title: PG1-Fib

description: SAMPLE 8

value: HGPS-Fib

value: Hutchinson-Gilford Progeria syndrome (HGPS) skin fibroblasts


title: MCF10A_rep2

status: Public on Dec 23 2010

type: RNA

city: Detroit

first: Andrea

last: Baillo

address: 4100 John R

country: USA

institute: Wayne State University

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit

growth_protocol: MCF10A cells were cultured in Ham's F-12 with 1 μg/ml hydrocortisone, 1 mg/ml bovine serum albumin, 10 mm Hepes, 5 mm ethanolamine, 5 μg/ml transferrin, 10 nm triiodothyronine, 50 nm sodium selenate, 5 μg/ml gentamicin, 2.5 μg/ml fungizone, and 5 μg/ml insulin. MCF10A+AREG cells were supplemented with 20ng/ml AREG and MCF10A cells were supplememnted with 10ng/ml EGF

extract_protocol: RNA was extracted with the QIAGEN Rneasy Plus kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanylizer and the Agilent RNA 6000 Nano Kit.

tag: agent

value: control

tag: cell type

value: immortalized human mammary epthelial cells

tag: cell line


title: MCF10A-AREG_rep1

description: replicate 1

value: -AREG


title: normal roots at panicle elongation stage, biological rep2

city: Beijing

first: pan

last: yajiao

address: Zhongguancun South Street No.12

country: China

institute: The chinese academy of agriculture sciences

description: DK151, a drought tolerant line from IR64

hyb_protocol: RNA from the three independent replicate samples were used for hybridization to the Affymetrix Genechips® Rice Genome Array chips, which contain probes to query 51,279 transcripts from two rice cultivars, including 48,564 japonica transcripts and 1,260 indica transcripts from Affymetrix (Santa Clara, CA).Hybridization to the arrays and quality control checks were carried out at the Company of CapitalBio Corporation, Beijing. (Affymetrix GeneChip Expression Analysis g of this fragmented target cRNA wasmTechnical Manual).

scan_protocol: Affy- Array Scanning

data_processing: The SAM (Significant Analysis of Microarray) software was applied to identify differentially regulated genes (DRGs) between samples using the two classes unpaired method based on the empirical criterion of more than two-fold change and significant q value (FDR adjusted P value) less than 0.05. A list of known or unknown genes was generated by performing a BLASTn search (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi) from the Affymetrix website

organism: Oryza sativa

source_name: Oryza DK151, root

label_protocol: Biotin labeled cRNA was produced with 5 ug of total RNA as starting material for each sample reaction.

growth_protocol: Rice plants were grown in PVC tubes (size: 75 cm×20 cm, each with a 20 cm hole from the bottom) with Turface and watered with 0.5×Yoshida.

extract_protocol: Total RNA were extracted using TRIzol reagents according to the instruction and then purified and concentrated using RNeasy MinElute Cleanup kit (Qiagen).

treatment_protocol: Drought stress was processed by slowly draining the solution until leaf relative water content was 65%–75%.

tag: tissue

value: root

tag: genotype

tag: age

value: panicle elongation stage


title: HES3-1

city: Singapore

first: FAN

last: ZHOU

address: 8A Biomedical Grove

country: Singapore

institute: Institute of Medical Biolog

description: SAMPLE 5

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization (Illumina BeadStudio 3.2).

source_name: hESC

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

extract_protocol: RNA was extracted with Trizol reagent, followed by the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: group name

value: HES

tag: tissue source

value: embryo

value: human embryonic stem cells


title: MCF10A-EGF_rep2

description: replicate 2

value: -EGF


title: H9-1

description: SAMPLE 6


title: MCF10A_rep1

description: replicate 1


title: N1-Fib

description: SAMPLE 7

source_name: normal skin fibroblasts

value: N-Fib

value: skin

value: normal skin fibroblasts


title: MCF10A+AREG_rep1

description: replicate 1

value: +AREG


title: 4TO7 Puro vec control for Cluster 1, repeat B

city: Princeton

first: Yibin

last: Kang

state: NJ

address: LTL 254, Washington Road

department: Molecular Biology

institute: Princeton University

hyb_protocol: Labeled cRNA (mixed Cy5-labeled and Cy3-labeled) was incubated with Blocking agent and Fragmentation buffer (Agilent Gene Expression Hybridization Kit) for 30min at 60°C. GEx Hybridization Buffer HI-RPM was then added to the mixture. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 16h. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner.Images were quantified using Agilent Feature Extraction Software (version 9.1.3).

data_processing: The data were analyzed with Genespring GX 7.3 Expression Analysis using Per Spot (divide by control channel), Per Chip (normalize to 50th percentile) and Per Gene (normalize to median) normalization methods.

organism: Mus musculus

source_name: 4TO7 cells-infected with pMSCV puro vector (Control for C1), repeat B

label_protocol: 175 ng of total RNA were primed with T7 promoter primer at 65°C for 10 min, then reversed transcribed to cDNA at 40°C for 2h with MMLV RT, and transcribed to cRNA with T7 RNA polymerase with dATP, dTTP, dGTP and Cy5-CTP or Cy3-CTP at 40°C for 2. Labeled cRNA was purified with Qiagen RNeasy mini kit.

growth_protocol: These sublines were maintained in DMEM with 10% FBS and antibiotics.

extract_protocol: Total RNA was extracted using Ambions MirVANA kit according to the manufacturer's instructions

source_name: Universal Mouse Reference RNA (Stratagene)

tag: reference

value: 11 mouse cell lines


title: PG1-iPSC-2

description: SAMPLE 4

source_name: iPSC, HGPS skin fibroblasts

value: HGPS-iPS

value: iPSC reprogrammed from Hutchinson-Gilford Progeria syndrome (HGPS) skin fibroblasts


title: MCF10A-EGF_rep1

description: replicate 1


title: 4TO7 Puro vec control for Cluster 1, repeat A

source_name: 4TO7 cells-infected with pMSCV puro vector (Control for C1), repeat A


title: normal roots at panicle elongation stage, biological rep1

value: DK151, a drought tolerant line from IR64


title: Drought treated leaves at panicle elongation stage, biological rep3

source_name: Oryza DK151, leaf

value: leaf


title: Invasive cancer originating in IPMN 1

city: Tokyo

first: Nobuyoshi

last: Hiraoka

address: 5-1-1 Tsukiji, Chuo-ku

department: Pathology Division

country: Japan

institute: National Cancer Center Research Institute

description: Gene expression data from microdissected epithelial cells of invasive cancer originating in IPMN

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 8000.

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 (GCOS1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: microdissected epithelial cells from invasive cancer originating in IPMN 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 30 ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Total RNA was obtained with Trizol extraction and purified with RNeasy Micro Kit according to the manufacturer's instructions.

value: pancreas

value: epithelial cells

tag: disease status

value: intraductal papillary-mucinous neoplasm (IPMN)


title: normal leaves at panicle elongation stage, biological rep3

value: panicle elongation stage


title: Invasive cancer originating in IPMN 3

source_name: microdissected epithelial cells from invasive cancer originating in IPMN 3


title: Invasive cancer originating in IPMN 2

source_name: microdissected epithelial cells from invasive cancer originating in IPMN 2


title: Drought treated leaves at panicle elongation stage, biological rep2


title: 4TO7 Cluster 1, repeat A

description: 4TO7 Cluster 1, repeat A

source_name: 4TO7 cells stably overexpressing cluster 1 microRNAs, repeat A


title: N1-iPSC-1

description: SAMPLE 1

source_name: iPSC, normal skin fibroblasts

value: N-iPS

value: iPSC reprogrammed from normal skin fibroblasts


title: IPMC 5

description: Gene expression data from microdissected epithelial cells of IPMC

source_name: microdissected epithelial cells from IPMC 5

value: intraductal papillary-mucinous carcinoma (IPMC)


title: 4TO7 CDH1, repeat B

description: 4TO7 CDH1, repeat B

source_name: 4TO7 cells stably overexpressing E-cadherin, repeat B


title: N1-iPSC-2

description: SAMPLE 2


title: normal leaves at panicle elongation stage, biological rep2


title: IPMC 6

source_name: microdissected epithelial cells from IPMC 6


title: Drought treated leaves at panicle elongation stage, biological rep1


title: 4TO7 CDH1, repeat A

description: 4TO7 CDH1, repeat A

source_name: 4TO7 cells stably overexpressing E-cadherin, repeat A


title: Array 100

city: Austin

first: Lin

last: Huffman

state: TX

address: 2400 Speedway, PAT 141

department: Institute for Cellular and Molecular Biology

institute: The University of Texas

hyb_protocol: Cy3- and Cy5-labeled samples were combined and mixed with yeast tRNA, polydA/dT, SSC, and SDS and heated to 100C for 2 minutes before being applied to microarray slides. Slides were cover slipped and incubated in custom hybridization chambers in a 65C water bath for 16 hours. Slides were then washed in a series of 3 solutions containing decreasing amounts of SSC and SDS before drying via centrifugation.

scan_protocol: Scanned using a GenePix 4000B array scanner and imaged using GenePix Pro 6.0.

data_processing: Scans were gridded and spots with diameter < 60 were removed from analysis. Intensities were normalized within each array using the LIMMA package for R by batch and print tip. A linear model was fit to each array using the lmFit function and significant differences between the two groups (M-cell and whole brain) were found using empirical Bayesian statistics via the function eBayes and corrected for multiple hypothesis testing using FDR. Individual arrays were analyzed by building a contrast matrix from the lmFit data and a Benjamini-Hochberg cut-off was applied to control for multiple hypothesis testing. Single-channel intensities were extracted from the normalized M-values using Microsoft Excel and sample M1 as a reference.

molecule: cytoplasmic RNA

organism: Haplochromis burtoni

label_protocol:
Two rounds of amplification using the picoRNA amplification kit (Ocimum Biosolutions).
500 ng of RNA were primed with 1 uL of 5 ug/ul oligodT and random hexamer solution at 70C for 10 minutes. RNA was reverse transcribed using SuperScriptII Reverse Transcriptase, amino allyl-dUTP/dNTP solution and DTT at 42C for 2 hours. Samples were treated with 1N NaOH and 0.5M EDTA at 65C for 15 minutes then neutralized with 1M HEPES. Samples were purified using the Qiagen MinElute kit and eluted with 0.1M Na bicarbonate. Samples were labeled by mixing 10 uL with Amersham CyDye Post-Labeling Reactive Dye dissolved in 1 uL DMSO in the dark for 1 hour, then neutralized with 3M NaOAc and cleaned using the Qiagen MinElute Kit.

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

value: Mauthner cell (M-cell)

value: whole brain


title: Array 97


title: Array 98


title: Array 99


title: 4TO7 CDH1 Puro vec control, repeat B

description: 4TO7 CDH1 Puro vec control, repeat B

source_name: 4TO7 cells-infected with pMSCV puro vector (Control for CDH1), repeat B


title: Drought treated roots at tillering stage, biological rep2

source_name: Oryza DK151, root

value: root

value: tillering stage


title: IPMC 4

source_name: microdissected epithelial cells from IPMC 4


title: 4TO7 CDH1 Puro vec control, repeat A

description: 4TO7 CDH1 Puro vec control, repeat A

source_name: 4TO7 cells-infected with pMSCV puro vector (Control for CDH1), repeat A


title: normal leaves at panicle elongation stage, biological rep1


title: Array 96


title: normal roots at tillering stage, biological rep3


title: normal roots at tillering stage, biological rep1


title: IPMC 1

source_name: microdissected epithelial cells from IPMC 1


title: normal roots at tillering stage, biological rep2


title: IPMA 5

description: Gene expression data from microdissected epithelial cells of IPMA

source_name: microdissected epithelial cells from IPMA 5

value: intraductal papillary-mucinous adenoma (IPMA)


title: 4TO7 Clusters 1+2, repeat B

description: 4TO7 Clusters 1+2, repeat B

source_name: 4TO7 cells overexpressing Clusters 1 and 2, repeat B

source_name: Universal Mouse Reference RNA (Stratagene)

value: 11 mouse cell lines


title: IPMC 2

source_name: microdissected epithelial cells from IPMC 2


title: 4TO7 Clusters 1+2, repeat A

description: 4TO7 Clusters 1+2, repeat A

source_name: 4TO7 cells overexpressing Clusters 1 and 2, repeat A


title: Drought treated roots at tillering stage, biological rep1


title: 4TO7 Hygro vec + Puro vec, repeat B

description: 4TO7 Hygro vec + Puro vec, repeat B

source_name: 4TO7 cells-infected with pMSCV-hygro and pMSCV-puro vectors (Control for C1+C2), repeat B


title: IPMC 3

source_name: microdissected epithelial cells from IPMC 3


title: 4TO7 Hygro vec + Puro vec, repeat A

description: 4TO7 Hygro vec + Puro vec, repeat A

source_name: 4TO7 cells-infected with pMSCV-hygro and pMSCV-puro vectors (Control for C1+C2), repeat A


title: IPMA 6

source_name: microdissected epithelial cells from IPMA 6


title: 7-day-old seedling of QK at HS condition, biological rep2

city: Shulin City, Taipei County

first: Hsiang-chin

last: Liu

address: 9F., No.332, Xuefu Rd.

country: Taiwan

institute: Academia sinica

description: Gene expression data from seedling at heat shock condition

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix® GeneChip® Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operation System 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Arabidopsis thaliana

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

growth_protocol: Col-0, Ws and QK were grown at 22°C on 0.5x MS plates containing 1% sucrose for 7 days.

extract_protocol: Total RNA was extracted using RNeasy RNA extraction kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Samples were incubated for 1 h at 37 °C then collected for RNA extraction.

value: seedling

value: QK mutant

value: 7 day old

tag: treatment

value: heat shocked


title: IPMA 4

source_name: microdissected epithelial cells from IPMA 4

value: pancreas


title: Array 95


title: Drought treated leaves at tillering stage, biological rep3

source_name: Oryza DK151, leaf

value: leaf

value: DK151, a drought tolerant line from IR64


title: 4TO7 Cluster 2, repeat A

description: 4TO7 Cluster 2, repeat A

source_name: 4TO7 cells overexpressing cluster 2 miRNAs, repeat A


title: Drought treated leaves at tillering stage, biological rep2


title: IPMA 2

source_name: microdissected epithelial cells from IPMA 2

value: epithelial cells


title: IPMA 3

source_name: microdissected epithelial cells from IPMA 3


title: 7-day-old seedling of QK at control condition, biological rep1

description: Gene expression data from seedling at control condition


title: Drought treated roots at tillering stage, biological rep3

source_name: Oryza DK151, root


title: PG1-iPSC-1

description: SAMPLE 3

source_name: iPSC, HGPS skin fibroblasts

value: HGPS-iPS

value: skin

value: iPSC reprogrammed from Hutchinson-Gilford Progeria syndrome (HGPS) skin fibroblasts


title: 7-day-old seedling of QK at control condition, biological rep2


title: 4TO7 Cluster 2, repeat B

description: 4TO7 Cluster 2, repeat B

source_name: 4TO7 cells overexpressing cluster 2 miRNAs, repeat B


title: 7-day-old seedling of QK at HS condition, biological rep1


title: normal leaves at tillering stage, biological rep3


title: normal main pancreatic duct 7

description: Gene expression data from microdissected epithelial cells of normal main pancreatic duct

source_name: microdissected epithelial cells from normal main pancreatic duct 7

value: normal


title: normal leaves at tillering stage, biological rep2


title: normal leaves at tillering stage, biological rep1


title: normal main pancreatic duct 6

source_name: microdissected epithelial cells from normal main pancreatic duct 6


title: Drought treated leaves at tillering stage, biological rep1


title: IPMA 1

source_name: microdissected epithelial cells from IPMA 1


title: 4TO7 Hygro vec, repeat B

description: 4TO7 Hygro vec, repeat B

source_name: 4TO7 cells-infected with pMSCV hygro vector (Control for C2), repeat B

source_name: Universal Mouse Reference RNA (Stratagene)


title: 4TO7 Hygro vec, repeat A

description: 4TO7 Hygro vec, repeat A

source_name: 4TO7 cells-infected with pMSCV hygro vector (Control for C2), repeat A


title: macroH2A2 shRNA, biological rep2

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

description: B16-F1 cells expressing mH2A2 shRNA

hyb_protocol: The resulting biotin-labeled cDNA was chemically fragmented, made into hybridization cocktail and hybridized to the Mouse Genome 430 Plus 2.0 arrays (Affymetrix) according to the Affymetrix GeneChip protocol.

scan_protocol: The array images were generated through a high-resolution GeneChip Scanner 3000 7G (Affymetrix) according to Affymetrix protocols.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: B16-F1 cells expressing mH2A2 shRNA

label_protocol: 150ng of total RNA was reverse transcribed using T7-poly(dT) primer and converted into double-stranded cDNA. The cDNA was used as a template for subsequent in vitro transcription with biotin-labeled UTP at 370C for 16 h using Genechip 3’ IVT express kit (Affymetrix).

growth_protocol: B16-F1 cells containing lentiviral shRNAs were grown in DMEM, 10%FBS, 5%CO2

extract_protocol: Total RNA was isolated from cell lines using RNeasy column purification per manufacturer's protocol (Qiagen). The quality of the RNA was evaluated using the Agilent BioAnalyzer RNA nano assay.

treatment_protocol: B16-F1 cells stably expressing lentiviral shRNAs were generated using standard protocols (See publication for details)

tag: strain

tag: disease

value: Melanoma


title: macroH2A1 shRNA, biological rep2

description: B16-F1 cells expressing mH2A1 shRNA

source_name: B16-F1 cells expressing mH2A1 shRNA


title: normal main pancreatic duct 5

source_name: microdissected epithelial cells from normal main pancreatic duct 5


title: macroH2A1 shRNA,  biological rep1

description: B16-F1 cells expressing mH2A1 shRNA


title: macroH2A2 shRNA,  biological rep1

description: B16-F1 cells expressing mH2A2 shRNA


title: normal main pancreatic duct 3

source_name: microdissected epithelial cells from normal main pancreatic duct 3


title: normal main pancreatic duct 2

source_name: microdissected epithelial cells from normal main pancreatic duct 2


title: normal main pancreatic duct 4

source_name: microdissected epithelial cells from normal main pancreatic duct 4


title: normal main pancreatic duct 1

source_name: microdissected epithelial cells from normal main pancreatic duct 1


title: MCF7-vector control cell

city: Salt Lake City

first: Jin

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

description: MCF7 cells vs Universal human reference RNA (Stratagene)

hyb_protocol: Agilent Two-color GE Hyb/Wash Protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1).

data_processing: Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: MCF7 cells

label_protocol: Agilent Two-Color LRILAK Labeling Protocol

growth_protocol: MCF10A cells were maintained in DMEM/F12 containing 5% horse serum, 20 ng/ml EGF, 0.5 µg/ml hydrocortisone, 10 µg/ml insulin, 50 U/ml penicillin, 50 µg/ml streptomycin and 8 µg/ml Blasticidin  at 37°C and 5% CO2. MCF7 cells were cultured in MEM containing 10% FBS, 10 µg/ml insulin, 1mM sodium pyruvate, 50 U/ml penicillin, 50 µg/ml streptomycin  and 4 µg/ml Blasticidin at 37°C and 5% CO2.

extract_protocol: Total RNA extracted using RNeasy kit  (Qiagen) following manufacturer's instructions

tag: transfection

value: vector control

value: MCF7 (HTB-22)

tag: donor gender

value: Female

tag: donor age

value: 69 years

tag: source organ

value: Mammary gland; breast

value: Epithelial

tag: donor disease state

value: Adenocarcinoma

tag: sample type

value: Universal human reference RNA (Stratagene), pooled RNA from 10 human cell lines


title: 7-day-old seedling of Col-0 at HS condition, biological rep1

value: seedling

value: 7 day old

value: heat shocked


title: 7-day-old seedling of Col-0 at control condition, biological rep1


title: MCF10A-vector control cell

description: MCF10A cells vs Universal human reference RNA (Stratagene)

source_name: MCF10A cells

tag: cell line

value: 36 years

tag: cell type

value: Fibrocystic disease


title: Control shRNA, biological rep2

description: B16-F1 cells expressing control shRNA

source_name: B16-F1 cells expressing control shRNA


title: Control shRNA, biological rep1

description: B16-F1 cells expressing control shRNA


title: wild type rep6

status: Public on Dec 22 2010

city: San Francisco

first: Alisha

last: Holloway

state: CA

address: 1650 Owens Street

institute: Gladstone Institutes

hyb_protocol: Affymetrix mouse Gene ST 1.0 arrays were hybridized and scanned according to manufacturer recommendations.

data_processing: Raw intensities from CEL files were analyzed using Affymetrix Power Tools (APT, version 1.10.1) to generate RMA (robust multi-array average; 49) expression intensities on a log2 scale for each probe set

source_name: mouse E11.5 hearts

label_protocol: Standard methods for biotin labeling were used.

growth_protocol: Embryonic hearts were dissected at E11.5

extract_protocol: Qiagen RNeasy Micro (December 2007)

value: C57Bl/6/BLKSW mix

tag: genotype/variation

value: wild type

tag: tissue

value: heart

tag: developmental stage


title: Tbx5+/- Brg1 +/- rep2

scan_protocol: Affymetrix mouse Gene ST 1.0 arrays were hybridized and scanned according to manufacturer recommendations.


title: Tbx5+/- Brg1 +/- rep3


title: MCF10A-TRIM29 shRNA cell

value: TRIM29 shRNA

source_name: Universal human reference RNA (Stratagene)


title: Tbx5+/- rep4


title: wild type rep4


title: wild type rep1


title: Tbx5+/- rep2


title: Tbx5+/- rep1


title: wild type rep3


title: wild type rep2


title: Nkx2-5+/- Brg1+/- rep1


title: Tbx5+/- Brg1 +/- rep1


title: Nkx2-5+/- Brg1+/- rep2


title: wild type rep5


title: Tbx5+/- rep5


title: Nkx2-5+/- rep4


title: Tbx5+/- rep3


title: Nkx2-5+/- Brg1+/- rep3


title: Nkx2-5+/- rep3


title: Brg1+/- rep3


title: Nkx2-5+/- rep1


title: Nkx2-5+/- rep2


title: Brg1+/- rep2


title: 4TO7 Cluster 1, repeat B

description: 4TO7 Cluster 1, repeat B

source_name: 4TO7 cells stably overexpressing cluster 1 microRNAs, repeat B

value: 11 mouse cell lines


title: Brg1+/- rep4


title: Brg1+/- rep1


title: ionomycin treated cells rep1

city: angers

first: frederique

last: savagner

address: 4 rue larrey

country: France

institute: Inserm

description: Biological replicate 1 of 2. Treated cells with ionomycin during 96h

hyb_protocol: Agilent hybridization protocol was used

scan_protocol: Agilent scanner

data_processing: Data tables contain Genespring software computed values. We have selected data after filtering normalized data on non variation for gene expression through all the chemical conditions (ionomycin and BAPTA treatment compared to non treated cells). The hierarchical gene clustering was computed on median-gene-centered and log-transformed data using average linkage and uncentered correlation distances. Computations and visualization were performed using Cluster and TreeView software (Eisen et al., 1998). The Expression Analysis Systematic Explorer (EASE) and Gene Set analysis were used to determine the statistical over represented and differentially expressed genes (Tusher et al., 2001).

source_name: RO82 W_1 ionomycin-rep1

label_protocol: RNA amplification and cDNA labeling using Cy3/Cy5 dyes according to manufacturer’s recommendations (Agilent)

growth_protocol: RO82 W-1 cells were grown in a mixed 60:30 DMEM-F12/endothelial basal medium supplemented with 10% fetal bovine serum, 1% L-glutamine, and an antibiotic cocktail

extract_protocol: Total RNA was isolated from cultured cells using the RNeasy kit . The integrity of RNA was determined using a Bio-Analyzer 2100

treatment_protocol: RO82 W-1 cells were treated five hours a day for four days with the calcium ionophore ionomycin  made up to a final concentration of 2 µM in the PSS medium containing 2mM calcium, that may increased intracellular calcium up to 2 nM. We further used the cytosolic calcium chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid-acetoxymethyl ester (BAPTA/AM)  made up to a final concentration of 2-8 µM, with a combination of ionomycin and BAPTA/AM or with equivalent volumes of DMSO for control cells. To avoid cell death due to the toxic effects of intracellular Ca++ ion chelation, the BAPTA/AM concentration was adjusted to cell density in the flask for each day of treatment as follows: 2 µM the first day, 4 µM the second day, 6 µM the third day, and 8 µM the fourth day

tag: disease state

value: carcinoma

value: ionomycin


title: control cells rep2

description: Biological replicate 2 of 2. Control cells, untreated

source_name: RO82 W_1 control-rep2


title: CTRL, biological rep 3

city: Bari

first: Pina

last: Iannelli

address: viale Orazio Flacco, 65

country: Italy

institute: National Cancer Centre "Giovanni Paolo II"

hyb_protocol: Hybridized arrays were labeled and washed using the Hybridization, Wash and Stain Kit on a GeneChip® Fluidics Station 450 with the appropriate fluidics scripts (Affymetrix).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G according to the Affimetrix protocol.

data_processing:
Data were processed using R software (http://www.r-project.org/, version 2.12.1).
The microarray data were processed using R software (http://www.r-project.org/, version 2.12.1 ) using RMA normalization protocol (affy package).

source_name: breast cell line MCF7/ADR

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Sense Target Labeling Assay (Affymetrix).

extract_protocol: After exposure, cells were pelletted and total RNA was extracted utilising Rneasy kit (QIAGEN) according to manifacturer's protocol.

treatment_protocol: Cells were exposed to 25 nM PB28 for 2 days, to 20 mM MC70 for 2 days, to 20 mM MC18 for 2 days. Drugs were provided by Prof. NA Colabufo, Dipartimento Farmacochimico, University of Bari, Bari, Italy.

tag: drug treatment

value: untreated cells


title: MC18, biological rep 1

value: MC18 treated cells


title: CTRL, biological rep 2


title: Brg1+/- rep5


title: PB28, biological rep 3

value: PB28 treated cells


title: ionomycin treated cells rep2

description: Biological replicate 2 of 2. Treated cells with ionomycin during 96h

source_name: RO82 W_1 ionomycin-rep2


title: BAPTA/AM treated cells rep2

description: Biological replicate 2 of 2. Treated cells with BAPTA/AM during 96h

source_name: RO82 W_1 BAPTA/AM-rep2

value: BAPTA/AM


title: PB28, biological rep 2


title: MC18, biological rep 2


title: CTRL, biological rep 1


title: MC70, biological rep 3

value: MC70 treated cells


title: Brg1+/- rep6


title: PB28, biological rep 1


title: control cells rep1

description: Biological replicate 1 of 2. Control cells, untreated

source_name: RO82 W_1 control-rep1


title: MC18, biological rep 3


title: BAPTA/AM treated cells rep1

description: Biological replicate 1 of 2. Treated cells with BAPTA/AM during 96h

source_name: RO82 W_1 BAPTA/AM-rep1


title: MC70, biological rep 2


title: MCF7-TRIM29 cell

value: MCF7 (HTB-22)

value: Female

value: 69 years

value: Mammary gland; breast

value: Epithelial

value: Adenocarcinoma

value: Universal human reference RNA (Stratagene), pooled RNA from 10 human cell lines


title: papilloma_412254156A_1_of_1

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

description: Gene expression data from papillomas induced on dorsal back skin by DMBA/TPA

hyb_protocol: 200 microliters of hybridization sample were incubated in the Affymetrix Hybridization Oven 640 instrument for 16 hours at 45C with 60 rpm rotation.  Arrays were processed with the Affymetrix Fluidics Station 450 instrument, using the FS450_0001 fluidics script and GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: The Affymetrix GCS3000 7G instrument was used to acquire the microarray image data.

data_processing: CEL files were background corrected and normalized with RMA using RMAExpress software and log2 transformed

source_name: papilloma induced on FVBBX dorsal back skin by DMBA/TPA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Mice (8–12 weeks old) received a dose of DMBA (25 mg per mouse in 200 ml acetone applied to shaved dorsal back skin). One week after initiation, tumours were promoted with TPA (200 ml of 1024 M solution in acetone) twice weekly for 20 weeks.

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol:
Tumors were initiated on dorsal back skin with a single dose of DMBA (25 µg per mouse in 200 µl acetone). Starting one week after the initiation tumors were promoted with TPA (200 µl of 10-4 M solution in acetone) twice weekly for 20 weeks.
Backcross mice were treated as noted

value: [SPRET/Ei X FVB/N] X FVB/N

tag: replicate

tag: origin

tag: cage

tag: sex

value: F

tag: coat

value: Agouti


title: papilloma_41214E6B49_2_of_2

tag: strain


title: papilloma_41214E6B49_1_of_2


title: Nlrc5-/- GM-DC, 2h

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

institute: AIST

description: gene expression data from GM-CSF induced Nlrc5 KO bone marrow dendritic cells infected with NDV, 2h after infection.

hyb_protocol: Following fragmentation, 2 micro g of cDNA were hybridized to Affymetrix Mouse Genome 430 2.0 array for 18 hours at 45 C. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Intensity data in CEL files were processed with using R and Bioconductor. Normalization was done with robust multiarray average algorithm with using Bioconductor package affy.

source_name: Dendritic cells induced from Nlrc5 KO bone marrow cells under GM-CSF treatment, and infected with NDV for 2h.

label_protocol: Biotinylated cDNA were prepared with using OVATION kit (NuGen) according to the manufacturer's instruction.

growth_protocol: Bone marrow cells were collected from Nlrc5+/+ (wild-type) and Nlrc5-/- mice, and then cultured with GM-CSF for 6 days.

extract_protocol: Total RNA were extracted with using Trizol (Invitrogen) and purified with using Rneasy mini kit (Qiagen) according to manufactures' instructions.

treatment_protocol: The induced dendritic cells were infected with Newcastle Disease virus at moi 1 for 0, 2, and 4 hours.

value: GM-CSF induced bone marrow dendritic cells

tag: genotype

value: Nlrc5 -/-

tag: infection

value: Newcastle disease virus infection

tag: time


title: MC70, biological rep 1


title: YUC.7DPA.R1

city: Ames

first: Lex

last: Flagel

state: IA

address: 251 Bessey Hall

institute: Iowa State Univ.

description: Wild Gossypium hirsutum (var. yucatanensis), 7 Days Post-Anthesis fiber, replicate 1

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

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

data_processing: Raw expression values for each unigene represented on the chip were obtained by median polishing the seven redundant probes for each gene using Tukey’s Biweight estimator.  Then polished values were natural log transformed, median centered and scale normalized prior to statistical analysis.

organism: Gossypium hirsutum

source_name: fiber from Gossypium hirsutum var yucatanensis

label_protocol: Labeling was performed using Cy3 by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: 50% Canadian Spagum Peat : 40% Coarse Perlite : 10% Mineral Soil; sun and 10 hour day sodium supplemental lighting @ Pohl Conservatory Iowa State Univ.; harvest at maturity (20+ weeks)

extract_protocol: Hot-borate / Li precipitation method (see: Wan & Wilkins. 1994. Analytical Biochemistry 223: 7-12.), followed by linear RNA amplification (see: Hovav et al. 2008. Planta 227:319–329)

value: Wild

tag: variety

value: yucatanensis

tag: days post-anthesis fiber


title: papilloma_4121141A53_1_of_1


title: Nlrc5+/+ GM-DC, 4h

description: gene expression data from GM-CSF induced wild-type bone marrow dendritic cells infected with NDV, 4h after infection.

source_name: Dendritic cells induced from wild-type bone marrow cells under GM-CSF treatment, and infected with NDV for 4h.

tag: cell type

value: Nlrc5 +/+


title: Nlrc5-/- GM-DC, 4h

description: gene expression data from GM-CSF induced Nlrc5 KO bone marrow dendritic cells infected with NDV, 4h after infection.

source_name: Dendritic cells induced from Nlrc5 KO bone marrow cells under GM-CSF treatment, and infected with NDV for 4h.


title: Nlrc5+/+ GM-DC, 2h

description: gene expression data from GM-CSF induced wild-type bone marrow dendritic cells infected with NDV, 2h after infection.

source_name: Dendritic cells induced from wild-type bone marrow cells under GM-CSF treatment, and infected with NDV for 2h.


title: YUC.2DPA.R3

description: Wild Gossypium hirsutum (var. yucatanensis), 2 Days Post-Anthesis fiber, replicate 3


title: YUC.25DPA.R3

description: Wild Gossypium hirsutum (var. yucatanensis), 25 Days Post-Anthesis fiber, replicate 3


title: Nlrc5-/- GM-DC, 0h

description: gene expression data from GM-CSF induced Nlrc5 KO bone marrow dendritic cells infected with NDV, 0h after infection.

source_name: Dendritic cells induced from Nlrc5 KO bone marrow cells under GM-CSF treatment, and infected with NDV for 0h.


title: YUC.7DPA.R3

description: Wild Gossypium hirsutum (var. yucatanensis), 7 Days Post-Anthesis fiber, replicate 3


title: YUC.25DPA.R2

description: Wild Gossypium hirsutum (var. yucatanensis), 25 Days Post-Anthesis fiber, replicate 2


title: YUC.2DPA.R2

description: Wild Gossypium hirsutum (var. yucatanensis), 2 Days Post-Anthesis fiber, replicate 2


title: papilloma_412256350E_2_of_2

value: M


title: YUC.7DPA.R2

description: Wild Gossypium hirsutum (var. yucatanensis), 7 Days Post-Anthesis fiber, replicate 2


title: Nlrc5+/+ GM-DC, 0h

description: gene expression data from GM-CSF induced wild-type bone marrow dendritic cells infected with NDV, 0h after infection.

source_name: Dendritic cells induced from wild-type bone marrow cells under GM-CSF treatment, and infected with NDV for 0h.


title: YUC.2DPA.R1

description: Wild Gossypium hirsutum (var. yucatanensis), 2 Days Post-Anthesis fiber, replicate 1


title: YUC.20DPA.R3

description: Wild Gossypium hirsutum (var. yucatanensis), 20 Days Post-Anthesis fiber, replicate 3


title: papilloma_4122726431_1_of_2

value: White


title: YUC.10DPA.R2

description: Wild Gossypium hirsutum (var. yucatanensis), 10 Days Post-Anthesis fiber, replicate 2


title: YUC.20DPA.R1

description: Wild Gossypium hirsutum (var. yucatanensis), 20 Days Post-Anthesis fiber, replicate 1


title: YUC.20DPA.R2

description: Wild Gossypium hirsutum (var. yucatanensis), 20 Days Post-Anthesis fiber, replicate 2


title: papilloma_4121484549_1_of_1

description: Gene expression data from papillomas induced on dorsal back skin by DMBA/TPA


title: YUC.10DPA.R1

description: Wild Gossypium hirsutum (var. yucatanensis), 10 Days Post-Anthesis fiber, replicate 1


title: YUC.10DPA.R3

description: Wild Gossypium hirsutum (var. yucatanensis), 10 Days Post-Anthesis fiber, replicate 3


title: papilloma_412103373C_1_of_2


title: papilloma_412103373C_2_of_2


title: papilloma_41211B6A7F_1_of_2


title: papilloma_4121514D20_2_of_2


title: YUC.25DPA.R1

description: Wild Gossypium hirsutum (var. yucatanensis), 25 Days Post-Anthesis fiber, replicate 1


title: papilloma_412256350E_1_of_2


title: TM1.2DPA.R3

description: Domesticated Gossypium hirsutum cultivar TM1, 2 Days Post-Anthesis fiber, replicate 3

source_name: fiber from Gossypium hirsutum cv. TM1

value: Domesticated

tag: cultivar


title: TM1.7DPA.R3

description: Domesticated Gossypium hirsutum cultivar TM1, 7 Days Post-Anthesis fiber, replicate 3


title: papilloma_4121093316_2_of_2


title: TM1.7DPA.R1

description: Domesticated Gossypium hirsutum cultivar TM1, 7 Days Post-Anthesis fiber, replicate 1


title: papilloma_4122726431_2_of_2


title: papilloma_4121514D20_1_of_2


title: papilloma_4217037671_2_of_2


title: TM1.25DPA.R3

description: Domesticated Gossypium hirsutum cultivar TM1, 25 Days Post-Anthesis fiber, replicate 3


title: TM1.7DPA.R2

description: Domesticated Gossypium hirsutum cultivar TM1, 7 Days Post-Anthesis fiber, replicate 2


title: TM1.2DPA.R1

description: Domesticated Gossypium hirsutum cultivar TM1, 2 Days Post-Anthesis fiber, replicate 1


title: papilloma_4217037671_1_of_2


title: TM1.20DPA.R3

description: Domesticated Gossypium hirsutum cultivar TM1, 20 Days Post-Anthesis fiber, replicate 3


title: papilloma_4121093316_1_of_2


title: papilloma_412254163_1_of_2


title: TM1.2DPA.R2

description: Domesticated Gossypium hirsutum cultivar TM1, 2 Days Post-Anthesis fiber, replicate 2


title: TM1.10DPA.R2

description: Domesticated Gossypium hirsutum cultivar TM1, 10 Days Post-Anthesis fiber, replicate 2


title: papilloma_412254163_2_of_2


title: papilloma_417F00555F_1_of_2


title: TM1.25DPA.R1

description: Domesticated Gossypium hirsutum cultivar TM1, 25 Days Post-Anthesis fiber, replicate 1


title: TM1.25DPA.R2

description: Domesticated Gossypium hirsutum cultivar TM1, 25 Days Post-Anthesis fiber, replicate 2


title: papilloma_4120701425_1_of_2


title: papilloma_417E2B3451_1_of_1


title: TM1.20DPA.R1

description: Domesticated Gossypium hirsutum cultivar TM1, 20 Days Post-Anthesis fiber, replicate 1


title: papilloma_417F196739_2_of_2


title: TM1.10DPA.R3

description: Domesticated Gossypium hirsutum cultivar TM1, 10 Days Post-Anthesis fiber,replicate 3


title: TM1.20DPA.R2

description: Domesticated Gossypium hirsutum cultivar TM1, 20 Days Post-Anthesis fiber, replicate 2


title: papilloma_417F254972_1_of_1

description: Gene expression data from papillomas induced on dorsal back skin by DMBA/TPA


title: papilloma_4120701425_2_of_2


title: papilloma_4213156654_2_of_2


title: TM1.10DPA.R1

description: Domesticated Gossypium hirsutum cultivar TM1, 10 Days Post-Anthesis fiber, replicate 1


title: Blood_Septic_Patient_13_Replicate_1

city: Giessen

first: Hamid

last: Hossain

address: Frankfurter Str. 107

department: University of Giessen

country: Germany

institute: Institute for Medical Microbiology

description: Gene expression analysis in polytrauma patients.

hyb_protocol: Purified cRNA was fragmented in fragmentation buffer (40 mM Tris-acetate pH 7.9, 100 mM KOAc, 31.5 mM MgOAc) at 94C for 20 minutes. For hybridization on CodeLink bioarrays, 10 ug of fragmented cRNA in 260 ul of hybridization solution was added to each bioarray via the Flex Chamber port and incubated for 18 hours in a Minitron shaker incubator (Infors AG, Germany) at 37C, 300 rpm. cRNA was hybridized onto microarrays at least in duplicate (technical replicates).

scan_protocol: Bioarrays were scanned using the GenePix 4000 B scanner and the GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA).

data_processing: A total of 26 patient samples were subjected to microarrays with at least two technical replicates per sample (total 70 arrays). Spot signals of CodeLink bioarrays were quantified using CodeLink System Software Batch Submission (V2.2.27) and Expression Analysis (V2.2.25) (GE Healthcare) as outlined in the user's manual. CodeLink Expression Software 1.21 generated background-corrected raw as well as median-centered intra-slide normalized data. The intra-slide normalized data were used for further analysis. The software automatically calculated thresholds for intra-slide normalized intensities for each array and flagged genes as TRUE when the gene intensity was higher than the threshold or FALSE when the intensity was lower than the threshold. Furthermore, the software flagged each gene value as GOOD, EMPTY, POOR, NEG or MSR defining quality measures. Only gene values flagged as GOOD or EMPTY were used for the analysis. Patients (arrays) were separated into two groups: A) 13 patients with sepsis in the latter time course and B) 13 patients without sepsis. Genes with missing values in  >= 50% of all arrays in a group were excluded from the analysis. Genes that were flagged as FALSE and GOOD or EMPTY in > 50% of arrays in each group were also excluded from the analysis. In this Dataset (Set1), missing values were imputed using sequential K-nearest neighbor (SKNN) imputation (Kim et al. 2004). To detect outlier values for a particular gene in a group, all gene values > median + 3 standard deviations (SD) or < median -3 SD in a group were flagged as BLANK. Exempted from this rule were those gene values being consistently (more then 50% of a patient's technical replicates) > median + 3 SD or < median -3 SD; in this case, the remaining values were flagged as BLANK since the consistency of these values in more then 50% among technical replicates of the same sample was considered as a biological feature rather than a technical outlier. All gene values that were flagged as BLANK were removed in Set1, which was then subjected to SKNN imputation. Finally, this set of 8551 genes was normalized using quantile normalization in R (Bolstad et al. 2003) and logged (base 2).

source_name: peripheral blood, polytrauma

label_protocol: Total RNA was subjected to cDNA synthesis using a polyA-binding primer containing the T7-polymerase promoter (CodeLink Expression Assay Kit). Double-stranded DNA fragments were purified using the QIAquickTM PCR Purification Kit (Qiagen, Germany). For target labeling, the cDNA was in-vitro transcribed (IVT) by partially substituting UTP with bio-16-UTP in the reaction mixture. Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Germany). The eluted cRNA was quantified with NanoDrop (NanoDrop Technologies) and quality was assessed with the Agilent 2100 bioanalyser (Agilent Technologies GmbH).

extract_protocol: Total RNA was extracted from the PAXgene Blood RNA System (PreAnalytiX, Heidelberg, Germany) using the manufacturer's recommendations (PreAnalytiX). Total RNA was quantified with Nanodrop (NanoDrop Technologies, Rockland DE, USA) and the quality of RNA was assessed using the Agilent 2100 Bioanalyzer Bioanalyzer (Agilent Technologies GmbH, Boeblingen, Germany).

tag: Human peripheral blood collected with the PAXgene Blood RNA System (PreAnalytiX, Heidelberg, Germany)

tag: Posttraumatic course

value: Complicated by sepsis


title: Blood_Septic_Patient_13_Replicate_2


title: Blood_Septic_Patient_12_Replicate_1


title: papilloma_417F196739_1_of_2


title: papilloma_4213156654_1_of_2


title: papilloma_417F00555F_2_of_2


title: Blood_Septic_Patient_12_Replicate_2


title: papilloma_417E3F3431_1_of_1


title: Blood_Septic_Patient_10_Replicate_3


title: Blood_Septic_Patient_11_Replicate_2


title: Blood_Septic_Patient_11_Replicate_1


title: Blood_Septic_Patient_09_Replicate_3


title: papilloma_417F000558_1_of_2


title: papilloma_417F000558_2_of_2


title: Blood_Septic_Patient_08_Replicate_1


title: papilloma_417E3B343D_2_of_2


title: papilloma_417F001308_2_of_2


title: Blood_Septic_Patient_07_Replicate_2


title: Blood_Septic_Patient_07_Replicate_3


title: Blood_Septic_Patient_09_Replicate_2


title: Blood_Septic_Patient_10_Replicate_2


title: papilloma_412153120B_2_of_2


title: papilloma_4122537175_1_of_2


title: Blood_Septic_Patient_08_Replicate_2


title: papilloma_417E3B343D_1_of_2


title: papilloma_417F001308_1_of_2


title: Blood_Septic_Patient_08_Replicate_3


title: papilloma_4122537175_2_of_2


title: Blood_Septic_Patient_06_Replicate_3


title: Blood_Septic_Patient_10_Replicate_1


title: papilloma_4121081A64_2_of_2


title: Blood_Septic_Patient_06_Replicate_2


title: papilloma_412153120B_1_of_2


title: papilloma_412112404D_1_of_2


title: Blood_Septic_Patient_05_Replicate_3


title: papilloma_4121081A64_1_of_2


title: papilloma_412112404D_2_of_2


title: Blood_Septic_Patient_04_Replicate_3


title: Blood_Septic_Patient_06_Replicate_1


title: Blood_Septic_Patient_04_Replicate_1


title: Blood_Septic_Patient_04_Replicate_2


title: Blood_Septic_Patient_02_Replicate_3


title: Blood_Septic_Patient_03_Replicate_1


title: Blood_Septic_Patient_03_Replicate_3


title: papilloma_4121340F03_1_of_2


title: Blood_Septic_Patient_09_Replicate_1


title: papilloma_40674E112D_1_of_2


title: papilloma_412156293F_2_of_2


title: papilloma_4121194F22_1_of_2


title: Blood_Septic_Patient_02_Replicate_2


title: papilloma_4121192A61_2_of_2


title: papilloma_4121340F03_2_of_2


title: Blood_Septic_Patient_05_Replicate_2


title: papilloma_4121194F22_2_of_2


title: Blood_Septic_Patient_05_Replicate_1


title: papilloma_4121192A61_1_of_2


title: papilloma_412156293F_1_of_2


title: papilloma_41211B6A7F_2_of_2


title: Blood_Septic_Patient_01_Replicate_3


title: Blood_Septic_Patient_02_Replicate_1


title: Blood_Septic_Patient_01_Replicate_2


title: papilloma_412115080D_2_of_2


title: Blood_Septic_Patient_01_Replicate_1


title: Blood_NonSeptic_Patient_13_Replicate_2

value: Not complicated by sepsis


title: papilloma_41212C0A01_2_of_2


title: papilloma_40674E112D_2_of_2


title: papilloma_412115080D_1_of_2


title: papilloma_41212C0A01_1_of_2


title: Blood_NonSeptic_Patient_13_Replicate_1


title: Blood_NonSeptic_Patient_12_Replicate_2


title: Blood_NonSeptic_Patient_11_Replicate_2


title: papilloma_4123071F02_2_of_2


title: Blood_NonSeptic_Patient_11_Replicate_1


title: papilloma_41211A1A6F_2_of_2


title: papilloma_4123071F02_1_of_2


title: Blood_NonSeptic_Patient_10_Replicate_3


title: papilloma_41211A1A6F_1_of_2


title: Blood_NonSeptic_Patient_09_Replicate_2


title: Blood_NonSeptic_Patient_12_Replicate_1


title: Blood_NonSeptic_Patient_10_Replicate_1


title: Blood_NonSeptic_Patient_10_Replicate_2


title: papilloma_4121057439_2_of_2


title: papilloma_4121057439_1_of_2


title: Blood_NonSeptic_Patient_09_Replicate_3


title: papilloma_41214F7246_1_of_2


title: Blood_NonSeptic_Patient_09_Replicate_1


title: papilloma_41214F7246_2_of_2


title: Blood_NonSeptic_Patient_08_Replicate_3


title: Blood_NonSeptic_Patient_08_Replicate_2


title: carcinoma_41215B6D13_1

hyb_protocol: 200 microliters of hybridization sample were incubated in the Affymetrix Hybridization Oven 640 instrument for 16 hours at 45C with 60 rpm rotation. Arrays were processed with the Affymetrix Fluidics Station 450 instrument, using the FS450_0001 fluidics script and GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: The Affymetrix GCS3000 7G instrument was used to acquire the microarray image data

source_name: carcinoma induced on FVBBX dorsal back skin by DMBA/TPA

extract_protocol: Trizol followed by Qiagen RNEasy clean-upl

tag: dx

value: SCC

tag: differentiation

value: poor

tag: valid


title: carcinoma_41207A546C_1

value: well

tag: origin


title: carcinoma_4121683825_1

value: [SPRET/Ei X FVB/N] X FVB/N

tag: cage


title: Blood_NonSeptic_Patient_07_Replicate_1


title: Blood_NonSeptic_Patient_07_Replicate_2


title: Blood_NonSeptic_Patient_06_Replicate_2


title: Blood_NonSeptic_Patient_07_Replicate_3


title: Blood_NonSeptic_Patient_08_Replicate_1


title: Blood_NonSeptic_Patient_06_Replicate_3


title: carcinoma_412254163_1

value: mod

tag: sex


title: Blood_NonSeptic_Patient_06_Replicate_1


title: carcinoma_4121663E37_1

value: F

tag: coat


title: carcinoma_4217037671_1

tag: strain


title: carcinoma_41247A0B40_1_1

value: Agouti


title: carcinoma_41247A0B40_1_2


title: carcinoma_4217072C08_1

value: spindle


title: carcinoma_4100614925_1


title: Blood_NonSeptic_Patient_05_Replicate_3


title: carcinoma_4122726431_1


title: carcinoma_417F254972_1


title: Blood_NonSeptic_Patient_04_Replicate_3


title: Blood_NonSeptic_Patient_04_Replicate_1


title: Blood_NonSeptic_Patient_04_Replicate_2


title: Blood_NonSeptic_Patient_05_Replicate_2


title: Blood_NonSeptic_Patient_02_Replicate_3


title: carcinoma_4120762510_1


title: carcinoma_417E3F3431_1


title: Blood_NonSeptic_Patient_03_Replicate_1


title: carcinoma_4122702E5D_1


title: Blood_NonSeptic_Patient_03_Replicate_2


title: carcinoma_4120627743_1


title: Blood_NonSeptic_Patient_01_Replicate_3


title: Blood_NonSeptic_Patient_03_Replicate_3


title: Blood_NonSeptic_Patient_05_Replicate_1


title: carcinoma_4122660C6D_1


title: carcinoma_417F00555F_1


title: carcinoma_417E2B3451_1


title: Blood_NonSeptic_Patient_02_Replicate_2


title: carcinoma_4122537175_1


title: carcinoma_417F000558_1


title: carcinoma_412254156A_2


title: carcinoma_41214E6B49_1


title: carcinoma_417F001308_1


title: carcinoma_417E3B343D_1


title: Blood_NonSeptic_Patient_02_Replicate_1


title: carcinoma_41205E4B42_1


title: carcinoma_41207B5D1D_1


title: carcinoma_41212B6361_2


title: carcinoma_412254156A_1


title: carcinoma_4121533C60_1


title: Blood_NonSeptic_Patient_01_Replicate_2

tag: Human peripheral blood collected with the PAXgene Blood RNA System (PreAnalytiX, Heidelberg, Germany).


title: Blood_NonSeptic_Patient_01_Replicate_1


title: carcinoma_412153120B_1


title: carcinoma_41212B6361_1


title: carcinoma_412112404D_1


title: carcinoma_4121340F03_1


title: carcinoma_4121134677_1


title: Peripheral blood mononuclear cells (PBMC)-Patient GM T0

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

institute: University of Bari

description: We used the default settings of GCOS software to scan the chips

hyb_protocol: Affymetrix GeneChips Human Genome U133 Array Set HG-U133A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions

data_processing: We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.

source_name: PBMC GM T0

label_protocol: The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions. The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays.

growth_protocol: Before RNA extraction, cells were thaw, counted and their viability determined by Trypan Blue exclusion (>90% PBMC were viable). A minimum of 5 milion cryopreserved PBMC were centrifuged, and immediately lysed for RNA extraction.

extract_protocol: Total RNA was extracted by RNeasy mini kit (QIAGEN Inc., Valencia, CA) according to the manufacturer’s instructions and resuspended in DEPC-treated Rnase-free distilled water. RNA concentration was determined by NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and its integrity was assessed by electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: PBMC were immediately isolated from 20 ml of whole blood by Ficoll–Hypaque (Flow Laboratories, Irvine, UK) density gradient centrifugation. Isolated cells were stored at –80°C in FBS+10% DMSO until use.

tag: Patient GM, stable renal transplant recipients, female, 53 years old, T0 (time of enrollment)


title: Peripheral blood mononuclear cells (PBMC)-Patient GM T1

scan_protocol: We used the default settings of GCOS software to scan the chips

source_name: PBMC GM T1

tag: Patient GM, stable renal transplant recipients, female, 53 years old, T1 (3 months after the switching of the therapy)


title: Peripheral blood mononuclear cells (PBMC)-Patient SE T1

source_name: PBMC SE T1

tag: Patient SE, stable renal transplant recipients, male, 31 years old, T1 (3 months after the switching of the therapy)


title: carcinoma_41212B5706_1


title: carcinoma_4121194F22_1


title: carcinoma_4121141A53_1


title: carcinoma_412156293F_1


title: Peripheral blood mononuclear cells (PBMC)-Patient SE T0

source_name: PBMC SE T0

tag: Patient SE, stable renal transplant recipients, male, 31 years old, T0 (time of enrollment)


title: carcinoma_412154011D_1


title: Peripheral blood mononuclear cells (PBMC)-Patient CV T1

source_name: PBMC CV T1

tag: Patient CV, stable renal transplant recipients, male, 58 years old, T1 (3 months after the switching of the therapy)


title: carcinoma_412115080D_1


title: carcinoma_4121192A61_1


title: carcinoma_41211B6A7F_1


title: Peripheral blood mononuclear cells (PBMC)-Patient CV T0

source_name: PBMC CV T0

tag: Patient CV, stable renal transplant recipients, male, 58 years old, T0 (time of enrollment)


title: carcinoma_40674E112D_1


title: carcinoma_4121362436_1


title: carcinoma_4123071F02_1


title: carcinoma_41212C0A01_1


title: Peripheral blood mononuclear cells (PBMC)-Patient CCo T0

source_name: PBMC CCo T0

tag: Patient CCo, stable renal transplant recipients, male, 38 years old, T0 (time of enrollment)


title: Peripheral blood mononuclear cells (PBMC)-Patient CCa T1

source_name: PBMC CCa T1

tag: Patient CCa, stable renal transplant recipients, female, 70 years old, T1 (3 months after the switching of the therapy)


title: Peripheral blood mononuclear cells (PBMC)-Patient CCa T0

source_name: PBMC CCa T0

tag: Patient CCa, stable renal transplant recipients, female, 70 years old, T0 (time of enrollment)


title: carcinoma_41216B4F5F_1

tag: dx

tag: differentiation


title: carcinoma_41211A1A6F_1

tag: valid

tag: origin


title: carcinoma_41214E3C43_1

tag: cage

tag: sex


title: carcinoma_4121514D20_3

tag: strain

tag: coat


title: Peripheral blood mononuclear cells (PBMC)-Patient CCo T1

source_name: PBMC CCo T1

tag: Patient CCo, stable renal transplant recipients, male, 38 years old, T1 (3 months after the switching of the therapy)


title: carcinoma_4121514D20_2


title: carcinoma_4121484549_1


title: CB_RA-pos_CB_CB023

city: Stanford

first: Ash

middle: A

last: Alizadeh

address: 269 Campus Drive, CCSR 1145c

department: Medicine, Divisions of Hematology and of Oncology

institute: Stanford University School of Medicine

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were normalized using MAS5

source_name: umbilical cord blood

label_protocol: Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual

extract_protocol: Total RNA was extracted using TRIzol reagent containing either glycogen or linear acrylamide according to the manufacturer's protocol, and then treated with DNaseI (Ambion).

tag: patient

tag: age group

value: fetus

tag: disease state

value: normal

tag: cell source

value: umbilical cord blood

tag: cell type (purified cell subset)


title: carcinoma_4121057439_1_2


title: carcinoma_4020685C21_1


title: BM_RA-pos_BM_NBM1440

source_name: bone marrow

value: adult

value: bone marrow


title: carcinoma_41214F7246_1

value: M

value: White


title: MXEMB_N2_RNA_EXPRESSION extraction4_array1 channel_1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Hybridizations to microarrays were performed using NimbleGen Hybridization System. Details can be found at manufacturer?s web site: http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf

scan_protocol: Scanning one-color NimbleGen arrays was done with a GenePix 4000B Scanner and associated software. Details can be found at manufacturer?s web site: http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf

data_processing: NimbleGen RNA data normalization:JL:1 protocol. This protocol describes a procedure to generate a normalized gene expression value (per gene) from raw data. Input files are raw one-color signal data per probe having XXX_532_pair.txt file extension. Output files are normalized expression value data per gene having XXX_RMA_calls.txt file extension. If the microarray platform is a 4-plex microarray (i.e. 4 arrays per a slide), there are 4 such input files and 4 such output files. This procedure is performed through NimbleScan software's function "RMA analysis" as described in NimbleGen Array User's Guide: Gene Expression Array's v5.0 (http://www.nimblegen.com/products/lit/expression_userguide_v5p0.pdf). For signal normalization, this procedure uses quantile normalization as described in Bolstad B, et al. (Bioinformatics, 19:185-193, 2003). To call a single expression value per gene from multiple probes, the software uses Robust Multichip Average (RMA) algorithm as described in Irizarry R. et al. (Biostatistics 4:249-264, 2003).  Processed data are obtained using following parameters: genome version is WS170

label: Cy3 dye

organism: Caenorhabditis elegans

label_protocol: Invitrogen Superscript Double-Stranded cDNA Synthesis Kit was used to synthesize double-stranded cDNA from 10 ug total RNA or 1 ug Poly-A RNA. 1 ug of cDNA was used for labeling with NimbleGen One-Color DNA Labeling Kit. Details can be found at manufacturer?s web site: http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol: Worm_RNA_extraction_v1. Sample in 10V Trizol was thawed at 37C, vortexed 30 seconds and re-frozen in liquid nitrogen. Freeze-cracking was repeated a total of four times. 1/5 V chloroform was added and vortexed for 30 seconds. After centrifugation of the sample at 13000 rpm for 5 minutes, aqueous phase containing RNA was recovered. RNA was precipitated by mixing with 0.8V isopropanol and incubation on ice, followed by centrifugation at 13000 rpm at 4C for 20 minutes. RNA was washed with 75% ethanol, dissolved in DEPC H2O and cleaned up using Qiagen RNeasy kit.

tag: developmental stage

value: Mixed Embryo

tag: genotype

value: wild type

tag: Sex

value: mixed Male and Hermaphrodite population


title: CB_RA-pos_CB_CB008


title: CB_RA-pos_CB_CB020


title: carcinoma_4122793F43_1

tag: dx

value: poor


title: US22502595_251269411211

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: Granulomas were isolated from tissue sections using a PALM Zeiss laser capture microdissection apparatus (Carl Zeiss, Jena, Germany) immediately after staining. Adhesive caps were used to collect multiple microdissected granulomas from 3-8 lung sections from each of three mice. Granulomas from a single mouse were digested with proteinase K solution overnight at 55°C.

hyb_protocol: 1.25 µg of each labeled cRNA was mixed, fragmented and hybridized to whole mouse genome 44k microarrays (Product no. G4122A) according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies). Features were extracted with an image analysis tool Version A4.045 (Agilent Technologies) using default settings.

data_processing: Data analysis was carried out on the Rosetta Inpharmatics (Seattle, WA, USA) platform (Resolver Built 3.0.0.3.22). Features detected as differentially regulated with a P-value ≤ 0.05 and at least ± 2-fold difference in signal intensity in both experiments were included in datasets. Datasets containing the GenBank accession numbers and fold changes were uploaded into Ingenuity pathway analysis software (Ingenuity Systems, Redwood City, CA, USA).

source_name: LCM Inf 5 week 4 B6

label_protocol: A total of 4 µg RNA was reverse transcribed using an oligo-dT-T7-promotor primer in a fluorescent linear amplification reaction (Agilent Technologies, Santa Clara, CA, USA). cRNA was labeled with Cyanine 3-CTP or Cyanine 5-CTP (NEB Life Science Products) in a T7 polymerase amplification reaction according to the supplier’s protocol.

extract_protocol: RNA was isolated using Paradise reagents and spin columns according to manufacturer’s instructions. RNA was quantified and measured for purity using a NanoSpec (Nanometrics, Sunnyvale, CA, USA).

tag: cell type

value: Granuloma

tag: protocol

value: Infected

tag: biological replicate

tag: time

value: week 4

value: wt C57BL/6

source_name: LCM Inf 5 week 6 B6

value: week 6


title: carcinoma_4121093316_1

value: [SPRET/Ei X FVB/N] X FVB/N

value: SCC

tag: differentiation

value: mod

tag: valid

tag: origin

tag: cage

tag: sex

value: F


title: US22502595_251269411209

source_name: LCM control Naive week 5 pool

value: control Naive

value: week 5

tag: strain


title: carcinoma_4121057439_1_1

value: well

value: M

tag: coat


title: MXEMB_N2_RNA_EXPRESSION extraction3_array1 channel_1

value: Mixed Embryo


title: US22502595_251269411212


title: carcinoma_412103373C_1

value: White


title: US22502595_251269411208

description: Granulomas were isolated from tissue sections using a PALM Zeiss laser capture microdissection apparatus (Carl Zeiss, Jena, Germany) immediately after staining. Adhesive caps were used to collect multiple microdissected granulomas from 3–8 lung sections from each of three mice. Granulomas from a single mouse were digested with proteinase K solution overnight at 55°C.

source_name: LCM Inf 4 week 6 B6

source_name: LCM Inf 4 week 4 B6


title: MXEMB_N2_RNA_EXPRESSION extraction2_array1 channel_1

growth_protocol: Worm_embryo_growth_and_harvest_v3. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol: Worm_embryo_RNA_extraction_v1. Embryo suspension in Trizol was brought to room temperature and vigorously mixed with one-fifth volume of chloroform. After centrifugation of the sample at 13000 rpm for 5 minutes, aqueous phase containing RNA was recovered. RNA was precipitated by 2-propanol, washed with 75% ethanol and dissolved in DEPC H2O. Quality of RNA was assessed by non-denatured agarose gel electrophoresis.

value: wild type

value: mixed Male and Hermaphrodite population


title: knockout mouse kidney - 3

city: london

first: Patrick

middle: J

last: Pollard

address: POBOX 123

country: United Kingdom

institute: Cancer Research UK

description: Macro-dissected renal cystic epithelial tissue from Fh1 knockout mouse

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: cel files were quantile normalized and signal estimates generated using RMA (Affymetrix package, Bioconductor)

source_name: murine kidney, cystic epithelial tissue,  Fh1 knockout mouse

label_protocol: standard Affymetrix procedures

extract_protocol: Column purification (SIGMA)


title: BM_MPP_BM_NBM1483

tag: patient

tag: age group

value: adult

tag: disease state

value: normal

tag: cell source

value: bone marrow


title: MXEMB_N2_RNA_EXPRESSION extraction1_array1 channel_1

tag: developmental stage

tag: genotype

tag: Sex


title: US22502595_251269411255

tag: cell type

value: Granuloma

tag: protocol

value: Infected

value: week 4

value: wt C57BL/6


title: knockout mouse kidney - 1

tag: Macro-dissected renal cystic epithelial tissue from Fh1 knockout mouse


title: Bombyx mori Middle Silk Gland SAGE library

type: SAGE

anchor: NlaIII

city: Villeurbanne

first: Pierre

middle: Marie

last: Couble

address: 16 rue Dubois

department: Biology - INSB

institute: CNRS-University Lyon 1

description:
Total RNA extracted prior to oligo-dT mRNA extraction.
RNAs controlled for quality and quantity on a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Tags  extracted from PSG library (3072 sequenced inserts) with the Sagenhaft software (Beissbarth et al., 2004) then identified with Identitag (Keime et al., 2004).

organism: Bombyx mori

source_name: Middle Silk Gland of Bombyx mori, fith instar, day 3

growth_protocol: Animals fed on fresh mulberry leaves

extract_protocol: Total RNA  extracted using Tri-Reagent (Sigma, USA).

tag: organism

value: Bombyx mori

tag: tissue

value: Middle Silk gland

value: F1 hybrids of 200 and 300

tag: stage

value: day 3, fifth instar


title: US22502595_251269411210

tag: biological replicate

tag: time

value: control Naive

value: week 5


title: BM_MPP_BM_NBM1481

tag: cell type (purified cell subset)


title: wild-type mouse kidney - 3

description: Macro-dissected renal epithelial tissue from wild-type littermate controls

source_name: murine kidney, wild-type littermate controls


title: BM_MPP_BM_NBM1444


title: Bombyx mori Posterior Silk Gland SAGE library

source_name: Posterior Silk Gland of Bombyx mori, fith instar, day 3

value: posterior silk glands

tag: strain


title: wild-type mouse kidney - 1

tag: Macro-dissected renal epithelial tissue from wild-type littermate controls


title: US22502595_251269411254


title: BM_MPP_BM_NBM1440

tag: patient

tag: age group


title: CENPK_Galactose_rep2

city: Gothenburg

first: wanwipa

last: vongsangnak

address: Kemivägen 10

department: Department of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

hyb_protocol: Array hybridization to Affymetrix Yeast Genome Y2.0 arrays were performed according to the manufacturer’s recommendations (Affymetrix GeneChip® Expression Analysis Technical Manual, 2005-2006 Rev. 2.0).

scan_protocol: Washing and staining of arrays were performed using the GeneChip Fluidics Station 450 and scanning with the Affymetrix GeneArray Scanner (Affymetrix, Santa Clara, CA).

data_processing: Affymetrix Microarray Suite v5.0 was used to generate CEL files of the scanned DNA microarrays.  These CEL files were then processed using the statistical language and environment R v5.3 (R Development Core Team, 2007, www.r-project.org), supplemented with Bioconductor v2.3 (Biconductor Development Core Team, 2008, www.bioconductor.org) packages Biobase, affy, gcrma, and limma (Smyth, 2005).  The probe intensities were normalized for background using the robust multiarray average (RMA) method only using perfect match (PM) probes after the raw image file of the DNA microarray was visually inspected for acceptable quality.  Normalization was performed using the qspline method and gene expression values were calculated from PM probes with the median polish summary. Statistical analysis was applied to determine differentially expressed genes using the limma statistical package.  Moderated t-tests between the sets of experiments were used for pair-wise comparisons.  Empirical Bayesian statistics were used to moderate the standard errors within each gene and Benjamini-Hochberg’s method was used to adjust for multi-testing.  A cut-off value of adjusted p<0.01 was used for statistical significance (Smyth, 2000).

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae grown on galactose medium

label_protocol: Labeling was performed according to the manufacturer’s recommendations (Affymetrix GeneChip® Expression Analysis Technical Manual, 2005-2006 Rev. 2.0).

extract_protocol: Total RNA was extracted using the FastRNA Pro RED kit (QBiogene, Carlsbad, USA) according to manufacturer’s instructions.

tag: culture condition

value: grown on galactose medium


title: knockout mouse kidney - 2


title: CENPK_Galactose_rep1


title: 129S1/SvImJ Oct4-EGFP+ cells_2

city: Bar Harbor

first: Steven

middle: C

last: Munger

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

hyb_protocol: 750ng of biotin-labelled cRNA was hybridized to MouseRef-8 v2.0 Expression BeadChips (Illumina BD-202-0202) according to Illumina protocols.

scan_protocol: BeadChips were scanned on the iScan BeadArray Reader (Illumina) following Illumina protocols.

data_processing: Raw probe level data was imported into GenomeStudio (Illumina) software, average normalized, and the background signal level was subtracted out. Genes that were not detected in at least one sample (detection p-value cutoff = 0.05) were removed from the analysis. The Illumina custom error model with false discovery rate (FDR) correction was applied to detect genes that were differentially expressed between strains. Expression differences were considered significant if the calculated Diffscore was ± 13 (equivalent to a p-value < 0.05).

source_name: germ cells

label_protocol: Total RNA was reverse transcribed to cDNA and then transcribed in vitro into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion #AMIL1791) according to manufacturer’s protocols.

extract_protocol: Total RNA was extracted from Oct4-EGFP+ sorted germ cell populations (C57BL/6J n=3, 129/SvJ n=2) using the RNeasy Micro kit (Qiagen #74004) with on-column DNase digestion according to manufacturer’s protocols.

tag: developmental stage

value: embryo

tag: age

tag: gender

value: XY

value: embryonic male gonads

value: germ cells

tag: testicular teratoma susceptibility

value: susceptible


title: CENPK_Glucose_rep2

source_name: Saccharomyces cerevisiae grown on glucose medium

value: grown on glucose medium


title: CENPK_Glucose_rep1


title: S288c_Galactose_rep2


title: iNOS d60 lung vs. iNOS d60 aIFNg lung

description: Microarray experiments were performed as dual-color hybridizations. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

hyb_protocol: Whole mouse genome 44k microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol Version 4.1

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies) and default settings (GE2-v4_95_Feb07).

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.9.5.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware, Build 6.1 (Rosetta Biosoftware).

source_name: iNOS d60 lung

label_protocol: RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled either with Cyanine 3-CTP.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen) using Glycogen as carrier.

treatment_protocol: The ear dermis of NOS2-/- knock-out (iNOS) mice was infected with 1e+4 c.f.u. Mtb in a volume of 10 µl. Mice were sacrificed at day 60 and lungs were  removed aseptically for total RNA preparation.

value: NOS2-/- knock-out (iNOS)

source_name: iNOS d60 aIFNg lung

label_protocol: RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled either with Cyanine 5-CTP.

treatment_protocol: The ear dermis of NOS2-/- knock-out (iNOS) mice was infected with 1e+4 c.f.u. Mtb in a volume of 10 µl. For antibody treatment, dermal infected mice were administered 500 µg XMG1.2 (ATCC) (anti-interferon gamma, aIFNg) in PBS intraperitoneally on day 7 and day 14 post infection.Mice were sacrificed at day 60 and lungs were  removed aseptically for total RNA preparation.


title: S288c_Galactose_rep1


title: CB_MPP_CB_CB023

value: fetus

tag: disease state

value: normal

tag: cell source

value: umbilical cord blood


title: 129S1/SvImJ Oct4-EGFP+ cells_1

tag: cell type


title: CB_MPP_CB_CB020


title: CB_MPP_CB_CB009


title: S288c_Glucose_rep1


title: C57BL/6J Oct4-EGFP+ cells_3

tag: tissue

value: resistant


title: C57BL/6J Oct4-EGFP+ cells_2


title: CB_MPP_CB_CB008


title: No-IP input DNA

type: genomic

city: Hong Kong

first: Yuk Ming

middle: Dennis

last: Lo

address: The Prince of Wales Hospital

department: Department of Chemical Pathology

institute: The Chinese University of Hong Kong

hyb_protocol: The labeled product was hybridized to the GeneChip® Human Tiling 2.0R Arrays according to manufacturer's standard procedures

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G.

data_processing:
Analysis with Tiling Array Software (TAS) version 1.1 (TAS): The CEL files of each sample were processed by TAS to calculate the signal of each IP-sample/no-IP control ratios within a 800-bp sliding window. The signal of each sample at a particular locus was normalized to give an average value of 1.00 for all loci. The signals of the 5 placentas were compared with those of the 5 maternal blood cells to calculate a signal log ratio. The resultant BED files were given as an EXCEL (Name: TAS_placenta vs blood cells_Signal_Log_Ratio_BED). Analysis with the Model-based Analysis of Tiling array (MAT): the CEL files of the 5 placentas were the TEST group while the CEL files of the 5 maternal blood cells were the CONTROL group when processed by MAT. The algorithms calculated the P-value to determine if there was significant difference between the signals of the two groups.
The BED format file of each MeDIP sample processed by TAS contain the average signal of IP-sample/no-IP control ratios within a 800-bp sliding window. The additional result file "TAS_placenta vs blood cells_Signal_Log_Ratio_BED" contains the signal log ratio of 5 placenta compared with 5 maternal blood cells.

molecule: genomic DNA

source_name: No-IP input DNA

label_protocol: Extracted DNA was sonicated and immunoprecipitated by antibody against 5-methylcytosines (Adcam, cat# 1884). The subsequent product was amplified and labeled using the dsDNA terminal labeling kit (Affymetrix)

extract_protocol: DNA was extracted from maternal peripheral blood cells using the Nucleon Blood DNA extraction kit (GE Healthcare-Biosciences) and from CVS and placental tissues using the QIAamp Tissue Kit (Qiagen).

tag: gestation

value: 1st trimester

value: Placental tissues (obtained via chorionic villus sampling)


title: BM_MEP_BM_NBM1483

value: adult

value: bone marrow


title: Maternal blood cells MeDIP DNA 5

source_name: Maternal blood cells MeDIP DNA

value: maternal blood cells


title: iNOS d30 aIFNg lung vs. iNOS d30 lung

source_name: iNOS d30 aIFNg lung

treatment_protocol: The ear dermis of NOS2-/- knock-out (iNOS) mice was infected with 1e+4 c.f.u. Mtb in a volume of 10 µl. For antibody treatment, dermal infected mice were administered 500 µg XMG1.2 (ATCC) (anti-interferon gamma, aIFNg) in PBS intraperitoneally on day 7 and day 14 post infection.Mice were sacrificed at day 30 and lungs were  removed aseptically for total RNA preparation.

source_name: iNOS d30 lung

treatment_protocol: The ear dermis of NOS2-/- knock-out (iNOS) mice was infected with 1e+4 c.f.u. Mtb in a volume of 10 µl. Mice were sacrificed at day 30 and lungs were  removed aseptically for total RNA preparation.


title: iNOS d30 lung vs. iNOS d30 aIFNg lung

treatment_protocol: The ear dermis of NOS2-/- knock-out (iNOS) mice was infected with 1e+4 c.f.u. Mtb in a volume of 10 μl. Mice were sacrificed at day 30 and lungs were  removed aseptically for total RNA preparation.

treatment_protocol: The ear dermis of NOS2-/- knock-out (iNOS) mice was infected with 1e+4 c.f.u. Mtb in a volume of 10 μl. For antibody treatment, dermal infected mice were administered 500 µg XMG1.2 (ATCC) (anti-interferon gamma, aIFNg) in PBS intraperitoneally on day 7 and day 14 post infection.Mice were sacrificed at day 30 and lungs were  removed aseptically for total RNA preparation.


title: S288c_Glucose_rep2


title: B6 d30 lung vs. B6 d30 aIFNg lung

source_name: B6 d30 lung

treatment_protocol: The ear dermis of C57BL/6 wild-type (B6) mice was infected with 1e+4 c.f.u. Mtb in a volume of 10 μl. Mice were sacrificed at day 30 and lungs were  removed aseptically for total RNA preparation.

value: C57BL/6 wild-type

source_name: B6 d30 aIFNg lung

treatment_protocol: The ear dermis of C57BL/6 wild-type (B6) mice was infected with 1e+4 c.f.u. Mtb in a volume of 10 Î¼l. For antibody treatment, dermal infected mice were administered 500 µg XMG1.2 (ATCC) (anti-interferon gamma, aIFNg) in PBS intraperitoneally on day 7 and day 14 post infection. Mice were sacrificed at day 30 and lungs were  removed aseptically for total RNA preparation.


title: BM_MEP_BM_NBM1444

source_name: bone marrow


title: C57BL/6J Oct4-EGFP+ cells_1

value: embryo


title: Maternal blood cells MeDIP DNA 4


title: B6 d30 aIFNg lung vs. B6 d30 lung

treatment_protocol: The ear dermis of C57BL/6 wild-type (B6) mice was infected with 1e+4 c.f.u. Mtb in a volume of 10 μl. For antibody treatment, dermal infected mice were administered 500 µg XMG1.2 (ATCC) (anti-interferon gamma, aIFNg) in PBS intraperitoneally on day 7 and day 14 post infection. Mice were sacrificed at day 30 and lungs were  removed aseptically for total RNA preparation.


title: wild-type mouse kidney - 2


title: iNOS d60 aIFNg lung vs. iNOS d60 lung


title: BM_MEP_BM_NBM1481


title: Maternal blood cells MeDIP DNA 3


title: B6 d30 lung vs. iNOS d30 lung


title: Hp mut5_8 vs. Hp wtG27

description: Microarray experiments were carried out as two-color hybridizations with a color-swap dye-reversal setting to compensate Cy-dye specific effects and to ensure statistically relevant data.

hyb_protocol: Cy3 and Cy5 labeled RNA samples (1.5 µg each) were pooled, heat denatured and mixed with hybridization buffer SlideHyb #3 (Ambion). Hybridization was performed in a humidified hybridization chamber for 16 h submerged in a 50°C water bath with LifterSlipsTM (Erie Scientific). Slides were washed twice with the first and low stringency washing buffer (2 × SSC, 0.1% SDS) for 10 min at 50°C, followed by the second washing buffer (0.5 × SSC, 0.1% SDS) for 10 min at 50°C and the third washing buffer (0.05 × SSC) for 5 min at 37°C.

scan_protocol: Slides were scanned with 10µm resolution using a  Agilent G2565AA scanner and default settings. Image Analysis / Feature Extraction software G2567AA (Version A.7.5.1 and A.9.5 ) using almost default settings for microarrays loaded with a grid file. Only the constant coefficient of variation for features and background was raised 5 fold. Intensities were normalized by local background correction and by rank consistency filtering with LOWESS normalization. The log intensity ratios were calculated by using the most conservative estimate of error between Universal Error Model and propagated error.

data_processing: Data analysis was carried out on the Rosetta Inpharmics platform Resolver Version 7.0. Ratio profiles were combined in an error-weighted fashion with Resolver to create ratio experiments. A twofold change expression threshold for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis set highly significant (P-value < 0.05), robust and reproducible.

organism: Helicobacter pylori

source_name: Hp mut5_8

label_protocol: Total RNA was labeled with ULS according the suppliers' protocol (http://tinyurl.com/c2jgfk).

extract_protocol: Bacterial cells grown on GC agar plates were scraped and washed with PBS twice. Total RNA was prepared with TRIzol® Reagents according the suppliers' protocol, using Glycogen as carrier (http://tinyurl.com/blu4uk). Samples were DNAse treated before labeling.

tag: The H. pylori G27 mutant 5_8 was grown on GC agar plates (Oxoid, Wesel, Germany) supplemented with 10% fetal bovine serum (FBS), vancomycin (10 mg/l), amphotericin B (4 mg/l) in a CO2 gas jar with a CampyPack (Oxoid) at 37ºC for 48 h.

source_name: Hp wtG27

tag: H. pylori wild-type G27 was grown on GC agar plates (Oxoid, Wesel, Germany) supplemented with 10% fetal bovine serum (FBS), vancomycin (10 mg/l), amphotericin B (4 mg/l) in a CO2 gas jar with a CampyPack (Oxoid) at 37ºC for 48 h.


title: ZNF145 MSC, biological rep2 (H5Z-1)

city: Singapore

first: Tongming

last: Liu

address: 60 Biopolis street

department: Cancer stem group

institute: Genome Institute of Singapore

description:
Gene expression data from patient 2 ZNF145-MSCs
H5Z-1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on HG_U133_plus 2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GenechipR Scanner 3000.

data_processing: The data were analyzed with Genespring Ver 7.3 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Human ZNF145-MSCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Human MSCs are isolated and purified from bone marrow, and cultured under standard condition.

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

treatment_protocol: Human primary MSCs are infected with lentivirus for overexpressing ZNF145 to generate ZNF145-MSCs

value: mesenchymal stem cells (MSCs)

tag: genotype/variation


title: iNOS d30 lung vs. B6 d30 lung

tag: strain


title: Maternal blood cells MeDIP DNA 2


title: AML_LSC_PB_SU031

source_name: peripheral blood

value: AML

value: peripheral blood

tag: cell type (purified cell subset)


title: Hp wtG27 vs. Hp mut5_8


title: ZNF145 MSC, biological rep2 (H5Z-2)

description:
Gene expression data from patient 2 ZNF145-MSCs
H5Z-2

tag: patient


title: Placenta MeDIP DNA 5

source_name: Placenta MeDIP DNA


title: AML_LSC_TLA_SU018

source_name: therapeutic leukapheresis

tag: age group

value: therapeutic leukapheresis


title: AML_LSC_TLA_SU032


title: ZNF145 MSC, biological rep1 (H4Z-2)

description:
Gene expression data from patient 1 ZNF145-MSCs
H4Z-2


title: Placenta MeDIP DNA 4


title: AML_LSC_TLA_SU014


title: AML_LSC_TLA_SU008


title: Control MSC, biological rep2 (H5D-1)

description:
Gene expression data from patient 2 control MSCs
H5D-1

source_name: Human control MSCs

value: control


title: AML_LSC_TLA_SU006


title: Control MSC, biological rep2 (H5D-2)

description:
Gene expression data from patient 2 control MSCs
H5D-2


title: ZNF145 MSC, biological rep1 (H4Z-1)

description:
Gene expression data from patient 1 ZNF145-MSCs
H4Z-1


title: Placenta MeDIP DNA 3


title: Control MSC, biological rep1 (H4D-2)

description:
Gene expression data from patient 1 control MSCs
H4D-2


title: AML_LSC_PB_SU004


title: Placenta MeDIP DNA 2


title: BM_MEP_BM_NBM07


title: US22502595_251269411256

source_name: LCM Inf 4 week 4 B6

value: Granuloma

tag: protocol

value: Infected

tag: biological replicate

tag: time

value: week 4

value: wt C57BL/6

source_name: LCM Inf 4 week 6 B6

value: week 6


title: Control MSC, biological rep1 (H4D-1)

description:
Gene expression data from patient 1 control MSCs
H4D-1


title: Placenta MeDIP DNA 1

value: 1st trimester


title: Maternal blood cells MeDIP DNA 1


title: AML_34pos38pos_TLA_SU032


title: AML_34pos38pos_PB_SU031


title: ZAPS

city: Sapporo

first: Akinori

last: Takaoka

address: Kita15, Nishi8, Kitat-ku

institute: Hokkaido University

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: GeneChip Scanner 3000 7G.

data_processing: MAS5.0 data analysis was performed with GeneChip Operating Software (Affymetrix).

source_name: HEK293T, ZAPS

label_protocol: Standard Affymetrix procedures.

extract_protocol: Total RNA was extracted with ISOGEN (Nippon gene) according to the manufacturer's instruction.

treatment_protocol: HEK293T cells were transfected with ZAPS expression vector or control for 48 hours.

tag: cell line

value: human embryonic kidney cells

tag: expression vector

value: ZAPS


title: Liver-low dose-rep4

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

description: no additional information

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added to 750 ng labeled experimental and reference samples.  Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers; 17 hrs overnight at 65 degrees C. After hybridization, slides were washed and dipped into acetonitrile.

scan_protocol: Scanned on an Agilent  scanner at ICBR, UF; Feature Extraction Software (version 9.1.3.1).

data_processing: GeneSpring version 9.0.3; two-color technology; threshold = 5, baseline to median, LOWESS

organism: Pimephales promelas

source_name: Adult male - 96 hr (experimental sample)

label_protocol: Agilent Low-RNA Input Linear Amplification Kit (LRILAK)

extract_protocol: Total RNA extracted using Qiagen RNEasy Plus columns following manufacturer's instructions

treatment_protocol: Aqueous static renewal.  Nominal concentrations of 0 (control), 1 mg/L (low dose) and 10 mg/L (high dose) of TiO2.

tag: agent

tag: nominal dose

value: 1 mg/L

source_name: Reference sample

tag: reference composition

value: Male & Female, Liver, gonad, brain


title: Liver-low dose-rep3

description: no additional information


title: monocytes_Q10H2_1

city: Kiel

first: Frank

last: Döring

address: Heinrich-Hecht-Platz 10

department: Human Nutrition and Food Science

institute: Christian-Albrechts-University Kiel

description: 24h Q10H2 preincubation, 4h LPS stimulation

hyb_protocol: 20 µg of fragmented cRNA was hybridized to a Human Genome U133 Plus 2.0 array for 16 hr at 45 °C at 60 rpm. Arrays were washed on GeneChip®  Fluidics station 450 (Affymetrix) and stained with streptavidin-phycoerythrin

scan_protocol: Microarrays were scanned with a GeneChip® Scanner 3000 7G (Affymetrix) using GCOS software.

data_processing: Expression data was normalized with GC-RMA algorithm.

source_name: blood, +Q10H2, +LPS

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (IVT Labeling Kit, Affymetrix).

growth_protocol: THP-1 cells were cultivated in RPMI medium 1640 (Invitrogen, Karlsruhe, Germany) supplemented with 10% FCS and 1% antibiotics (penicillin/ streptomycin) in a humidified incubator containing 5% CO2 at 37°C. Twenty four hours before pre-incubation, cells were plated at a density of 3 x 106 per well in a 6-well plate.

extract_protocol: Cells were collected in Qiazol-lysis buffer (Qiagen, Hilden, Germany) and stored at -80 °C until isolation of total RNA.

treatment_protocol: In 6-well plates, cells were pre-incubated with 10 µM ubiquinol (Q10H2), or the respective vehicle controls (KANEKA Corporation, Japan). After 24 hours, cell culture medium was removed and fresh lipopolysaccharide (LPS, E. coli, O55:B5, Sigma Aldrich, Taufkirchen, Germany) containing medium (1 µg/ ml) was added for 4 hours, except in the negative control wells (-LPS).

tag: cell type

value: myeloid monocytic cells


title: CL1-1 H3K9K14ac_2 h

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

institute: National Cheng Kung University

description: Chip-chip CL1-1 cells_2 h H3K19K14ac

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: H3K9K14ac ChIP DNA from CL1-1 cells_2 h

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: CL1-1 cells were cultured in the Dulbecco's Modified Eagle's Medium containing 10% fetal bovine serum and 1% penicillin-streptomycin  and incubated at 37°C in a 5% CO2 humidified incubator.

extract_protocol: 4 x 10E6 cells seeded on 100-mm culture dishes in DMEM medium containing 10% FBS were grown to approximately 80–90% confluency and treated with DMSO or 2.5 μM OSU-HDAC-44 for 2 h, and then cross-linked with 1% formaldehyde. Lysate was sonicated to shear DNA and ChIP was as described above. Immunoprecipitation was performed with anti-acetylated lysine 9 and lysine 14 of histone H3 (H3K9K14Ac) for 16 h at 4C.

treatment_protocol: CL1-1 cells were treated with 2.5 uM OSU-HDAC-44 for 2 hours.

tag: chip antibody

source_name: Input DNA from CL1-1 cells_2 h

value: none, input DNA


title: monocytes_Q10H2_3

value: 24h Q10H2 preincubation, 4h LPS stimulation


title: monocytes_Q10H2_2


title: Liver-low dose-rep2

description: no additional information


title: CL1-1 H3K9K14ac_0 h

description: Chip-chip CL1-1 cells_0 h H3K19K14ac

source_name: H3K9K14ac ChIP DNA from CL1-1 cells_0 h

treatment_protocol: CL1-1 cells were left untreated with OSU-HDAC-44.

source_name: Input DNA from CL1-1 cells_0 h


title: AML_34pos38pos_TLA_SU008

value: adult

tag: disease state

value: AML

tag: cell source


title: AML_LSC_TLA_SU001

value: therapeutic leukapheresis


title: AML_34pos38pos_TLA_SU028


title: monocytes_-LPS_2

description: 28h medium

source_name: blood, -LPS

treatment_protocol: In 6-well plates, cells were pre-incubated with 10 µM oxidized ubiquinone (Q10), or the respective vehicle controls (KANEKA Corporation, Japan). After 24 hours, cell culture medium was removed and fresh lipopolysaccharide (LPS, E. coli, O55:B5, Sigma Aldrich, Taufkirchen, Germany) containing medium (1 µg/ ml) was added for 4 hours, except in the negative control wells (-LPS).

value: 28h medium


title: Control

source_name: HEK293T, control

value: control


title: RWPE ni vs. RWPE 266 24h

description:
Human RWPE cells were infected with Propionibacterium acnes strain 266 and samples were isolated 24h post infection. Uninfected cells isolated at 24h were used as a control.
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies) using default settings and the GE2_105_Dec08 protocol.

hyb_protocol: After precipitation, purification and quantification, 1.25 µg of each labeled cRNA was fragmented and subsequent hybridized to whole human genome 44k microarrays (AMADID-014850) according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Hybridized microarrays were washed using the SSC washing protocol (Agilent Technologies). Scanning of microarrays was performed with extended mode (100% and 10%) at 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: The extracted MAGE-ML files were further analyzed with the Rosetta Resolver Biosoftware, Build 7.2 (Rosetta Biosoftware, Seattle, WA, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

source_name: RWPE ni 24h

label_protocol: RNA labeling was performed with the Quick Amp Labeling Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled with either Cyanine 3-CTP or Cyanine 5-CTP according the suppliers instructions

extract_protocol: total RNA was extracted with Trizol (invitrogen) according the suppliers instructions using Glycogen as carrier

value: prostate epithelial

tag: infection

source_name: RWPE 266 24h

value: Propionibacterium acnes strain 266


title: H1299 H3K9K14ac_2 h

description: Chip-chip H1299 cells_2 h H3K19K14ac

source_name: H3K9K14ac ChIP DNA from H1299 cells_2 h

growth_protocol: H1299 cells were cultured in the Dulbecco's Modified Eagle's Medium containing 10% fetal bovine serum and 1% penicillin-streptomycin  and incubated at 37°C in a 5% CO2 humidified incubator.

treatment_protocol: H1299 cells were treated with 2.5 uM OSU-HDAC-44 for 2 hours.

source_name: Input DNA from H1299 cells_2 h


title: AML_34pos38pos_TLA_SU014

source_name: therapeutic leukapheresis

extract_protocol: Total RNA was extracted using TRIzol reagent containing either glycogen or linear acrylamide according to the manufacturer's protocol, and then treated with DNaseI (Ambion).


title: A549 H3K9K14ac_2 h

description: Chip-chip A549 cells_2 h H3K19K14ac

source_name: H3K9K14ac ChIP DNA from A549 cells_2 h

growth_protocol: A549 cells were cultured in the Dulbecco's Modified Eagle's Medium containing 10% fetal bovine serum and 1% penicillin-streptomycin  and incubated at 37°C in a 5% CO2 humidified incubator.

treatment_protocol: A549 cells were treated with 2.5 uM OSU-HDAC-44 for 2 hours.

source_name: Input DNA from A549 cells_2 h


title: AML_LPC_TLA_SU006


title: RWPE ni vs. RWPE P6 2wk

description:
Human RWPE cells were infected with Propionibacterium acnes strain P6 and samples were isolated 2 weeks post infection. Uninfected cells isolated at 2wk were used as a control.
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies) using default settings and the GE2_105_Dec08 protocol.

source_name: RWPE ni 2wk

source_name: RWPE P6 2wk

value: Propionibacterium acnes strain P6


title: monocytes_-LPS_3

description: 28h medium


title: RWPE KPA vs. RWPE ni 24h

description:
Human RWPE cells were infected with Propionibacterium acnes strain KPA and samples were isolated 24h post infection. Uninfected cells isolated at 24h were used as a control.
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies) using default settings and the GE2_105_Dec08 protocol.

source_name: RWPE KPA 24h

value: Propionibacterium acnes strain KPA


title: AML_34pos38pos_PB_SU004

source_name: peripheral blood

value: peripheral blood


title: H1299 H3K9K14ac_0 h

description: Chip-chip H1299 cells_0 h H3K19K14ac

source_name: H3K9K14ac ChIP DNA from H1299 cells_0 h

treatment_protocol: H1299 cells were left untreated with OSU-HDAC-44.

source_name: Input DNA from H1299 cells_0 h


title: Liver-high dose-rep3

description: no additional information

source_name: Adult male - 96 hr (experimental sample)

value: 10 mg/L

source_name: Reference sample


title: monocytes_Q10_3

description: 24h Q10 preincubation, 4h LPS stimulation

source_name: blood, +Q10, +LPS


title: monocytes_-LPS_1

description: 28h medium

source_name: blood, -LPS


title: Liver-low dose-rep1

description: no additional information


title: RWPE P6 vs. RWPE ni 2wk


title: AML_LPC_TLA_SU001


title: monocytes_Q10_2

value: 24h Q10 preincubation, 4h LPS stimulation