biotinylated anti-streptavidin Ab. Restaining with SAPE was followed by a second scan at 570 nm.

data_processing: The remaining data mass for each microarray was then normalised to itself, making the median of all the present measurements one. The subsequent analysis of results was carried out on the genes present in all three replicates of a sample type.

organism: Drosophila melanogaster

source_name: Drosophila adult flies 8 days after SINV infection

label_protocol: For each experimental type, three biologically independent samples were used. Biotinylated RNA was produced and hybridized to Affymetrix Drosophila GeneChip microarrays (Part Number 510548; Affymetrix, Santa Clara, USA) according to the method published in Irving et al, 2001.

growth_protocol: Flies were fed on standard cornmeal–agar medium at 25°C and used in infection experiments.

extract_protocol: Samples of 45 flies were ground to a fine powder were ground to a fine powder using matched glass pestle and grinder, followed by the immediate addition of 600 µl of RNeasy lysis buffer (QIAGEN, Courtaboeuf, France). After initial tissue disruption, total RNA was extracted using the RNeasy system, following the manufacturer’s instructions.

treatment_protocol: Infections were performed with 4–6 days old adult flies by intrathoracic injection (Nanoject II apparatus, Drummond Scientific) with viral particles.

tag: strain

value: Oregon R

tag: time

value: 8 days

tag: infection

value: Sindbis virus


title: NS_P-41

source_name: normal skin

value: lower back

value: normal unexposed epidernis


title: AK_P-05

type: genomic

hyb_protocol: Hybridizations were performed at the Leiden Genome Technology Center according to the manufacturer's instructions

data_processing:
Image analysis and quality control (call rate > 98%) was performed in Illumina's BeadStudio Version 3.2 software using the genotyping module. Each BeadChip was self-normalized using information contained within the array. Further analysis and visualization was performed with the Illumina Genome Viewer in Beadstudio. First, tumor data was paired with data from their corresponding normal control. Subsequently, examination of the log R ratio (signal intensity tumor/signal intensity normal control) and B allele frequency (BAF) was analyzed for the presence of copy number variations (CNVs) and/or loss of heterozygosity (LOH) in the tumor samples. By plotting the log R ratio across a chromosome, CNVs could be visualized by an increase or decrease in baseline signal. Secondly, the BAF was plotted across each chromosome to detect regions of LOH in tumor cells. A region with LOH was defined as a stretch of heterozygous SNPs in normal DNA but homozygous in the matched tumor DNA.
Matrix signal (ie, The signal intensities of all SNPs for each sample) is linked as a supplementary file on the Series record.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: actinic keratosis

label_protocol: 400 ng of genomic DNA was labelled according to Illumina's standard protocol

extract_protocol: DNA was isolated from SCC and AK samples that contained at least 70% tumor cells, as determined by haematoxylin and eosin stained frozen sections. DNA from the tumor samples was isolated using the Genomic-tips 20/G kit (Qiagen). A salting-out procedure was used to isolate genomic DNA from the peripheral blood samples. DNA was quantified using a Nanodrop (NanoDrop technologies) and evaluated for degradation on agarose gel.

value: actinic keratosis (AK)

value: forearm


title: BLD1_P-41

source_name: peripheral blood

value: peripheral blood

value: lymphocyte


title: LMNA siRNA repeat2

country: USA

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

value: LMNA siRNA


title: BLD1_P-05


title: SINV 8d rep1


title: ARV+PP (5937290092_B)

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
Pigtail macaque
Sample name: 5937290092_B

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

organism: Macaca nemestrina

source_name: CD45+ LIVE COLON

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

extract_protocol: CD45+ (clone MB4-6D6) leukocytes were sorted from thawed colon samples. RNA isolated with Qiagen RNeasy Micro kit.

tag: treatment protocol

value: ARV + probiotics

tag: tissue

value: colon

value: CD45+ (clone MB4-6D6) leukocytes


title: BLD1_P-33

value: female

value: kidney


title: AK_P-41

value: male

value: azathioprine + prednison

value: actinic keratosis


title: SCC_P-41

value: squamous cell carcinoma (SCC)

value: keratinocyte

value: unknown


title: AK_P-41


title: AK_P-03

value: mycophenolate mofetil + prednison


title: SINV 8d rep3

value: Oregon R

value: 8 days

value: Sindbis virus


title: SCC_P-33

value: shoulder


title: Negative Control siRNA repeat 2

value: Negative Control siRNA


title: SCC_P-41

value: squamous cell carcinoma


title: SINV 4d rep2

source_name: Drosophila adult flies 4 days after SINV infection

value: 4 days


title: LMNA pro-siRNA repeat1

value: LMNA pro-siRNA


title: SINV 4d rep1


title: NS_P-38

value: female

value: lower back

value: normal unexposed epidernis


title: LMNA siRNA repeat1

value: LMNA siRNA


title: AK_P-44

value: actinic keratosis (AK)

value: forearm

value: male

value: kidney

value: azathioprine + prednison


title: BLD2_P-41

value: peripheral blood

value: lymphocyte


title: FHV 72h rep2

source_name: Drosophila adult flies 72 hours after FHV infection

value: Oregon R

value: 72 hours

value: flock house virus


title: BLD2_P-33


title: MaSC Ezh2 knock-down, rep 3

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The scanner operating software, GenomeStudio (v.1.1.1), converts the signal on the array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID:20929874]. This analysis was was carried out in R (v.2.11.0) using the limma package (v.3.4.0).

organism: Mus musculus

source_name: MaSC Ezh2 knock-down

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

extract_protocol: RNA was extracted using QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: FVB/N and C57BL/6

tag: genotype/variation

value: Ezh2T/+ F/F

value: 8 weeks

value: mammary epithelium

value: FACS isolated mammary cells

tag: cell subpopulation

value: MaSC-enriched (CD29hiCD24+) cells

tag: infected with

value: virus expressing cre recombinase

value: MaSC Ezh2 KO

tag: animal pool


title: FHV 72h rep1


title: MaSC empty vector control, rep 3

source_name: MaSC empty vector control

value: control virus

value: MaSC control


title: SINV 4d rep3

value: 4 days

value: Sindbis virus


title: AK_P-33

value: actinic keratosis (AK)

value: keratinocyte

value: forearm

tag: patient

value: female

value: kidney

value: azathioprine + prednison


title: BLD1_P-38

value: peripheral blood

value: lymphocyte

tag: gender


title: AK_P-33

tag: age

value: actinic keratosis


title: Lum Ezh2 knock-down, rep 3

source_name: Lum Ezh2 knock-down

value: FVB/N and C57BL/6

value: Ezh2T/+ F/F

value: 8 weeks

value: mammary epithelium

value: FACS isolated mammary cells

value: luminal (CD29loCD24+) cells

value: Lum Ezh2 KO


title: AK_P-39

tag: location

value: upper arm


title: FHV 48h rep1

source_name: Drosophila adult flies 48 hours after FHV infection

value: Oregon R

value: 48 hours

value: flock house virus


title: BLD1_P-03

value: male

tag: transplanted organ

value: mycophenolate mofetil + prednison


title: FHV 48h rep2


title: AK_P-27

value: female

value: forearm

value: liver

tag: immunosuppressive drugs

value: tacrolimus + prednison

value: keratinocyte


title: NS_P-27

value: lower back

tag: sample type

value: normal unexposed epidernis


title: BLD1_P-44

value: peripheral blood

value: lymphocyte

value: kidney

value: azathioprine + prednison


title: SCC_P-33

value: shoulder

value: squamous cell carcinoma

tag: cell type


title: BLD2_P-05


title: Lum empty vector control, rep 2

source_name: Lum empty vector control

tag: strain

value: FVB/N and C57BL/6

value: Ezh2T/+ F/F

value: 8 weeks

value: mammary epithelium

value: FACS isolated mammary cells

value: luminal (CD29loCD24+) cells

value: control virus

value: Lum control


title: FHV 48h rep3

value: Oregon R

tag: time

value: 48 hours

value: flock house virus


title: Lum empty vector control, rep 3


title: BLD1_P-39

value: peripheral blood

value: female


title: AK_P-38

value: forearm

value: kidney

value: actinic keratosis

value: keratinocyte


title: Lum Ezh2 knock-down, rep 2

value: FVB/N and C57BL/6

value: virus expressing cre recombinase

value: Lum Ezh2 KO


title: Mouse bone marrow-derived mast cells treated with IL3+IL33, rep 6

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+IL33, rep 6 of 6.

hyb_protocol: Hybridization and fluidics were performed according to standard Affymetrix protocols (http://www.affymetrix.com).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus according to standard Affymetrix protocols.

data_processing: The data were analyzed with GCOS 1.4 and EC 1.1 using Affymetrix default settings except the trimmed mean target intensity of each array was arbitrarily set to 1250.

label_protocol: Affymetrix GeneChip targets were made by amplification of 50 ng RNA using the WT-Ovation RNA Amplification System (Nugen Inc., San Carlos, CA).

growth_protocol: Bone marrow-derived mast cells (BMMCs) were developed from bone marrow obtained from the femurs of C57BL/6 mice (The Jackson Laboratory, Bar Harbor, ME) as described (Kuehn, H. S., M. A. Beaven, H. T. Ma, M. S. Kim, D. D. Metcalfe, and A. M. Gilfillan. 2008. Synergistic activation of phospholipases Cγ and Cβ: a novel mechanism for PI3K-independent enhancement of FcεRI-induced mast cell mediator release. Cell Signal 20:625-636 (PMID 18207701)).

extract_protocol: RNAs were extracted using an RNeasy 96 kit (Qiagen, Valencia, CA) with each sample treated with 27 units DNase I during the extraction process.

treatment_protocol: Essentially, the cells were cultured for 4-6 weeks in media containing mouse recombinant IL-3 (30 ng/ml) (Peprotech, Rocky Hill, NJ) and mouse IL-33 (10 ng/ml). The cells were maintained at 37 ˚C in a humidified incubator gassed with 95% air and 5% CO2. The purity of the cultures, as assessed by toluidine blue staining and FceRIa and KIT expression, was >99%.

value: bone marrow-derived mast cells

tag: treatment

value: interleukin 3 and interleukin 33


title: SCC_P-27

value: shoulder

value: liver

value: tacrolimus + prednison

value: squamous cell carcinoma


title: BLD1_P-24

value: lymphocyte

value: male

value: azathioprine + prednison


title: NS_P-33

value: female

value: lower back

value: normal unexposed epidernis


title: SCC_P-05

value: squamous cell carcinoma (SCC)

value: lower arm

value: kidney


title: FHV 72h rep3

value: Oregon R

value: 72 hours

tag: infection

value: flock house virus


title: Lum empty vector control, rep 1

value: FVB/N and C57BL/6

value: Ezh2T/+ F/F

value: 8 weeks

tag: tissue

value: mammary epithelium

value: FACS isolated mammary cells

value: luminal (CD29loCD24+) cells

value: control virus

value: Lum control


title: BLD1_P-11

value: peripheral blood

value: lymphocyte

value: female

value: azathioprine + prednison


title: Mouse bone marrow-derived mast cells treated with IL3+IL33, rep 4

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+IL33, rep 4 of 6.

value: bone marrow-derived mast cells

value: interleukin 3 and interleukin 33


title: MaSC Ezh2 knock-down, rep 2

tag: genotype/variation

value: MaSC-enriched (CD29hiCD24+) cells

value: virus expressing cre recombinase

value: MaSC Ezh2 KO


title: Mouse bone marrow-derived mast cells treated with IL3+IL33, rep 3

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+IL33, rep 3 of 6.


title: AK_P-24

value: male

value: forearm

value: kidney

value: actinic keratosis

value: keratinocyte


title: MaSC empty vector control, rep 2

value: FVB/N and C57BL/6

value: Ezh2T/+ F/F

value: 8 weeks

value: mammary epithelium

value: FACS isolated mammary cells

tag: cell subpopulation

value: MaSC control


title: Mouse bone marrow-derived mast cells treated with IL3+IL33, rep 2

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+IL33, rep 2 of 6.


title: AK_P-24

value: actinic keratosis (AK)

value: azathioprine + prednison


title: MaSC Ezh2 knock-down, rep 1

tag: infected with


title: SCC_P-24

value: lower leg

value: squamous cell carcinoma


title: NS_P-18

value: lower back

value: kidney + pancreas

value: normal unexposed epidernis


title: AK_P-38

value: forearm

value: female


title: SCC_P-18

value: male

value: dorsal hand


title: MaSC empty vector control, rep 1

value: FVB/N and C57BL/6

value: MaSC-enriched (CD29hiCD24+) cells

value: control virus

tag: animal pool


title: Mouse bone marrow-derived mast cells treated with IL3+IL33, rep 5

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+IL33, rep 5 of 6.

value: bone marrow-derived mast cells

value: interleukin 3 and interleukin 33


title: AK_P-18

tag: patient

value: actinic keratosis

value: keratinocyte


title: Negative Control siRNA repeat 1

tag: cell line

tag: sirna transfection

value: Negative Control siRNA


title: Mouse bone marrow-derived mast cells treated with IL3+IL33, rep 1

description: Gene expression data from mouse bone marrow-derived mast cells treated with IL3+IL33, rep 1 of 6.


title: NS_P-24

tag: gender

tag: age

tag: location

value: kidney

value: azathioprine + prednison


title: SCC_P-38

value: shoulder

tag: transplanted organ

tag: immunosuppressive drugs

tag: sample type

value: squamous cell carcinoma


title: Lum Ezh2 knock-down, rep 1

tag: strain

value: Ezh2T/+ F/F

value: 8 weeks

value: mammary epithelium

tag: cell type

value: FACS isolated mammary cells

value: luminal (CD29loCD24+) cells

value: virus expressing cre recombinase

value: Lum Ezh2 KO


title: BLD2_P-24_repeat

value: peripheral blood

value: lymphocyte

value: male


title: Dcp1a+Dcp2 siRNA_rep2

city: Prague 4

first: Matyas

last: Flemr

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics

description: Gene expression data from in vitro matured mouse MII eggs injected with Dcp1a+Dcp2 siRNAs

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The data were loaded into R software and normalized using AffyPLM package of the Bioconductor software. GCRMA algorithm was used for normalization. The values lower than 10.0 represent detection absent (with detection call P-value P>0.05).

label_protocol: cRNA samples were amplified and labelled according to Affymetrix protocol  GeneChip Eukaryotic Small Sample Target Labelling Assay Version II.

growth_protocol: Microinjected oocytes were cultured in CZB with milrinone for 20 h and then transferred to milrinone-free medium and allowed to mature to MII for 18 h. The MII eggs were then used for RNA extraction and microarray analysis.

extract_protocol: Total RNA was extracted from pools of 30 MII eggs per samples using Pico-Pure RNA Isolation kit (Acturus).

treatment_protocol: Full-grown GV oocytes were injected with Dcp1a siRNA (Dharmacon, On-TARGETplus SMARTpool, L-065144-01) or Dcp2 siRNA (Dharmacon, On-TARGETplus SMARTpool L-040353-01).  Dcp1a&Dcp2 double knockdown were achieved by injecting a mixture of the above siRNAs.

tag: condition

value: Dcp1a+Dcp2 siRNA

tag: developmental stage

value: MII egg


title: 297C2 on hFib+rLIF p19_iPSCs

city: San Francisco

first: Kiichiro

last: Tomoda

state: CA

address: 1650 Owens Street

institute: The Gladstone Institutes, UCSF

description: Gene expression in pluripotent stem cells

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: gProcessedSignal(normalized) columns were genereated using GeneSpringGX (Agilent).

source_name: Female hiPSC

label_protocol: Agilent standard protocol

growth_protocol: Cultured on indicated feeder cells in KDMEM medium containing 20% KSR and bFGF with or without rLIF.

extract_protocol: Total RNA was isolated with Trizol.

value: human fibroblasts (hFib) + recombinant (r)LIF

tag: passage


title: BLD2_P-39

value: female

value: kidney


title: 297C2 on SNL P21(+15)_iPSCs

value: SNLs


title: AK_P-11

value: forearm

value: azathioprine + prednison

value: actinic keratosis

value: keratinocyte


title: NS_P-11

value: lower back

value: normal unexposed epidernis


title: SCC_P-24_repeat

value: squamous cell carcinoma (SCC)

value: lower leg


title: 297C2 on hFib p19_iPSCs

value: human fibroblasts (hFib)


title: Dcp1a+Dcp2 siRNA_rep3

source_name: MII eggs injected with Dcp1a+Dcp2 siRNAs


title: Dcp2 siRNA_rep3

description: Gene expression data from in vitro matured mouse MII eggs injected with Dcp2 siRNA

source_name: MII eggs injected with Dcp2 siRNA

value: Dcp2 siRNA


title: Dcp1a+Dcp2 siRNA_rep1


title: Dcp2 siRNA_rep1


title: 297C2 on hFib p7_iPSCs


title: Dcp2 siRNA_rep2


title: SCC_P-57

value: tibia


title: NS_P-05

value: male


title: BLD2_P-57

value: peripheral blood

value: lymphocyte


title: SCC_P-11

value: female

value: squamous cell carcinoma


title: 297C1 on SNL P21(+15)_iPSCs

value: SNLs


title: SCC_P-39

value: kidney


title: AK_P-05

value: forearm

value: azathioprine + prednison


title: Dcp1a siRNA_rep2

description: Gene expression data from in vitro matured mouse MII eggs injected with Dcp1a siRNA

source_name: MII eggs injected with Dcp1a siRNA

value: Dcp1a siRNA

value: MII egg


title: SCC_P-05

source_name: cutaneous squamous cell carcinoma

value: lower arm

value: keratinocyte


title: 297C1 on hFib p7_iPSCs

value: passage (p)7


title: Dcp1a siRNA_rep3


title: 297C1 on hFib p19_iPSCs

value: human fibroblasts (hFib)


title: SCC_P-03

value: upper leg

value: mycophenolate mofetil + prednison


title: NS_P-03

value: male

value: lower back

value: normal unexposed epidernis


title: control siRNA_rep3

description: Gene expression data from in vitro matured mouse MII eggs injected with control siRNA

source_name: MII eggs injected with control siRNA

value: control siRNA


title: AK_P-03

value: actinic keratosis


title: Dcp1a siRNA_rep1


title: control siRNA_rep2


title: BLD2_P-44

value: peripheral blood

value: lymphocyte


title: NS_P-40

source_name: normal skin

value: buttocks

value: kidney


title: 297C1 on hFib+rLIF p19_iPSCs

value: human fibroblasts (hFib) + recombinant (r)LIF


title: SCC_P-44

value: squamous cell carcinoma (SCC)

value: dorsal hand

value: azathioprine + prednison


title: AK_P-40

source_name: actinic keratosis

value: forearm

value: keratinocyte


title: AK_P-11

value: actinic keratosis (AK)

value: female


title: NS_P-39


title: SCC_P-03

value: upper leg

value: male

value: mycophenolate mofetil + prednison


title: 660-7

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

country: Italy

institute: University of Parma

hyb_protocol: Hybridization of labeled test DNA to these microarrays was performed according to CombiMatrix protocols (http://www.combimatrix.com/support_docs.htm).

scan_protocol: Fluorescence scanning was performed employing a MicroArray scanner (InnoScan 700).

data_processing: Signal intensities for each spot were determined using Microarray Imager 5.8 software (CombiMatrix). Signal background was calculated as the mean of negative controls plus two times the SD. A global quantile normalization was performed, and log2 ratios among the reference sample (Bifidobacteriaadolescentis ATCC15703) and the other samples analyzed were calculated. The distribution of the log2-transformed ratios for each hybridization reaction was calculated separately. Log2-ratio data of Sample over reference is linked to the Series record.

organism: Bifidobacterium sp.

label_protocol: DNA was labeled with Cy5-ULS using the Kreatech ULS array CGH Labeling kit (Kreatech Diagnostics) according to the supplier’s instructions.

growth_protocol: Each strain was grown in MRS over night and the DNA was extracted.

extract_protocol: Total DNA was isolated using phenol/chloroform extraction method. Briefly, cells pellet were resuspended in 10 ml of TES, lysozyme and mutanolysin and incubated for 2h at 37°C. Pellets were washed and resuspended in TE, 10% SDS, Proteinase K and CTAB/NaCl solution and incubatated for 2h. Then, washing with  phenol/chloroform was performed following the Sambrook and Russell protocol. Finally, DNA was precipitated using EtOH 96% and resuspended in water.


title: 676-1


title: SCC_P-24

value: lower leg


title: BLD2_P-24

source_name: peripheral blood


title: AK_P-39

value: upper arm

value: actinic keratosis


title: SCC_P-40

value: squamous cell carcinoma


title: MB271


title: Em39A

city: Yufu-shi

first: Kaei

last: Nasu

state: Oita

address: Idaigaoka 1-1, Hasama-machi

department: Obstetrics and Gynecology

country: Japan

institute: Oita University, Faculty of Medicine

description: miRNA expression in primary cultured NESCs

hyb_protocol: After Cy3-labeling, RNA was dried up and re-solved with 18 ul RNase-free water.  And then, 4.5 ul of 10x Gene expression blocking agent and 22.5 ul of 2x hybridization buffer HI-RPM were added to the RNA sample, and the mixture hybridized to Agilent Human miRNA Microarrays (G4470C, Human Rel. 12.0, Agilent Technologies) for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 5 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 5% and 100%, extended dynamic range scan mode).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent Technologies) using default parameters (protocol miRNA-v1_95_May07 and Grid: 021827_D_20081121) to obtain background subtracted Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: NESC

label_protocol: One hundred ng of total RNA was labeled with Cy3 using a miRNA labeling and hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Endometriotic tissues were obtained from premenopausal patients who had undergone salpingo-oophorectomy or evisceration for ovarian endometriotic cysts. Normal endometrial tissues were obtained from premenopausal patients who had undergone hysterectomies for subserousal leiomyoma and had no evidence of endometriosis. None of the patients had received any hormonal treatments for at least 2 years prior to operation. All the specimens were diagnosed as being in the mid- to late-proliferative phases according to the pathological observation and/or the menstrual cycles.  ECSCs and NESCs were isolated from ovarian endometriotic tissues by enzymatic digestion with collagenase as previously described (Nishida et al., J Clin Endocrinol Metab 2004; 89: 5094-5100).  Isolated ECSCs and NESCs were cultured in DMEM supplemented with 100 IU/ml of penicillin, 50 mg/ml of streptomycin, and 10% heat-inactivated fetal bovine serum at 37°C in 5% CO2 in air.   ECSCs and NESCs in the monolayer culture after the third passage were >99% pure as determined by immunocytochemical staining with antibodies to vimentin, CD10, cytokeratin, factor VIII, and leukocyte common antigen, and were used for the following experiments (Nishida et al., J Clin Endocrinol Metab 2004; 89: 5094-5100).

extract_protocol: Total RNA from cultured ECSCs and NESCs was extracted with a miRNeasy Mini kit (QIAGEN) following the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: ECSCs and NESCs isolated and cultured as described above were subjected to miRNA microarray analysis. Cells subjected to microarray did not undergo any stimulation during culture.

tag: tissue

value: endometrial tissue

value: NESC


title: glnR_Low_Nitrogen_rep3

city: Vicksburg

first: Dawn

middle: E

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

description: This sample is of Gordonia sp. KTR9 mutant GlnR eposed to 0.9 mM Ammonium sulfate. It is the third of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Two micrograms of the labeled DNA was used for subsequent hybridization to Nimblegen Bacterial Gene Expression Arrays for Salmonella typhimurium LT2 X4. The hybridized arrays were washed using the Nimblegen Wash Buffer Kit.

scan_protocol: Washed arrays were scanned using the Agilent Microarray Scanner

data_processing: Microarray images were analyzed using Nimblescan v2.5.26 software (Nimblegen) and ArrayStar v4.0.0 (DNAstar, Madison, WI) software. Expression data were log2 transformed and statistical significance was determined using a moderated t-test for binary transcriptome comparisons (i.e. control vs. experimental). The P-value was set at 0.05 and only those genes induced or repressed at least fivefold were considered in this paper.  Differentially expressed transcripts were assigned to their functional classifications based on the Comprehensive Microbial Resource genome annotation from the J. Craig Venter Institute.

organism: Gordonia sp. KTR9

source_name: GlnR exposed to Low Nitrogen conditions

label_protocol: The cDNA was labeled with the One-Color DNA Labeling Kit (Nimblegen, Madison, WI) and the concentration verified using the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA).

growth_protocol:
Gordonia sp. KTR9 exposed to high nitrogen were grown in mineral salts media supplemented with succinate (20 mM) and ammonium sulfate (4 mM) for 48 h at 30°C shaking at 150 rpm.
Gordonia sp. KTR9 exposed to low nitrogen were grown in mineral salts media supplemented with succinate (20 mM) and ammonium sulfate (0.9 mM) for 48 h at 30°C shaking at 150 rpm.
Gordonia sp. KTR9 mutant GlnR exposed to high nitrogen were grown in mineral salts media supplemented with succinate (20 mM) and ammonium sulfate (4 mM) for 48 h at 30°C shaking at 150 rpm.
Gordonia sp. KTR9 mutant GlnR exposed to low nitrogen were grown in mineral salts media supplemented with succinate (20 mM) and ammonium sulfate (0.9 mM) for 48 h at 30°C shaking at 150 rpm.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and according to the manufacturer’s instructions for RNA cleanup with an added enzymatic lysis step and mechanical disruption step added before cleanup. Enzymatic lysis and mechanical disruption was performed by resuspending the cell pellet in 100 uL TE buffer and 200 uL lysozyme (20 mg/mL), transferring the resuspended pellet to a MP Biomedicals (Solon, OH) Lysing Matrix B tube and vortexing for 1 min. The optional on column DNA digestion using the Qiagen RNase-Free DNase Kit was performed to remove DNA. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer. The RNA was used to generate cDNA using the Superscript II Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s directions. At each step the quality of the RNA and cDNA was analyzed using the Agilent 2100 Bioanalyzer and DNA 1000 Kit (Agilent).

tag: genotype/variation

value: GlnR mutant


title: SCC_P-39

value: kidney


title: DSM16992

organism: Bifidobacterium catenulatum DSM 16992 = JCM 1194 = LMG 11043


title: BLD2_P-03

value: peripheral blood

value: lymphocyte


title: hlyA1- 2C

city: Bethesda

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89565.gif

hyb_protocol: not provided

scan_protocol: Scanner model: G2505C

data_processing: VALUE is Log Red/Green

source_name: 850 ng of amplified infected mouse bladder cDNA harvested 24 hours post infection

label_protocol: not provided

extract_protocol: not provided

value: bladder

tag: infection (e. coli genotype)

source_name: 850 ng of amplified normal mouse bladder cDNA


title: control siRNA_rep1

value: control siRNA

value: MII egg


title: glnR_Low_Nitrogen_rep2

description: This sample is of Gordonia sp. KTR9 mutant GlnR eposed to 0.9 mM Ammonium sulfate. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Em28-5


title: 853B


title: SCC_P-38

value: squamous cell carcinoma (SCC)

value: keratinocyte

value: shoulder

tag: patient

value: female

value: azathioprine + prednison


title: Em21-5


title: glnR_Low_Nitrogen_rep1

description: This sample is of Gordonia sp. KTR9 mutant GlnR eposed to 0.9 mM Ammonium sulfate. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: 318B


title: BLD2_P-11


title: 660-1


title: SCC_P-27

value: liver

value: tacrolimus + prednison


title: glnR_High_Nitrogen_rep3

description: This sample is of Gordonia sp. KTR9 mutant GlnR eposed to 4 mM Ammonium sulfate. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: GlnR exposed to High Nitrogen conditions


title: hlyA1- 5C

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89567.gif


title: Em19-5A


title: 249B


title: glnR_High_Nitrogen_rep2

description: This sample is of Gordonia sp. KTR9 mutant GlnR eposed to 4 mM Ammonium sulfate. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Em18B


title: 202B

organism: Bifidobacterium sp. 202


title: WT CP9 5A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89558.gif

value: wt


title: SCC_P-18_repeat

value: dorsal hand

value: male

value: kidney + pancreas


title: BLD2_P-18_repeat


title: SCC_P-11

value: tibia

value: kidney


title: glnR_High_Nitrogen_rep1

description: This sample is of Gordonia sp. KTR9 mutant GlnR eposed to 4 mM Ammonium sulfate. It is the first of three biological replicates used in this experiment, each from separate cultures.

value: GlnR mutant


title: BLD2_P-27

value: peripheral blood

value: lymphocyte


title: Em6

value: endometrial tissue

value: NESC


title: Em8A


title: DSM20438

organism: Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505


title: BLD2_P-38


title: KTR9wt_Low_Nitrogen_rep3

description: This sample is of Gordonia sp. KTR9 eposed to 0.9 mM Ammonium sulfate. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: KTR9 exposed to Low Nitrogen conditions

value: wild type


title: 145B

data_processing: Signal intensities for each spot were determined using Microarray Imager 5.8 software (CombiMatrix). Signal background was calculated as the mean of negative controls plus two times the SD. A global quantile normalization was performed, and log2 ratios among the reference sample (B. adolescentis ATCC15703) and the other samples analyzed were calculated. The distribution of the log2-transformed ratios for each hybridization reaction was calculated separately. The log2 ratio data of Sample over reference is linked to the Series record.

organism: Bifidobacterium adolescentis


title: 22L


title: KTR9wt_Low_Nitrogen_rep2

description: This sample is of Gordonia sp. KTR9 eposed to 0.9 mM Ammonium sulfate. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Em3


title: KTR9wt_Low_Nitrogen_rep1

description: This sample is of Gordonia sp. KTR9 eposed to 0.9 mM Ammonium sulfate. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: KTR9wt_High_Nitrogen_rep3

description: This sample is of Gordonia sp. KTR9 eposed to 4 mM Ammonium sulfate. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: KTR9 exposed to High Nitrogen conditions


title: BLD2_P-40

value: mycophenolate mofetil + prednison


title: PBS control 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89581.gif

value: bladder

value: PBS control


title: C35

description: miRNA expression in primary cultured ECSCs

source_name: ECSC

value: ovarian endometriotic tissue

value: ECSC


title: C31


title: 703B


title: hlyA1- 7C 3/5/2010

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89570.gif


title: SCC_P-40

value: squamous cell carcinoma (SCC)

value: keratinocyte


title: KTR9wt_High_Nitrogen_rep2

description: This sample is of Gordonia sp. KTR9 eposed to 4 mM Ammonium sulfate. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: 369B


title: 153B


title: C27


title: PBS control 4 6/18/2010

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89583.gif


title: BLD2_P-18

value: male

value: azathioprine + prednison


title: BLD1_P-40


title: C25-8


title: hlyA1- 2C 4/13/2010

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89569.gif


title: KTR9_High_Nitrogen_rep3

growth_protocol:
Gordonia sp. KTR9 exposed to RDX were grown in mineral salts media supplemented with succinate (20 mM) and RDX (40 ppm) for 48 h at 30°C shaking at 150 rpm.
Gordonia sp. KTR9 exposed to RDX and high nitrogen were grown in mineral salts media supplemented with succinate (20 mM), RDX (40 ppm), and ammonium sulfate (4 mM) for 48 h at 30°C shaking at 150 rpm.
Gordonia sp. KTR9 exposed to low nitrogen were grown in mineral salts media supplemented with succinate (20 mM) and ammonium sulfate (0.9 mM) for 48 h at 30°C shaking at 150 rpm.
Gordonia sp. KTR9 exposed to RDX were grown in mineral salts media supplemented with succinate (20 mM) and ammonium sulfate (4 mM) for 48 h at 30°C shaking at 150 rpm.


title: 125B


title: ATCC15703


title: KTR9_High_Nitrogen_rep2


title: C24p-6


title: C20


title: SCC_P-18

value: dorsal hand

value: kidney + pancreas


title: KTR9_High_Nitrogen_rep1

description: This sample is of Gordonia sp. KTR9 eposed to 4 mM Ammonium sulfate. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: reo mutant+IPTG Induced pEcfO rep3

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

state: NC

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

description: reo (anti-ecfO) mutant with IPTG induced expression of ecfO experiment

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., using standard protocol as described on their website.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., using standard protocol as described on their website.

data_processing:
Raw data (pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185) using NimbleGen Systems DEVA 1.1 software as described on their web site.
Two of the .pair files (ecfO_bio_rep3.pair and reo+pEcfO_bio_rep4.pair) are missing some chip quality control/tracking information resulting less data rows that other raw data files

organism: Bacteroides fragilis 638R

source_name: reo (anti-ecfO) null_IPTG induced expression of ecfO

label_protocol: Labeling was performed by NimbleGen Systems Inc., using standard protocol as described on their website.

growth_protocol:
Overnight cultures of the vector control or IPTG inducible strain were diluted 1/50 into complex media.  IPTG was added and cultures were grown under anaerobic conditions at 37C
to mid-logarithmic phase at A550 of 0.3

extract_protocol: Total RNA was isolated by the hot phenol method and treated as described by Sund et al, 2008, Mol. Microbiol.67:129-142.

value: reo (anti-ecfO) mutant with ecfO gene in pFD1146


title: hlyA1- 1C

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89564.gif


title: C13


title: KTR9_Low_Nitrogen_rep3


title: AK_P-18

value: actinic keratosis (AK)

value: forearm


title: KTR9wt_High_Nitrogen_rep1


title: BLD1_P-18

value: peripheral blood

value: lymphocyte


title: reo mutant+IPTG Induced pEcfO rep2


title: KTR9_Low_Nitrogen_rep2


title: C7


title: hlyA1- 4C

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89566.gif


title: WT CP9 3A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89556.gif

value: wt


title: KTR9_Low_Nitrogen_rep1


title: AK_P-40

value: kidney

value: mycophenolate mofetil + prednison


title: ecfO mutant rep1

description: ecfO mutant with empty vector control for IPTG induced expression of ecfO experiment

source_name: ecfO null_empty vector

value: ecfO null mutant with empty vector control


title: reo mutant+IPTG Induced pEcfO rep1


title: KTR9_RDX_High_Nitrogen_rep3

description: This sample is of Gordonia sp. KTR9 eposed to 40 ppm RDX and 4 mM Ammonium sulfate. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: KTR9 exposed to RDX and High Nitrogen conditions


title: cnf1- 7B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89563.gif

value: bladder


title: ecfO mutant rep2


title: KTR9_RDX_rep3

description: This sample is of Gordonia sp. KTR9 eposed to 40 ppm RDX. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: KTR9 exposed to RDX


title: ecfO mutant rep3


title: Host transcriptional responses in mouse BMDM infected with T. gondii [RH_WT]

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

description: Gene expression data from BMDM infected with indicated T. gondii strain, 18 h post-infection

hyb_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Genome Oligo Array (4x44K, Agilent Technologies).

scan_protocol: After washing, slides were scanned with the Agilent DNA microarray Scanner. Data was extracted and normalized using Agilent Feature Extraction Software (version 11.0.1.1).

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 6 out of 9 samples have flags in Detected or Not Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering.

source_name: mouse BMDM infected with T. gondii RH_WT

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling. Dyes used were Cy3

growth_protocol:
Bone marrow-derived macrophages were obtained from 8-10-week old C57BL/6 mice purchased from JANVIER (France). Bone marrow
was isolated by flushing hind tibias and femurs using a 25-gauge needle and DMEM media supplemented with 10% heat-inactivated FBS (Invitrogen), 1 mM L-glutamine, 50 µg/mL each of penicillin and streptomycin. ~5 x 10^6 cells were resuspended in DMEM supplemented with 20 ng/mL M-CSF (Invitrogen)and plated in 10-cm nontissue culture-treated dishes (Corning). Cells were incubated at 37°C, with 5% CO2 in humidified air for 6 days. Adherent cells were harvested in cold-PBS(4°C) using a cell scraper, and replated at 8 x 10e6 cells per 10-cm2 plate for the assay.

treatment_protocol: Mouse BMDM were infected with Toxoplasma gondii tachyzoites (prepared from infected HFFs and washed in PBS) of the indicated strain at multiplicity of infection ~3; 18 hours post-infection, adherent cells and cells in the supernatent were harvested and lysed in Trizol reagent for RNA extraction.

tag: host cell

value: Mouse bone marrow-derived macrophages (BMDM)

tag: parasites

value: RH delta ku80 wild type

tag: time point

value: 18 h post-infection


title: KTR9_RDX_rep2

description: This sample is of Gordonia sp. KTR9 eposed to 40 ppm RDX. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: 923M3 on MEF p15

description: Gene expression in pluripotent stem cells

source_name: Female hiPSC

value: MEFs


title: PBS control 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89579.gif

value: PBS control


title: KTR9_RDX_rep1

description: This sample is of Gordonia sp. KTR9 eposed to 40 ppm RDX. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: reo mutant+IPTG Induced pEcfO rep4


title: Host transcriptional responses in mouse BMDM infected with T. gondii [Pru_WT]

source_name: mouse BMDM infected with T. gondii Pru_WT

value: Prugniaud delta ku80 wild type


title: cnf1- 5B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89561.gif


title: WT CP9 2A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89555.gif


title: 923M3 on SNL p15

value: SNLs


title: cnf1- 4B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89560.gif


title: BMI1-silenced LNCaP cells

status: Public on Feb 05 2013

city: AUSTIN

first: MOHAMMAD

middle: SALEEM

last: BHAT

state: MN

address: 801, 16th AVE NE

institute: UNIVERSITY OF MINNESOTA

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.

label: SYBR

source_name: Prostate

label_protocol: PCR assays were performed using prosate cancer Pathway PCR assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 1 microgram total RNA using. Quantitative real-time PCR were performed (Applied biosystem) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with Trizol method followed by DNase I treatment (Invitrogen)

treatment_protocol: BMI1-silenced by siRNA

tag: cell line

value: LNCaP

tag: treatment

value: BMI1 silenced


title: 923M2 on MEF p4_iPSCs


title: Control LNCaP cell

description: Control

value: control


title: 923M3 on MEF p4


title: GRA16-dependent host transcriptional responses in mouse BMDM infected with T. gondii [Pru_GRA16-KO]

source_name: mouse BMDM infected with T. gondii Pru_GRA16-KO

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling.  Dyes used were Cy5

growth_protocol:
Bone marrow-derived macrophages were obtained from 8-10-week  old C57BL/6 mice purchased from JANVIER (France). Bone marrow
was isolated by flushing hind tibias and femurs using a 25-gauge needle and DMEM media supplemented with 10% heat-inactivated FBS (Invitrogen), 1 mM L-glutamine, 50 µg/mL each of penicillin and streptomycin. ~5 x 10^6 cells were resuspended in DMEM supplemented with 20 ng/mL M-CSF (Invitrogen)and plated in 10-cm nontissue culture-treated dishes (Corning). Cells were incubated at 37°C, with 5% CO2 in humidified air for 6 days. Adherent cells were harvested in cold-PBS(4°C) using a cell scraper, and replated at 8 x 10e6 cells per 10-cm2 plate for the assay.

tag: parasite

value: Pruku80(deltaGRA16) mutant


title: WT CP9 1A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89554.gif


title: 923M2 on MEF+rLIF p15_iPSCs

value: MEFs + recombinant (r)LIF


title: GRA16-dependent host transcriptional responses in mouse BMDM infected with T. gondii [RH_GRA16-KO]

source_name: mouse BMDM infected with T. gondii RH_GRA16-KO

value: RHku80(deltaGRA16) mutant


title: PBS control 2 6/18/2010

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89582.gif


title: hlyA1- 6C

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89568.gif


title: 923M2 on MEF P15_iPSCs


title: cnf1- 6B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89562.gif


title: 923M2 on SNL p15_iPSCs


title: Cdx2-Hnf4a D knockout expression array-2

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Microarray expression: RMA (bioconductor) with custom CDF (Mouse4302_Mm_REFSEQ) for background elimination and normalization. Limma for detection of differentially expressed genes between controls and Cdx2 KO, HNF4A KO or Cdx2-Hnf4a DKO.

source_name: Cdx2-Hnf4a D knockout gene expression profiling

label_protocol: and prepared for arrays using manufacturer's instructions (biotin, Affymetrix).

growth_protocol: mice were treated with tamoxifen for 5 consecutive days (1mg/day) to inactivate the relevant TF.

extract_protocol: RNA was extracted using the Trizol method

treatment_protocol: The jejunal epithelium was harvested 3-4 days after completion of the timecourse.

value: jejunum epithelium

value: 129xC57BL6 mixed background

value: Cdx2-Hnf4a Double knockout


title: Cdx2 knockout expression array-1.2

source_name: Cdx2 knockout gene expression profiling

value: Cdx2 knockout


title: Cdx2-Hnf4a D knockout expression array-1


title: cnf1- 1B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89559.gif

source_name: 850 ng of amplified infected mouse bladder cDNA harvested 24 hours post infection

value: bladder

source_name: 850 ng of amplified normal mouse bladder cDNA


title: Hnf4a knockout expression array-1

source_name: Hnf4a knockout gene expression profiling

value: Hnf4a knockout


title: Cdx2-Hnf4a D knockout expression array-3


title: PBS control 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89580.gif


title: Cdx2 knockout expression array-2.2


title: Control expression array-3.2

source_name: control gene expression profiling

value: littermate controls


title: active TB infection 7

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

institute: Utrecht University

description: whole blood, active TB infection

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Affymetrix powertools: apt-probeset-summarize –a rma -a plier-gcbg -qc-probesets HuEx-1_0-st-v2.r2.qcc -o output -c HuEx-1_0-st-v2.r2.clf --bgp-file HuEx-1_0-st-v2.r2.antigenomic.bgp -p HuEx-1_0-st-v2.r2.pgf -m HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: whole blood, active TB infection

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: RNA was isolated using the PAXgene Blood RNA kit (PreAnalytix) following the manufacturer’s protocol. RNA quality was checked using the RNA 6000 Nano Kit on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA)

treatment_protocol: From every child, 2.5 ml of peripheral whole blood was collected in PAXgene RNA tubes (PreAnalytix) and stored at -80°C prior to processing

tag: Sex

value: Male

tag: age (years)

tag: culture results

value: Negative

tag: tuberculin skin test

tag: qft-git

value: Positive

tag: cxr findings

value: Adult-type disease with unilateral bronchopneumonic consolidation, lymph node disease with unilateral hyperinflation


title: active TB infection 6

description: whole blood, active TB infection

value: Female

value: Ghon focus with bilateral bronchopneumonic consolidation, lymph node disease with tracheal compression, pleural effusion


title: Cdx2 knockout expression array-3.2

tag: strain


title: Hnf4a knockout expression array-2

tag: tissue


title: active TB infection 9

description: whole blood, active TB infection

value: Adult-type disease with bilateral cavitation and unilateral bronchopneumonic consolidation


title: Control expression array-2.2

tag: genotype/variation


title: active TB infection 8

description: whole blood, active TB infection

value: Adult-type disease with unilateral cavitation, lymph node disease with lobar alveolar consolidation and unilateral hyperinflation


title: Control expression array-1.2


title: Control expression array-4


title: WT CP9 4A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-09/89557.gif

tag: infection (e. coli genotype)

value: wt


title: KTR9_RDX_High_Nitrogen_rep1

description: This sample is of Gordonia sp. KTR9 eposed to 40 ppm RDX and 4 mM Ammonium sulfate. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: active TB infection 5

description: whole blood, active TB infection

value: Ghon focus with bilateral bronchopneumonic consolidation, lymph node disease with bronchial compression and unilateral hyperinflation


title: KTR9_RDX_High_Nitrogen_rep2

description: This sample is of Gordonia sp. KTR9 eposed to 40 ppm RDX and 4 mM Ammonium sulfate. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: active TB infection 3

description: whole blood, active TB infection

value: Adult-type disease with unilateral cavitation and bilateral bronchopneumonic consolidation, lymph node disease with bronchial compression


title: NTHi 86-028NPrpsL∆fur, exponential growth, biological rep3

city: Columbus

first: Alistair

last: Harrison

state: OH

address: 700 Children's Drive

department: Center for Microbial Pathogenesis

institute: The Research Institute at Nationwide Children's Hospital

description: Gene expression data from fur mutant of rpsL mutant strain

hyb_protocol: Hybridization was carried out using the  Agilent One Color Microarray-Based Gene Expression Analysis labeling protocol

scan_protocol: Slides were scanned with an Agilent G2505C Microarray Scanner, at 2 µm resolution.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.9). This data is stored in the FE “.txt” files. The raw intensity values from these files is imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process.  The median green (Cy3) intensities are normalized between the arrays using the Quantile Normalization package in “R” (Bolstad et al., 2003). Quantile normalization is a non-linear probe-level normalization that results in the same empirical distribution of intensities for each array This is a significantly more robust approach than simply normalizing to the median value of each array.

organism: Haemophilus influenzae 86-028NP

label_protocol: First strand DNA synthesis was performed on 5ug of total RNA and cleaned up using the Qiagen MinElute Reaction Cleanup kit.  Material was then labeled using Cy3 reactive dye packs from GE Healthcare.  A final MinElute Reaction Cleanup was performed before moving into the Agilent One Color Microarray-Based Gene Expression Analysis labeling protocol.

growth_protocol: Strains were grown on chocolate plates, overnight at 37˚C in  a 5% CO2 atmosphere.  Cells were then harvested and diluted into iron depeleted  RPMI base medium (DIS) and grown statically overnight at 37˚C in  a 5% CO2 atmosphere.  Cells were then diluted into DIS supplemented with 10 µg human hemoglobin /ml and grown into mid-log phase.

extract_protocol: Two volumes of cells were harvested and extracted with 1 vol. Trizol and 1/10 vol. chloroform.  RNA was purifed using QIAGEN RNeasy Mini Kit, according to the manufacturers' instructions.

treatment_protocol: Cells in mid-log phase were placed on ice then harvested by centrifugation at 4˚C prior to RNA extraction.

tag: source material

value: whole cells

tag: growth phase

value: exponential


title: 144_G07_nasal_epithelium_healthy_subject

city: Amsterdam

first: Ariane

last: Wagener

address: Meibergdreef 9

institute: Academic Medical Center

hyb_protocol: According to standard Affymetrix protocol.

data_processing:
Array images were analyzed by Affymetrix Expression Console using the robust multichip analysis (RMA) algorithm. The normalized data were further analysed using R (version 2.9) and the Bioconductor Limma package (v.3.14.1). Probesets without a known geneID were excluded for further analyses.
The data was further normalized in R by quantile normalization between the arrays

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Isolated airway epithelial cells were grown in fully humidified air containing 5% CO2 at 37°C, and culture medium was replaced every other day.

treatment_protocol: Cells were cultured to 80% confluence and were pre-incubated with BEBM for 48 hours prior to the removement of supernatant and RNA extraction

tag: gender

value: male

tag: subject group

value: healthy controls

value: nasal epithelium

tag: cell type

value: isolated and cultured nasal epithelial cells

tag: condition

value: healthy

tag: paired samples


title: NTHi 86-028NPrpsL∆fur, exponential growth, biological rep4


title: active TB infection 4

description: whole blood, active TB infection

tag: Sex

value: Negative

value: Indeterminate

value: Ghon focus with cavitation and bilateral bronchopneumonic consolidation, lymph node disease with tracheal compression


title: 139_F05_bronchial_epithelium_rhinitis_subject

scan_protocol: According to standard Affymetrix protocol.

value: female

value: patients with rhinitis

value: bronchial epithelium

value: isolated and cultured bronchial epithelial cells

value: rhinitis


title: NTHi 86-028NP∆fur::Tn903, exponential growth, biological rep3

description: Gene expression data from fur mutant of parental strain


title: 132_B09_nasal_epithelium_rhinitis_subject


title: NTHi 86-028NPrpsL, exponential growth, biological rep4

description: Gene expression data from rpsL mutant of parental strain

source_name: NTHi 86-028NPrpsL, exponential growth


title: NTHi 86-028NPrpsL∆fur, exponential growth, biological rep1


title: NTHi 86-028NPrpsL∆fur, exponential growth, biological rep2


title: 923M3 on MEF+rLIF p15

description: Gene expression in pluripotent stem cells

value: MEFs + recombinant (r)LIF

tag: passage


title: NTHi 86-028NP∆fur::Tn903, exponential growth, biological rep4


title: 138_C05_nasal_epithelium_asthma_subject

value: patients with asthma

value: asthma


title: latent TB infection 7

description: whole blood, latent TB infection

source_name: whole blood, latent TB infection

value: Female

tag: age (years)

tag: culture results

value: not performed

value: Positive

value: No abnormalities observed


title: active TB infection 1

description: whole blood, active TB infection

tag: tuberculin skin test

tag: qft-git

value: Ghon focus with unilateral bronchopneumonic consolidation


title: latent TB infection 9

description: whole blood, latent TB infection

value: Male

tag: cxr findings


title: NTHi 86-028NP, exponential growth, biological rep4

description: Gene expression data from parental strain

source_name: NTHi 86-028NP, exponential growth

value: whole cells

value: exponential


title: NTHi 86-028NPrpsL, exponential growth, biological rep2


title: 120_G05_bronchial_epithelium_healthy_subject

value: male

value: healthy controls

tag: tissue

value: healthy


title: 129_H07_nasal_epithelium_asthma_subject

value: female

value: nasal epithelium

value: isolated and cultured nasal epithelial cells


title: 126_A09_nasal_epithelium_asthma_subject


title: NTHi 86-028NP∆fur::Tn903, exponential growth, biological rep1


title: NTHi 86-028NPrpsL, exponential growth, biological rep1


title: NTHi 86-028NPrpsL, exponential growth, biological rep3


title: NTHi 86-028NP∆fur::Tn903, exponential growth, biological rep2


title: active TB infection 2

description: whole blood, active TB infection

value: Adult-type disease with bilateral bronchopneumonic consolidation, lymph node disease


title: 117_H05_bronchial_epithelium_asthma_subject

value: patients with asthma

value: bronchial epithelium

value: isolated and cultured bronchial epithelial cells


title: NTHi 86-028NP, exponential growth, biological rep2


title: 114_C05_bronchial_epithelium_healthy_subject


title: NTHi 86-028NP, exponential growth, biological rep3


title: NTHi 86-028NP, exponential growth, biological rep1


title: latent TB infection 8

description: whole blood, latent TB infection

value: Female

value: not performed


title: 108_E09_nasal_epithelium_healthy_subject


title: Benign prostate tissue 19

city: New York

first: Pei-Chun

last: Lin

state: NY

address: 1300 York Ave

department: Pathology and Laboratory Medicine

institute: Cornell Weill Medical College

description: benign prostate tissue

hyb_protocol: According to manufacturer's protocol.

scan_protocol: Probe level (.CEL file) data were generated using Affymetrix Command Console v1.1

data_processing: Arrays were processed using the GCOS software. Data were extracted from the Affymatrix miRNA QC tool using RMA background correction and median polish summarization. Variance Stabilization Normalization (VSN) procedure was carried out for global noralization

source_name: Bening prostate tissue 19

label_protocol: Total RNA (100ng per sample) was labeled using the FlashTag Biotin HSR kit (Genisphere)

extract_protocol: TRIzol according to manufacturer's protocol

value: Benign, prostate tissue


title: 98_E07_nasal_epithelium_rhinitis_subject

value: patients with rhinitis

value: rhinitis


title: latent TB infection 6

description: whole blood, latent TB infection

value: Male

value: Positive

value: No abnormalities observed


title: latent TB infection 3

description: whole blood, latent TB infection


title: Benign prostate tissue 16

description: benign prostate tissue

source_name: Bening prostate tissue 16


title: Benign prostate tissue 15

description: benign prostate tissue

source_name: Bening prostate tissue 15


title: Benign prostate tissue 18

description: benign prostate tissue

source_name: Bening prostate tissue 18


title: Benign prostate tissue 21

description: benign prostate tissue

source_name: Bening prostate tissue 21


title: latent TB infection 5

description: whole blood, latent TB infection

value: Negative


title: Benign prostate tissue 17

description: benign prostate tissue

source_name: Bening prostate tissue 17


title: latent TB infection 4

description: whole blood, latent TB infection


title: Benign prostate tissue 20

description: benign prostate tissue

source_name: Bening prostate tissue 20


title: latent TB infection 2

description: whole blood, latent TB infection


title: Clinically localized primary prostate cancer 20

description: clinical localized prostate cancer tissue

value: Primary, Prostate cancer, localized


title: Benign prostate tissue 12

description: benign prostate tissue

source_name: Bening prostate tissue 12


title: 103_B07_nasal_epithelium_rhinitis_subject

value: male


title: Clinically localized primary prostate cancer 19


title: 87_E05_nasal_epithelium_healthy_subject

value: female

value: healthy controls

value: nasal epithelium

value: healthy


title: healthy control 9

description: whole blood, healthy control

source_name: whole blood, healthy control


title: healthy control 8

description: whole blood, healthy control


title: 79_A07_nasal_epithelium_healthy_subject

value: isolated and cultured nasal epithelial cells


title: 88_A05_bronchial_epithelium_healthy_subject

value: bronchial epithelium

value: isolated and cultured bronchial epithelial cells


title: healthy control 7

description: whole blood, healthy control

value: not performed


title: Clinically localized primary prostate cancer 18


title: Clinically localized primary prostate cancer 16


title: Clinically localized primary prostate cancer 17


title: Benign prostate tissue 13

description: benign prostate tissue

source_name: Bening prostate tissue 13

value: Benign, prostate tissue


title: Benign prostate tissue 14

description: benign prostate tissue

source_name: Bening prostate tissue 14


title: Clinically localized primary prostate cancer 15


title: Clinically localized primary prostate cancer 21


title: Clinically localized primary prostate cancer 14


title: latent TB infection 1

description: whole blood, latent TB infection


title: Clinically localized primary prostate cancer 13


title: 68_C05_bronchial_epithelium_asthma_subject

value: patients with asthma

value: asthma


title: healthy control 5

description: whole blood, healthy control

value: Female


title: 101_A05_2_bronchial_epithelium_asthma_subject


title: 62_D09_nasal_epithelium_healthy_subject


title: healthy control 4

description: whole blood, healthy control


title: Benign prostate tissue 11

description: benign prostate tissue

source_name: Bening prostate tissue 11


title: Benign prostate tissue 10

description: benign prostate tissue

source_name: Bening prostate tissue 10


title: Benign prostate tissue 9

description: benign prostate tissue

source_name: Bening prostate tissue 9


title: Benign prostate tissue 8

description: benign prostate tissue

source_name: Bening prostate tissue 8


title: Clinically localized primary prostate cancer 12


title: 55_H09_bronchial_epithelium_asthma_subject


title: Benign prostate tissue 5

description: benign prostate tissue

source_name: Bening prostate tissue 5


title: Benign prostate tissue 7

description: benign prostate tissue

source_name: Bening prostate tissue 7


title: Benign prostate tissue 6

description: benign prostate tissue

source_name: Bening prostate tissue 6


title: Benign prostate tissue 4

description: benign prostate tissue

source_name: Bening prostate tissue 4


title: Benign prostate tissue 3

description: benign prostate tissue

source_name: Bening prostate tissue 3


title: 48_D05_bronchial_epithelium_asthma_subject


title: healthy control 1

description: whole blood, healthy control

value: Male


title: healthy control 2

description: whole blood, healthy control

value: No abnormalities observed


title: healthy control 6

description: whole blood, healthy control

value: Negative


title: 43_B07_nasal_epithelium_asthma_subject


title: 59_C09_nasal_epithelium_asthma_subject


title: 49_G09_bronchial_epithelium_healthy_subject


title: healthy control 3

description: whole blood, healthy control


title: Benign prostate tissue 2

description: benign prostate tissue

source_name: Bening prostate tissue 2


title: Benign prostate tissue 1

description: benign prostate tissue

source_name: Bening prostate tissue 1


title: Clinically localized primary prostate cancer 11

value: Primary, Prostate cancer, localized


title: 34_E05_bronchial_epithelium_rhinitis_subject

value: male

value: patients with rhinitis

value: rhinitis


title: 26_E09_nasal_epithelium_asthma_subject

value: female

value: nasal epithelium


title: 30_H09_nasal_epithelium_rhinitis_subject

value: isolated and cultured nasal epithelial cells


title: Clinically localized primary prostate cancer 10


title: Sima07607,ERR1/ERR2 double mutant larvae at late-L3, hypoxia biological rep2

city: Richmond

first: Keith

middle: D

last: Baker

state: VA

address: 1220 E. Broad St.

department: Biochemistry & Molecular Biology

institute: VCU School of Medicine

description: Gene expression data from late-L3 partial clear gut dHIF,dERR double mutant animals hand sorted and treated in 4% oxygen for 6 hours

hyb_protocol: Hybridizations to Affymetrix GeneChip Drosophila Genome 2.0 arrays were performed using the manufacturers recommendations.

scan_protocol: Every chip was scanned at a high resolution by the Affymetrix GeneChip® Scanner 3000 according to the GeneChip Expression Analysis Technical Manual procedures

data_processing: Raw data were normalized using RMA

source_name: Drosophila larvae at partial clear gut stage (-10 to -4 hr prior to pupariation) challenged with 6 hours of 4% oxygen grown at 25C on yeast paste in nomoxia

label_protocol: Template labelings were performed using the GeneChip 3' IVT Express Kit according to the manufacturer’s  specifications (Affymetrix, Santa Clara, CA).

growth_protocol: Fly eggs were collected onto egg caps with yeast paste . The caps were replaced after overnight incubation periods and kept at 25ºC, until mid-L2. At mid-L2, larvae were transferred to a fresh egg cap with blue yeast paste (0.3% bromophenol blue), and allowed to develop until achieving the partial clear gut L3 stage (-10 to -4 hrs prior to metamorphic onset). Appropriately staged animals were moved to fresh agar plates and allowed to age an additional 6 hours at 25ºC.

extract_protocol: Larvae were placed in TRIzol (Invitrogen, Carlsbad, CA) and homogenized using VWR disposable pellet mixer. Total RNA was isolated using a TRIzol/RQ1 DNase (Promega, Madison, WI) hybrid extraction protocol.

treatment_protocol: Appropriately staged animals were moved to fresh agar plates ~36 hours after hatching and allowed to continue development. Wandering larvae were manually selected for size, vitality, and appropriate spiracle formation, and, importantly, blue food content of the gut. Selected animals were allowed to age an additional 6 hours at 25ºC (normoxia). Alternatively, animals were placed in an airtight Modular Incubator Chamber for 6 hours at 25ºC after a gas mixture containing 4% oxygen balanced with nitrogen was flashed into the chamber (hypoxic treatment). After either treatment, larvae were rinsed with 1xPBS and frozen at -80C until further processing.

value: whole larvae

tag: genotype

value: Sima07607,dERR1/Sima07607,dERR2 (product of the cross of parents Sima07607,dERR1/TM3,tw-GFP x Sima07607,dERR2/TM3,tw-GFP)

tag: age

value: late-L3 partial clear gut (-10 to -4 hrs prior to metamorphic onset) as judged by blue food content in gut


title: Clinically localized primary prostate cancer 6


title: Clinically localized primary prostate cancer 7


title: Clinically localized primary prostate cancer 9


title: Clinically localized primary prostate cancer 3


title: ERR1/ERR2 mutant larvae at late-L3, hypoxia biological rep2

description: Gene expression data from late-L3 partial clear gut dERR mutant animals hand sorted and treated in 4% oxygen for 6 hours

value: dERR1/dERR2 (product of the cross of parents dERR1/TM3,tw-GFP x dERR2/TM3,tw-GFP)


title: Sima07607,ERR1/ERR2 double mutant larvae at late-L3, hypoxia biological rep1


title: Sima07607 mutant larvae at late-L3, hypoxia biological rep3

description: Gene expression data from late-L3 partial clear gut dHIF mutant animals hand sorted and treated in 4% oxygen for 6 hours

value: dHIF/dHIF (product of the cross of parents Sima07607/TM3,tw-GFP x Sima07607/TM3,tw-GFP)


title: ERR1/ERR2 mutant larvae at late-L3, hypoxia biological rep1


title: Clinically localized primary prostate cancer 4


title: ERR1/ERR2 mutant larvae at late-L3, hypoxia biological rep3


title: Sima07607 mutant larvae at late-L3, hypoxia biological rep2


title: 9_H07_bronchial_epithelium_rhinitis_subject

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

value: bronchial epithelium

value: isolated and cultured bronchial epithelial cells


title: 22_A09_bronchial_epithelium_asthma_subject

value: patients with asthma

value: asthma


title: 20_F05_bronchial_epithelium_healthy_subject

value: healthy controls

value: healthy


title: Clinically localized primary prostate cancer 1

data_processing: Arrays were processed using the GCOS software. Data were extracted from the Affymatrix miRNA QC tool using RMA background correction and median polish summarization. Variance Stabilization Normalization (VSN) procedure was carried out for global normalization

value: Primary, Prostate cancer, localized


title: 6_D05_nasal_epithelium_rhinitis_subject

value: patients with rhinitis


title: Clinically localized primary prostate cancer 5


title: Clinically localized primary prostate cancer 8


title: Clinically localized primary prostate cancer 2


title: Control larvae at late-L3, hypoxia biological rep5

description: Gene expression data from late-L3 partial clear gut wild type animals hand sorted and treated in 4% oxygen for 6 hours

value: w1118 parents


title: Sima07607 mutant larvae at late-L3, hypoxia biological rep1


title: Control larvae at late-L3, hypoxia biological rep3


title: 16_D09_bronchial_epithelium_rhinitis_subject

value: female

value: rhinitis


title: 13_F09_nasal_epithelium_healthy_subject

value: nasal epithelium

value: isolated and cultured nasal epithelial cells


title: 1_G07_bronchial_epithelium_healthy_subject


title: 10_B05_bronchial_epithelium_rhinitis_subject


title: Sima07607,ERR1/ERR2 double mutant larvae at late-L3, hypoxia biological rep3

value: whole larvae

value: Sima07607,dERR1/Sima07607,dERR2 (product of the cross of parents Sima07607,dERR1/TM3,tw-GFP x Sima07607,dERR2/TM3,tw-GFP)


title: Control larvae at late-L3, hypoxia biological rep1

value: late-L3 partial clear gut (-10 to -4 hrs prior to metamorphic onset) as judged by blue food content in gut


title: Control larvae at late-L3, hypoxia biological rep2


title: ERR1/ERR2 mutant larvae at late-L3, normoxia biological rep3

description: Gene expression data from late-L3 partial clear gut dERR mutant animals hand sorted and treated in normoxia

source_name: Drosophila larvae at partial clear gut stage (-10 to -4 hr prior to pupariation) grown at 25C on yeast paste in nomoxia

value: dERR1/dERR2 (product of the cross of parents dERR1/TM3,tw-GFP x dERR2/TM3,tw-GFP)


title: Sima07607,ERR1/ERR2 double mutant larvae at late-L3, normoxia biological rep2

description: Gene expression data from late-L3 partial clear gut dHIF,dERR double mutant animals hand sorted and treated in normoxia


title: embryoid body, TKO at d4, biological replicate 1

city: Planegg-Martinsried

first: Fabio

last: Spada

state: Bavaria

address: Grosshaderner Str. 2

department: Biology

country: Germany

institute: Ludwig Maximilian University Munich

description: Gene expression data from TKO embryoid bodies differentiated for 4 days

hyb_protocol: Samples were hybridized to GeneChip Human Gene 1.0 ST microarrays following the instructions from the supplier (Affymetrix)

scan_protocol: Scanning was performed with a GeneChip Scanner 3000 7G following the instructions from the supplier (Affymetrix)

data_processing:
The data was processed using the affy (rma normalization) package from Bioconductor.
RMA signal intensity. Note that this expression measure is given to you in log base 2 scale.

source_name: embyroid bodies at day 4

label_protocol: Labeling of samples for array analysis was performed using the GeneChip Whole transcript WT Sense Target Labeling Assay (Affymetrix) with 300 ng input RNA.

growth_protocol: Embryonic stem cells were harvested in the undifferentiated state (day 0) or differentiated as embyroid bodies (EBs) using the hanging drop method; EB samples were harvested at day 4 and 16 of differentiation.

treatment_protocol: Embryoid bodies and stem cells were directly lysed in Trizol and frozen at -80C until all samples were collected.

value: embyroid bodies at day 4

tag: developmental stage

value: embryoid bodies, d4

tag: strain

value: dnmt1-/-, dnmt3a-/-, dnmt3b-/- (TKO)


title: embryoid body, TKO at d16, biological replicate 2

description: Gene expression data from TKO embryoid bodies differentiated for 16 days

source_name: embyroid bodies at day 16

value: embyroid bodies at day 16

value: embryoid bodies, d16


title: embryonic stem cells, TKO at d0, biological replicate 2

description: Gene expression data from TKO undifferentiated embyronic stem cells

source_name: undifferentiated embryonic stem cells

value: undifferentiated embryonic stem cells

value: undifferentiated state


title: Control larvae at late-L3, hypoxia biological rep4


title: Sima07607,ERR1/ERR2 double mutant larvae at late-L3, normoxia biological rep1


title: embryoid body, TKO at d4, biological replicate 2


title: ERR1/ERR2 mutant larvae at late-L3, normoxia biological rep2


title: embryoid body, dnmt1-/- at d16, biological replicate 1

description: Gene expression data from dnmt1-/- embryoid bodies differentiated for 16 days


title: Sima07607,ERR1/ERR2 double mutant larvae at late-L3, normoxia biological rep3


title: embryoid body, TKO at d16, biological replicate 1


title: embryoid body, dnmt1-/- at d16, biological replicate 2


title: embryonic stem cells,TKO at d0, biological replicate 1


title: embryoid body, dnmt1-/- at d4, biological replicate 1

description: Gene expression data from dnmt1-/- embryoid bodies differentiated for 4 days


title: embryonic stem cells, dnmt1-/- at d0, biological replicate 1

description: Gene expression data from dnmt1-/- undifferentiated embyronic stem cells


title: Sima07607 mutant larvae at late-L3, normoxia biological rep2

description: Gene expression data from late-L3 partial clear gut dHIF mutant animals hand sorted and treated in normoxia

value: dHIF/dHIF (product of the cross of parents Sima07607/TM3,tw-GFP x Sima07607/TM3,tw-GFP)


title: Sima07607 mutant larvae at late-L3, normoxia biological rep3


title: ERR1/ERR2 mutant larvae at late-L3, normoxia biological rep1


title: embryoid body, dnmt1-/- at d4, biological replicate 2


title: embryoid body, wildtype at d16, biological replicate 2

description: Gene expression data from wt embryoid bodies differentiated for 16 days

value: wild type


title: BaP 1 µM treated

city: Bergen

first: Fekadu

last: Yadetie

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

hyb_protocol: Hybridization was performed according to by NimbleGen protocols Gene Expression User Guide (Roche NimbleGen). See www.nimblegen.com.

scan_protocol: Axon 4000B scanner (Axon Instruments Inc., Union City, CA) was used.

data_processing: Array data were quantile normalized separately. Background correction was performed by subtracting the top 2% of negative control intensity values. For a gene to be considered as expressed, at least 50 percent of the probes covering exons of the gene had to have a positive intensity. A gene was assigned the median intensity of the positive probes covering it.

organism: Oikopleura dioica

source_name: BaP 1 µM treated

label_protocol: BaP and Clo treated samples were labeled using Cy3-coupled random nonamers and DMSO controls were labeled using Cy5-coupled random nonamers.

extract_protocol: RNeasy Mini Kit according manufacturer’s protocols (QIAGEN, Hilden, Germany).

tag: sample type

value: Sexually immature mixed sex animals

tag: treatment

value: 1 µM treated Benzo[a]pyrene


title: Clofibrate 5 µM DMSO control

source_name: DMSO control

value: 5 µM DMSO


title: Clofibrate 5 µM treated

source_name: Clofibrate 5 µM treated

value: 5 µM Clofibrate


title: embryoid body, wildtype at d16, biological replicate 1

tag: cell type


title: Clofibrate 1 µM DMSO control

value: 1 µM DMSO


title: Liver HF-Q replicate 12

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.5.1.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: liver tissue, high fat diet supplemented with 0.33 % (w/w) quercetin

label_protocol: 1 µg of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al., (Anal Biochem 2007;363:315-7).

extract_protocol: Total RNA was isolated from liver tissue using TRIzol reagent according to the manufacturer’s instruction, followed by purification with RNeasy Mini columns (Qiagen), quantified using Nanodrop (IsoGen Life Science) and qualified using Experion Automated Electrophoresis System (BioRad).

treatment_protocol: All mice started with a three week adaptation phase, in which they were fed a mild-high-fat diet (30 en% fat). Twelve mice were sacrificed immediately after the adaptation phase (t=0). The other 24 mice received the same mild-high-fat diet without (HF) or with supplementation of 0.33% (w/w) quercetin (HF-Q) for 12 weeks. Animals were fasted for minimal 2 hr prior anaestetization and sacrification.

tag: gender

value: male

tag: development stage

value: adult

value: liver

source_name: liver, reference pool of all samples


title: embryonic stem cells, dnmt1-/- at d0, biological replicate 2


title: embryoid body, wildtype at d4, biological replicate 1

description: Gene expression data from wt embryoid bodies differentiated for 4 days

value: embyroid bodies at day 4


title: Clofibrate 1 µM treated

source_name: Clofibrate 1 µM treated

value: 1 µM Clofibrate


title: BaP 0.2 µM treated

source_name: BaP 0.2 µM treated

value: 0.2 µM treated Benzo[a]pyrene


title: Liver HF-Q replicate 11

value: high fat diet supplemented with 0.33 % (w/w) quercetin


title: Sima07607 mutant larvae at late-L3, normoxia biological rep1

value: whole larvae

value: late-L3 partial clear gut (-10 to -4 hrs prior to metamorphic onset) as judged by blue food content in gut


title: embryoid body, wildtype at d4, biological replicate 2

value: embryoid bodies, d4


title: Liver HF-Q replicate 10


title: embryonic stem cells, wildtype at d0, biological replicate 2

description: Gene expression data from wt undifferentiated embyronic stem cells

value: undifferentiated embryonic stem cells

value: undifferentiated state


title: Control larvae at late-L3, normoxia biological rep3

description: Gene expression data from late-L3 partial clear gut wild type animals hand sorted and treated in normoxia

value: w1118 parents


title: D16_2

city: Bronx

first: Yiting

last: Yu

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ,Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing:
Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background.PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.)
ratio_matrix.txt: normalized log2 (HpaII/MspI) ratio

source_name: CD34+ early stem/hematopoietic cell culture on day 16

label_protocol: Random 9-mers pre-labeled with either Cy5 or Cy3

growth_protocol: CD34+ early stem/hematopoietic cells were purified from growth factor mobilized peripheral blood of healthy donors purchased from All Cells Inc. Purified stem/progenitor cells were cultured in media containing 15% fetal calf serum, 15% human serum Iscove¡¯s modified Dulbecco¡¯s medium (IMDM), 10 ng/ml IL-3, 2 U/ml EPO and 50 ng/ml SCF. During the initial 7 days of culture cells were fed on days 3 and 6 by adding equal volume of fresh culture media supplemented with growth factors. However, no new IL-3 was added after the initial addition on day 0 and the amount of SCF added to the fresh media was gradually decreased at each feeding (day 3, 25 ng/ml; day 6, 10 ng/ml; day 8, 2 ng/ml). The amount of EPO added was 2 U/ml during each feeding. On day 7 of culture cells were flow cytometry sorted for CD71 positive (transferrin receptor) cells using a MoFlo high-speed flow cytometer. The purity of the population isolated by this method was 98-99%. Sorted cells were cultured in the same media as before with EPO and SCF except the concentration of SCF was reduced to 2 ng/ml. Cells were fed one more time on day 10 of culture by adding equal volume of fresh media with only EPO (2 U/ml) during this final feeding. Cells were collected for DNA and RNA isolation on days 0, 3, 7, 10, 13 and 16 days of culture.

extract_protocol: Genomic DNA from neutrophils isolated from peripheral blood via Ficoll-gradient density separation was prepared using Qiagen reagents.

value: CD34+ early stem/hematopoietic cell

tag: restriction enzyme

value: MspI representation of genomic DNA

value: HpaII representation of genomic DNA


title: Control larvae at late-L3, normoxia biological rep1


title: Control larvae at late-L3, normoxia biological rep2


title: embryonic stem cells, wildtype at d0, biological replicate 1

value: wild type


title: Liver HF-Q replicate 09

value: male


title: Liver HF-Q replicate 08

value: adult


title: D13_2

source_name: CD34+ early stem/hematopoietic cell culture on day 13


title: D7_2

source_name: CD34+ early stem/hematopoietic cell culture on day 7


title: D10_2

source_name: CD34+ early stem/hematopoietic cell culture on day 10


title: NHEK_6 (array B)

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

institute: Hyogo College of Medicine

description: neonatal human epidermal keratinocytes

hyb_protocol: hybridization buffer : 50% formamide-6 x SSC-0.2% SDS-5 x denhardt’s-0.2 mg/ml denatured salmon sperm, hybridization : at 70°C for 16 h, washing : three times with 2× SSC, 0.2% SDS at 65°C for 10 min, and rinsed once with 0.05 × SSC at room temperature

scan_protocol: Scanned on an Affymetrix 428 Array Scanner Images were quantified using ImaGene version 6.0  (Biodiscovery Inc., CA, USA)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Probes with poor-quality signals (S/N <1.2) and having null data at the frequency of more than 35% in all samples were filtered out using the microarray data analysis software, Expressionist (GeneData AG, Basel, Switzerland).

source_name: Cascade Biologics HEKn　Cat No: C-001-5C，Lot No: 5C0579

label_protocol: 4 µg of total RNA were labeled with Cy3 or Cy5 monoreactive dyes (Amersham, Buckinghamshire, UK) using RNA Transcript SureLABEL™ Core Kit (TaKaRa Bio) according to the manufacture’s instructions

growth_protocol: cultured in Defined Keratinocyte-SFM medium （DK-SFM, GIBCO/Invitrogen Co., CA） at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol: Total RNA extracted using Trizol (Invitrogen, CA) and purified using RNeasy kit (QIAGEN, Hilden, Germany) following manufacturer's instructions

treatment_protocol: third or fourth passaged cells in log phase cultures

source_name: Reference RNA

value: a mixture of NHEK total RNA and Universal Human Reference RNA (Stratagene Corporation, CA, USA)


title: BaP 0.2 µM DMSO control

value: Sexually immature mixed sex animals

value: 0.2 µM DMSO


title: BaP 1 µM _DMSO control

value: 1 µM DMSO


title: NHEK_5 (array B)

description: neonatal human epidermal keratinocytes

source_name: Cascade Biologics HEKn　Cat No: C-001-5C，Lot No: 3C1272


title: D16_1


title: D0_2

source_name: CD34+ early stem/hematopoietic cell culture on day 0


title: D3_2

source_name: CD34+ early stem/hematopoietic cell culture on day 3


title: D13_1


title: NHEK_4 (array B)

description: neonatal human epidermal keratinocytes

source_name: Cascade Biologics HEKn　Cat No: C-001-5C，Lot No: 5C0571


title: NHEK_3 (array B)

description: neonatal human epidermal keratinocytes

source_name: Cambrex；NHEK-Neo　Cat No: CC2503，Lot No: 4F1363


title: NHEK_2 (array B)

description: neonatal human epidermal keratinocytes

source_name: Kurabo; NHEK(F)　Lot No.4C1163


title: NHEK_1 (array B)

description: neonatal human epidermal keratinocytes

source_name: Kurabo; NHEK(F)　Lot No.3C1272


title: BDK_donor18 (array B)

description: bulge–derived keratinocytes

source_name: donor 18

tag: disease

value: atopic dermatitis


title: Liver HF-Q replicate 07

source_name: liver tissue, high fat diet supplemented with 0.33 % (w/w) quercetin

value: liver

source_name: liver, reference pool of all samples


title: Liver HF-Q replicate 05

value: high fat diet supplemented with 0.33 % (w/w) quercetin


title: Liver HF-Q replicate 06


title: Liver HF-Q replicate 04


title: ILEUM APCmin/+/VP16 (CTRL) 4

city: Santa Maria Imbaro

first: Antonio

last: Moschetta

address: Via Nazionale 8A

institute: University of Bari & Consorzio Mario Negri Sud

description:
ILEUM APCmin/+/VP16 (CTRL) 4
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <100 in both groups were excluded.

source_name: Intestinal (ileal) Tumor

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina® TotalPrepTM RNA  Amplification Kit

extract_protocol: RNA was extracted with QIAzol reagent, following manufacturer's instructions. Quality control was performed with Biorad Experion.

value: C57BL/6J-FVBN Mixed Strain

value: 8 months

value: Intestinal (ileal) Tumor

tag: genotype/variation

value: APCmin/+/VP16 (control)


title: Liver HF-Q replicate 02


title: ILEUM APCmin/+/VP16 (CTRL) 3

description:
ILEUM APCmin/+/VP16 (CTRL) 3
replicate 1


title: ILEUM APCmin/+/VP16 (CTRL) 2

description:
ILEUM APCmin/+/VP16 (CTRL) 2
replicate 1


title: ILEUM APCmin/+/VP16LXRa 7

description:
ILEUM APCmin/+/VP16LXRa 7
replicate 1


title: ILEUM APCmin/+/VP16LXRa 5

description:
ILEUM APCmin/+/VP16LXRa 5
replicate 1


title: ILEUM APCmin/+/VP16LXRa 8

description:
ILEUM APCmin/+/VP16LXRa 8
replicate 1


title: Liver HF-Q replicate 01


title: ILEUM APCmin/+/VP16LXRa 6

description:
ILEUM APCmin/+/VP16LXRa 6
replicate 1


title: D10_1

value: CD34+ early stem/hematopoietic cell


title: D7_1

value: MspI representation of genomic DNA


title: BDK_donor17 (array B)

description: bulge–derived keratinocytes

source_name: donor 17


title: BDK_donor16 (array B)

description: bulge–derived keratinocytes

source_name: donor 16


title: D3_1

value: HpaII representation of genomic DNA


title: Liver HF-Q replicate 03


title: Liver HF replicate 12

source_name: liver tissue, high fat diet

value: high fat diet